Daily Papers

Existing imitation learning (IL) methods such as inverse reinforcement learning (IRL) usually have a double-loop training process, alternating between learning a reward function and a policy and tend to suffer long training time and high variance. In this work, we identify the benefits of differentiable physics simulators and propose a new IL method, i.e., Imitation Learning via Differentiable Physics (ILD), which gets rid of the double-loop design and achieves significant improvements in final performance, convergence speed, and stability. The proposed ILD incorporates the differentiable physics simulator as a physics prior into its computational graph for policy learning. It unrolls the dynamics by sampling actions from a parameterized policy, simply minimizing the distance between the expert trajectory and the agent trajectory, and back-propagating the gradient into the policy via temporal physics operators. With the physics prior, ILD policies can not only be transferable to unseen environment specifications but also yield higher final performance on a variety of tasks. In addition, ILD naturally forms a single-loop structure, which significantly improves the stability and training speed. To simplify the complex optimization landscape induced by temporal physics operations, ILD dynamically selects the learning objectives for each state during optimization. In our experiments, we show that ILD outperforms state-of-the-art methods in a variety of continuous control tasks with Brax, requiring only one expert demonstration. In addition, ILD can be applied to challenging deformable object manipulation tasks and can be generalized to unseen configurations.

This work focuses on addressing two major challenges in the context of large-scale nonconvex Bi-Level Optimization (BLO) problems, which are increasingly applied in machine learning due to their ability to model nested structures. These challenges involve ensuring computational efficiency and providing theoretical guarantees. While recent advances in scalable BLO algorithms have primarily relied on lower-level convexity simplification, our work specifically tackles large-scale BLO problems involving nonconvexity in both the upper and lower levels. We simultaneously address computational and theoretical challenges by introducing an innovative single-loop gradient-based algorithm, utilizing the Moreau envelope-based reformulation, and providing non-asymptotic convergence analysis for general nonconvex BLO problems. Notably, our algorithm relies solely on first-order gradient information, enhancing its practicality and efficiency, especially for large-scale BLO learning tasks. We validate our approach's effectiveness through experiments on various synthetic problems, two typical hyper-parameter learning tasks, and a real-world neural architecture search application, collectively demonstrating its superior performance.

The dominant paradigm for building LLM based agents is the Agent Loop, an iterative cycle where a single language model decides what to do next by reading an ever growing context window. This paradigm has three structural weaknesses: implicit dependencies between steps, unbounded recovery loops, and mutable execution history that complicates debugging. We characterize the Agent Loop as a single ready unit scheduler: at any moment, at most one executable unit is active, and the choice of which unit to activate comes from opaque LLM inference rather than an inspectable policy. This perspective places Agent Loops and graph based execution engines on a single semantic continuum. We propose SGH, Structured Graph Harness, which lifts control flow from implicit context into an explicit static DAG. SGH makes three commitments: execution plans are immutable within a plan version, planning execution and recovery are separated into three layers, and recovery follows a strict escalation protocol. These choices trade some expressiveness for controllability, verifiability, and implementability. Our contributions are fourfold: a scheduler unified framework that applies classical scheduling theory to LLM agent execution and identifies challenges introduced by non deterministic LLM nodes; a trade off analysis of controllability, expressiveness, and implementability across 70 surveyed systems; a formal specification including a node state machine with termination and soundness guarantees; and an attributable experimental framework with a seven group design for future validation. This is a position paper and design proposal. We provide a theoretical framework, design analysis, and experimental protocol, not a production implementation or empirical results.

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and task generalization. However, their application to structured data analysis remains fragile due to inconsistencies in schema interpretation, misalignment between user intent and model output, and limited mechanisms for self-correction when failures occur. This paper introduces the STROT Framework (Structured Task Reasoning and Output Transformation), a method for structured prompting and feedback-driven transformation logic generation aimed at improving the reliability and semantic alignment of LLM-based analytical workflows. STROT begins with lightweight schema introspection and sample-based field classification, enabling dynamic context construction that captures both the structure and statistical profile of the input data. This contextual information is embedded in structured prompts that guide the model toward generating task-specific, interpretable outputs. To address common failure modes in complex queries, STROT incorporates a refinement mechanism in which the model iteratively revises its outputs based on execution feedback and validation signals. Unlike conventional approaches that rely on static prompts or single-shot inference, STROT treats the LLM as a reasoning agent embedded within a controlled analysis loop -- capable of adjusting its output trajectory through planning and correction. The result is a robust and reproducible framework for reasoning over structured data with LLMs, applicable to diverse data exploration and analysis tasks where interpretability, stability, and correctness are essential.

A robot's effective ``mind'' need not reside in a single policy. It can emerge when specialized components perceive, reason, predict, act, verify, and remember within a shared orchestration process. EMERGE-Policy turns this perspective into a graph-structured agentic framework that coordinates both capability invocation and information exchange. A Main Agent retains task-level state within an active context window, while role-specific Sub Agents process perception, execution monitoring, verification, and memory consolidation in isolated contexts and return structured, task-relevant evidence. Role-specific contexts control information load by exposing only decision-relevant evidence to the Main Agent, while the functional Skill interface composes heterogeneous backends as Operational, Imagination, and Evaluation Skills. Criterion-grounded verification, textual failure diagnosis, and Branch Stack recovery provide localized correction, with token-aware external memory preserving task-relevant state. Together, their closed-loop interaction realizes the system-level policy captured by the name EMERGE-Policy. Without additional fine-tuning, we achieved outstanding performance on several public benchmark that have had a wide-reaching impact, and conducted a series of real robot experiments. These system-level results suggest that through the division of different functional sub-tasks among multiple agents and their concurrent collaboration, as well as the technical paradigm where the model is regarded as a skill and called within the framework, EMERGE-Policy can extend the robust robot policies beyond isolated runs.

We present Context Window Lifecycle (CWL), a context-management scheme that gives long-horizon LLM agents an effectively unbounded working horizon. As a session accumulates history, CWL keeps the context within budget through graduated, semantically-aware eviction: the agent annotates its trajectory as typed, dependency-linked episodes as work proceeds, and a deterministic, LLM-free policy evicts content in priority order within that structure when a token budget is exceeded. CWL preserves user turns and the exploratory context the agent is actively reasoning over, while aggressively shedding action episodes whose effects are already persisted in the environment, keeping active context near a stable ceiling that also avoids the performance degradation associated with very large prompts. Compared to summarization-based compaction, CWL avoids four well-known limitations: unpredictable lossiness, destruction of causal structure, blocking model cost, and compression-induced hallucination. Compared to recency truncation, CWL is semantically aware: it drops the oldest-and-most-recoverable content according to the dependency graph rather than oldest-in-time regardless of relevance. We describe the annotation protocol, the episode graph, the eviction policy, and the token-accounting loop, and evaluate CWL on long-horizon agentic benchmarks: a single agent session completing 89 sequential tasks across 80 million tokens with no measurable degradation in task accuracy relative to per-task isolated sessions

Understanding ultra-long videos such as egocentric recordings, live streams, or surveillance footage spanning days to weeks, remains a challenge. For current multimodal LLMs: even with million-token context windows, frame budgets cover only tens of minutes of densely sampled video, and most evidence is discarded before inference begins. Memory-augmented and agentic approaches help with scale, but their retrieval remains fragmented across modalities and lacks long-range narrative summaries that span days or weeks. We propose MAGIC-Video, a training-free framework built around a multimodal memory graph with interleaved narrative chain: the graph unifies episodic, semantic, and visual content through six typed edges and supports cross-modal retrieval, while the chain distils long-horizon entity biographies and recurring activity events. At inference time, an agentic loop interleaves graph retrieval with narrative fact injection, covering both the modality and time dimensions of ultra-long video in a single retrieval pipeline. On EgoLifeQA, Ego-R1 and MM-Lifelong, MAGIC-Video consistently outperforms strong general-purpose, long-video, and agentic baselines, with gains of 10.1, 7.4, and 5.9 points over the prior best agentic system on each benchmark. Code is available at https://github.com/lijiazheng0917/MAGIC-video.

LLM-based coding agents can localize bugs, generate patches, and run tests with diminishing human oversight, yet the scaffolding code that surrounds the language model (the control loop, tool definitions, state management, and context strategy) remains poorly understood. Existing surveys classify agents by abstract capabilities (tool use, planning, reflection) that cannot distinguish between architecturally distinct systems, and trajectory studies observe what agents do without examining the scaffold code that determines why. This paper presents a source-code-level architectural taxonomy derived from analysis of 13 open-source coding agent scaffolds at pinned commit hashes. Each agent is characterized across 12 dimensions organized into three layers: control architecture, tool and environment interface, and resource management. The analysis reveals that scaffold architectures resist discrete classification: control strategies range from fixed pipelines to Monte Carlo Tree Search, tool counts range from 0 to 37, and context compaction spans seven distinct strategies. Five loop primitives (ReAct, generate-test-repair, plan-execute, multi-attempt retry, tree search) function as composable building blocks that agents layer in different combinations; 11 of 13 agents compose multiple primitives rather than relying on a single control structure. Dimensions converge where external constraints dominate (tool capability categories, edit formats, execution isolation) and diverge where open design questions remain (context compaction, state management, multi-model routing). All taxonomic claims are grounded in file paths and line numbers, providing a reusable reference for researchers studying agent behavior and practitioners designing new scaffolds.

Phenotyping is fundamental to rare disease diagnosis, but manual curation of structured phenotypes from clinical notes is labor-intensive and difficult to scale. Existing artificial intelligence approaches typically optimize individual components of phenotyping but do not operationalize the full clinical workflow of extracting features from clinical text, standardizing them to Human Phenotype Ontology (HPO) terms, and prioritizing diagnostically informative HPO terms. We developed RARE-PHENIX, an end-to-end AI framework for rare disease phenotyping that integrates large language model-based phenotype extraction, ontology-grounded standardization to HPO terms, and supervised ranking of diagnostically informative phenotypes. We trained RARE-PHENIX using data from 2,671 patients across 11 Undiagnosed Diseases Network clinical sites, and externally validated it on 16,357 real-world clinical notes from Vanderbilt University Medical Center. Using clinician-curated HPO terms as the gold standard, RARE-PHENIX consistently outperformed a state-of-the-art deep learning baseline (PhenoBERT) across ontology-based similarity and precision-recall-F1 metrics in end-to-end evaluation (i.e., ontology-based similarity of 0.70 vs. 0.58). Ablation analyses demonstrated performance improvements with the addition of each module in RARE-PHENIX (extraction, standardization, and prioritization), supporting the value of modeling the full clinical phenotyping workflow. By modeling phenotyping as a clinically aligned workflow rather than a single extraction task, RARE-PHENIX provides structured, ranked phenotypes that are more concordant with clinician curation and has the potential to support human-in-the-loop rare disease diagnosis in real-world settings.

We study how to predict the downstream closed-loop performance of a learned latent world model from validation-time diagnostics alone. Choosing the right checkpoint from a world-model training run is difficult: validation loss and multi-step prediction RMSE keep improving long after closed-loop performance has collapsed. We present a suite of structural validation-time diagnostics drawn from optimal-control theory and apply them to Gymnasium's LunarLander v3, which features shaped rewards. We train an RSSM [5, 4] world model on it and treat per checkpoint CEM-MPC return as the oracle for closed-loop quality. By evaluating 40 metrics against this oracle, we find that the strongest single predictor is the Reward Observability Fraction (ROF), which measures the reward predictor's dependence on the observable subspace. We combine ROF with three structural regularizers into a single-number offline checkpoint selection score, the Composite Reward Observability Fraction (CROF). The CROF-selected world model trains a model-based A2C policy that beats a fairly evaluated model-free A2C baseline by ~24.5 return points while using ~65x fewer real-environment interactions, and the same world model also drives a strong zero-shot CEM-MPC policy. Code and data: https://github.com/nsmoly/LunarLander_RSSM.

Motif-scaffolding systems commonly follow a generate-then-filter paradigm, in which candidate proteins are generated independently and structural evaluation is used primarily for terminal screening or ranking. This paradigm underuses evaluation: failed predictions contain state-specific evidence about whether a design requires repair of motif geometry, global foldability, or other structural constraints. We introduce ELMS (Evidence-based LLM-guided Monte Carlo Search), an evaluator-in-the-loop search framework for motif scaffolding that turns such evaluator feedback into targeted design actions. Effective reuse of structural feedback is nontrivial because different scaffold states exhibit different failure modes, and repeatedly refining a single trajectory can prematurely commit computation to an unproductive region of sequence space. ELMS therefore retains evaluated scaffolds as persistent search states: a Critic Agent diagnoses state-local structural failures, a Policy Agent selects targeted operators with execution parameters, motif-locked operators realize legal sequence modifications, and MCTS determines which historical states should receive further design effort. Under the standard GeomMotif protocol (100 candidates per task), ELMS achieves Successful rates of 86.41\% on single-motif tasks and 84.57\% on paired-motif tasks, exceeding the strongest prior baseline by 19.3 and 21.9 percentage points, respectively. On MotifBench, under a matched 100-candidate search budget, it solves 26.7 of 30 tasks on average (88.89\% Task Success), compared with 16.0 tasks (53.33\%) for the strongest baseline. These results establish ELMS as an effective approach for converting structural evaluation from a terminal filter into actionable guidance for iterative motif scaffolding.

Enterprise back office workflows require agentic systems that are auditable, policy-aligned, and operationally predictable, capabilities that generic multi-agent setups often fail to deliver. We present POLARIS (Policy-Aware LLM Agentic Reasoning for Integrated Systems), a governed orchestration framework that treats automation as typed plan synthesis and validated execution over LLM agents. A planner proposes structurally diverse, type checked directed acyclic graphs (DAGs), a rubric guided reasoning module selects a single compliant plan, and execution is guarded by validator gated checks, a bounded repair loop, and compiled policy guardrails that block or route side effects before they occur. Applied to document centric finance tasks, POLARIS produces decision grade artifacts and full execution traces while reducing human intervention. Empirically, POLARIS achieves a micro F1 of 0.81 on the SROIE dataset and, on a controlled synthetic suite, achieves 0.95 to 1.00 precision for anomaly routing with preserved audit trails. These evaluations constitute an initial benchmark for governed Agentic AI. POLARIS provides a methodological and benchmark reference for policy-aligned Agentic AI. Keywords Agentic AI, Enterprise Automation, Back-Office Tasks, Benchmarks, Governance, Typed Planning, Evaluation

Scaling Transformer-based click-through rate (CTR) models by stacking more parameters brings growing computational and storage overhead, creating a widening gap between scaling ambitions and the stringent industrial deployment constraints. We propose LoopCTR, which introduces a loop scaling paradigm that increases training-time computation through recursive reuse of shared model layers, decoupling computation from parameter growth. LoopCTR adopts a sandwich architecture enhanced with Hyper-Connected Residuals and Mixture-of-Experts, and employs process supervision at every loop depth to encode multi-loop benefits into the shared parameters. This enables a train-multi-loop, infer-zero-loop strategy where a single forward pass without any loop already outperforms all baselines. Experiments on three public benchmarks and one industrial dataset demonstrate state-of-the-art performance. Oracle analysis further reveals 0.02--0.04 AUC of untapped headroom, with models trained with fewer loops exhibiting higher oracle ceilings, pointing to a promising frontier for adaptive inference.

Looped Transformers scale latent computation by repeatedly applying shared blocks, but sequential looping increases latency and KV-cache memory with the loop count. Parallel loop Transformers (PLT) alleviate this cost through cross-loop position offsets (CLP) and shared-KV gated sliding-window attention, making loop count a practical design choice. We therefore study PLT loop-count selection through a gain--cost view: an extra loop may refine representations, but CLP also introduces a positional mismatch at each loop boundary. We instantiate this study by training LoopCoder-v2, a family of 7B PLT coders with different loop counts, from scratch on 18T tokens, followed by matched instruction tuning and evaluation. Empirically, the two-loop variant delivers broad gains over the non-looped baseline across code generation, code reasoning, agentic software engineering, and tool-use benchmarks, improving SWE-bench Verified from 43.0 to 64.4 points and Multi-SWE from 14.0 to 31.0 points. In contrast, variants with three or more loops regress, revealing a strongly non-monotonic loop-count effect. Our diagnostics show that loop 2 provides the main productive refinement, while later loops yield diminishing, oscillatory updates and reduced representational diversity. Because the CLP-induced mismatch remains roughly fixed as refinement gains shrink, the offset cost increasingly dominates. This gain--cost trade-off explains PLT's saturation at two loops and provides diagnostics for loop-count selection.

Modeling dynamical systems and unraveling their underlying structural dependencies is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and stochastic in nature, and admit only partial, noisy state measurements. Our primary motivating setting is single-cell biology, where destructive measurements yield unpaired population snapshots rather than longitudinal trajectories of the same cells. This poses a significant challenge for addressing the problems of modeling the underlying dynamics and inferring the network structure of these systems. Existing methods are typically tailored either for structure learning or modeling dynamics at the population level, but are limited in their ability to address both problems together. In this work, we address both problems simultaneously: we present StructureFlow, a novel and principled simulation-free training approach for jointly learning the structure and stochastic population dynamics of physical systems. We showcase the utility of StructureFlow for the tasks of structure learning from interventions and dynamical (trajectory) inference of conditional population dynamics. We empirically evaluate our approach on high-dimensional synthetic systems, a set of biologically plausible simulated systems, and an experimental single-cell dataset. We show that StructureFlow can learn the structure of underlying systems while simultaneously modeling their conditional population dynamics --- a key step toward model-based mechanistic understanding of systems behavior.

Looped Transformers have drawn growing attention because looping improves multi-step reasoning and increases the executed depth of a model without adding parameters. They achieve this by reusing a stack of L layers for N loops. However, increasing the loop count N not only destabilizes training but also shifts the best hyperparameters, so they must be searched again for every loop count. Inspired by Depth-μP (Yang et al., 2024), which multiplies each residual branch by L^{-1/2} for depth L so that a learning rate tuned on a shallow untied network transfers to a deep one, we study how the residual branches and the learning rate should scale with the loop count N. We find that loops cannot simply be treated as extra depth, because the loops share weights. At initialization, distinct layers add nearly uncorrelated increments to the residual stream, so their sum grows as L, whereas a shared layer adds positively correlated increments at every loop, so their sum grows linearly in N. For a single layer looped N times, we show in the infinite-width limit that multiplying the residual branch by 1/N and keeping the learning rate independent of N is the only parameterization with both a stable forward pass and maximal residual-stream updates. We then generalize the analysis to a stack of L distinct layers looped N times to obtain a parameterization we call Loop-μP, in which the loop factor 1/N combines with the depth factor L^{-1/2}. Empirically, we find in language modeling that the base learning rate tuned on the smallest model stays best under Loop-μP for loop counts up to 8 and executed depths up to 384 layers. These results make Loop-μP a practical recipe for scaling looped Transformers.

We reformulate the problem of supervised learning as learning to learn with two nested loops (i.e. learning problems). The inner loop learns on each individual instance with self-supervision before final prediction. The outer loop learns the self-supervised task used by the inner loop, such that its final prediction improves. Our inner loop turns out to be equivalent to linear attention when the inner-loop learner is only a linear model, and to self-attention when it is a kernel estimator. For practical comparison with linear or self-attention layers, we replace each of them in a transformer with an inner loop, so our outer loop is equivalent to training the architecture. When each inner-loop learner is a neural network, our approach vastly outperforms transformers with linear attention on ImageNet from 224 x 224 raw pixels in both accuracy and FLOPs, while (regular) transformers cannot run.

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA folding model. Understanding the specific local structures (i.e., "motifs") that contribute to undesignability is crucial for refining RNA folding models and determining the limits of RNA designability. Despite its importance, this problem has received very little attention, and previous efforts are neither scalable nor interpretable. We develop a new theoretical framework for motif (un-)designability, and design scalable and interpretable algorithms to identify minimal undesignable motifs within a given RNA secondary structure. Our approach establishes motif undesignability by searching for rival motifs, rather than exhaustively enumerating all (partial) sequences that could potentially fold into the motif. Furthermore, we exploit rotational invariance in RNA structures to detect, group, and reuse equivalent motifs and to construct a database of unique minimal undesignable motifs. To achieve that, we propose a loop-pair graph representation for motifs and a recursive graph isomorphism algorithm for motif equivalence. Our algorithms successfully identify 24 unique minimal undesignable motifs among 18 undesignable puzzles from the Eterna100 benchmark. Surprisingly, we also find over 350 unique minimal undesignable motifs and 663 undesignable native structures in the ArchiveII dataset, drawn from a diverse set of RNA families. Our source code is available at https://github.com/shanry/RNA-Undesign and our web server is available at http://linearfold.org/motifs.

Language model agents increasingly automate post-training, but when given the full training stack they converge on supervised fine-tuning and spend most effort revising training data. Existing systems give the agent one kind of control, selecting rows from a fixed pool or calling a generator, whereas a human data engineer adjusts proportions, prunes, repairs, replaces and synthesizes the data. We design a data action space for these changes and ask whether an automated system can make the full range rather than one of them, and what structure that requires. We first run this loop with a single agent, and it reaches only one action, adjusting category proportions, while its context fills with execution output and is discarded mid-search. We therefore introduce AutoSFT, a multi-agent system where a meta agent separates execution from analysis, gathers proposals from independent angles, and calls a synthesis subagent for capabilities the pool cannot cover, with the model, the trainer, and the budget fixed within each comparison. Adding each component in turn helps: the executor halves context loss, the analysis subagents lift the best IFEval by +6.5, and synthesis adds +3.4 IFEval and +2.9 IFBench. The same loop transfers to code, where analysis adds +3.7 MBPP+ over a single agent that does not improve. Every result comes from runs that retrain from the base model each round, so each component's effect is individually attributable. Our findings suggest that automating SFT data research depends more on covering diverse data actions than on a stronger single action.

The complementarity-determining regions of antibodies are loop structures that are key to their interactions with antigens, and of high importance to the design of novel biologics. Since the 1980s, categorizing the diversity of CDR structures into canonical clusters has enabled the identification of key structural motifs of antibodies. However, existing approaches have limited coverage and cannot be readily incorporated into protein foundation models. Here we introduce ImmunoGlobulin LOOp Tokenizer, Igloo, a multimodal antibody loop tokenizer that encodes backbone dihedral angles and sequence. Igloo is trained using a contrastive learning objective to map loops with similar backbone dihedral angles closer together in latent space. Igloo can efficiently retrieve the closest matching loop structures from a structural antibody database, outperforming existing methods on identifying similar H3 loops by 5.9\%. Igloo assigns tokens to all loops, addressing the limited coverage issue of canonical clusters, while retaining the ability to recover canonical loop conformations. To demonstrate the versatility of Igloo tokens, we show that they can be incorporated into protein language models with IglooLM and IglooALM. On predicting binding affinity of heavy chain variants, IglooLM outperforms the base protein language model on 8 out of 10 antibody-antigen targets. Additionally, it is on par with existing state-of-the-art sequence-based and multimodal protein language models, performing comparably to models with 7times more parameters. IglooALM samples antibody loops which are diverse in sequence and more consistent in structure than state-of-the-art antibody inverse folding models. Igloo demonstrates the benefit of introducing multimodal tokens for antibody loops for encoding the diverse landscape of antibody loops, improving protein foundation models, and for antibody CDR design.

Typed decision models answer a declared question without generating text: a decision head returns a probability for each of the declared options in a single forward pass. A single pass is fast, intuitive System 1 thinking. We study what lies between one pass and generated reasoning: looping, in which the same layers are recursively applied several times before one typed readout. Each loop lets the model revise its hidden state before it commits to an answer, without generating a token; we call this System 1.5 thinking. We propose SanSi, which turns a pre-trained looped language model into a typed decision model. The option probabilities are read after every loop, and every loop is trained with a proper scoring rule, so that one model serves every budget from one loop to eight in a single run. On 10,027 test decisions from 59 sources, SanSi reaches 72.0% accuracy: 13.5 points above a non-looped model of the same shape trained with the same recipe, 5.3 points above a newer non-looped model of its size, and 1.8 points below one with three times the parameters. On two depth-controlled tasks, loops extend the solvable depth beyond the depths seen in training, where the larger single-pass model fails. Used as the judge for policy optimization with reinforcement learning, without gold answers, SanSi raises the generator's F1 by 7.7 points.

A latent recurrent language model applies a shared block of layers repeatedly, so one checkpoint can trade inference compute for accuracy by changing the loop count. At one loop, however, such models typically fall well short of a non-recurrent model of the same size, a one-loop tax that makes a separate non-recurrent model the better choice whenever latency matters. We present Elastic Latent Recurrence (ELR), a recipe for training looped language models without this tax. At one loop, an ELR model costs the same to serve as a non-recurrent model of the same size and, trained on the same data, reaches similar accuracy. Each additional loop then buys more accuracy for more inference compute. Three choices make this work: a gated state update with a learned step size, loop counts mixed within each optimizer update, and conditioning each pass on its loop index and budget. The first two preserve one-loop accuracy, and the third lowers loss at every additional loop. Mixed depths can be introduced late in pretraining to limit the added training cost, and with zero-initialized conditioning added at the switch, this late schedule reaches lower loss than mixed-depth training from scratch. In MoE models, reusing first-loop expert routes on later loops cuts mixed-depth update time by 11.7% with no measurable change in accuracy. At inference, keeping only the last loop's attention KV cache holds attention KV memory at its one-loop level while retaining most of the gain from additional loops. On 4B dense and 30B-A3B MoE hybrid models, ELR at one loop is 0.52 points below and 1.04 points above its matched baseline on a ten-task average, and four loops add 7.25 and 4.75 points. Carried through post-training, the recipe yields Koi-4B, a single checkpoint that scores an estimated 18 on the Artificial Analysis Intelligence Index at one loop, matching Qwen3.5-4B, and 29 at four loops.

In mid-2026 a slogan reorganized how practitioners talk about coding agents: stop prompting your agent, start designing the loop that prompts it. We take this claim seriously and give it a careful treatment. We call the object of the new practice the loop specification: a bounded, reusable artifact, made of a trigger, a goal, a verification step, a stopping rule and a memory, that a human hands to an agent harness (such as Claude Code or Codex) so the agent pursues a goal on its own, in place of step-by-step prompting. We distinguish this external loop specification from two things it is often confused with: an ordinary programming loop, and the internal perceive-act-observe cycle that the harness already provides as plumbing. We position loop engineering as a new layer in the progression from prompt to context to harness to loop, and we argue, against the stronger headlines, that it does not retire prompt engineering; loop and prompt are distinct tools with distinct uses. We offer four contributions: a definition and scope for the discipline; an anatomy and taxonomy of loop specifications organized around trigger, goal type, a five-level verification ladder, architecture, and named terminal states; a descriptive analysis of the Loop Library, a public corpus of fifty real loops that we code by hand; and a set of design principles and anti-patterns grounded in the scientific literature on self-correction, reward hacking and model-as-judge fragility. The corpus shows that practice has matured most where the discipline says it matters: seventy percent of loops verify in the autonomous zone of the ladder and seventy-four percent name their terminal states, while automated triggering and durable memory remain comparatively underdeveloped. We close with the limits the practice must respect, including the verification burden, comprehension debt and the risk of cognitive surrender.

Loop invariants are fundamental to reasoning about programs with loops. They establish properties about a given loop's behavior. When they additionally are inductive, they become useful for the task of formal verification that seeks to establish strong mathematical guarantees about program's runtime behavior. The inductiveness ensures that the invariants can be checked locally without consulting the entire program, thus are indispensable artifacts in a formal proof of correctness. Finding inductive loop invariants is an undecidable problem, and despite a long history of research towards practical solutions, it remains far from a solved problem. This paper investigates the capabilities of the Large Language Models (LLMs) in offering a new solution towards this old, yet important problem. To that end, we first curate a dataset of verification problems on programs with loops. Next, we design a prompt for exploiting LLMs, obtaining inductive loop invariants, that are checked for correctness using sound symbolic tools. Finally, we explore the effectiveness of using an efficient combination of a symbolic tool and an LLM on our dataset and compare it against a purely symbolic baseline. Our results demonstrate that LLMs can help improve the state-of-the-art in automated program verification.

Looped Transformers provide a parameter-efficient approach to depth scaling by repeatedly applying shared Transformer blocks. Recent reasoning models have likewise highlighted the value of scaling test-time computation through longer computation trajectories. However, the principles for designing effective loop transitions remain poorly understood. We view the looped hidden state as a fast weight that is updated throughout the depth. We formulate loop transitions as local gradient-based updates, with recurrent blocks predicting implicit targets at each depth. Our framework derives loop transitions in closed form from a projection, a local objective and an optimizer update rule. Mapping representative loop transitions into this framework reveals mismatches between their transitions and projections. We first align the input maps of existing transitions. We then derive OperLoop, which combines explicit weight decay, adaptive step size and a delta objective. The aligned variants reduce training loss and improve average commonsense accuracy. OperLoop improves average generative performance over the compared looped and non-looped baselines under matched training FLOPs. These results support the framework's usefulness for loop design. We extend the analysis to additional loop models and outline a roadmap for future loop transition design.

Looped Transformers introduce recurrent depth as a new scaling axis for LLMs: by repeatedly applying shared Transformer blocks, they increase effective depth without increasing parameter count. However, the benefits of looping remain unclear for large MoE LLMs under FLOPs-matched comparisons. The main reason is that the gains from additional iterations diminish quickly and can even turn into degradation, so the extra FLOPs spent on looping yield little substantial improvement. Consequently, prior work typically settles on two loops. We identify two main obstacles to scaling looped MoE. First, looping inherits and amplifies the curse of depth: hidden-state variance grows with each iteration as residual updates accumulate, which destabilizes deep recurrence and causes representations to drift. Second, looped MoE suffers from expert selection collapse: routers repeatedly select the same experts across loops, so extra iterations add computation without adding computational diversity. Guided by this diagnosis, we propose LOOM, built on a single principle: each loop should contribute new computation while keeping the recurrent state stable. LOOM stabilizes recurrence by scaling residual updates to bound variance growth and re-injecting the input embedding at every loop, and diversifies it through per-loop routers that engage different experts and a Looping Residual that carries earlier outputs forward. Experiments across 100M-1.7B models show stable scaling to 9-12 loops. Under near-iso-FLOP, the 700M model performs best at 5 loops, reducing perplexity from 18.36 to 16.54 and improving average zero-shot accuracy from 38.84% to 39.53% over the non-looped baseline. Without FLOP matching, the 1.7B model trained on 60B tokens peaks at 9 loops, reducing perplexity from 9.62 to 7.77 and improving average zero-shot accuracy from 42.4% to 47.7%. Code is available https://github.com/hed-ucas/LOOM.

We seek a hierarchical resolution of residual error under a composite learning objective as a principled mechanism for identifying and exploiting additional information, particularly under distribution shift and perturbation. Inspired by the System 1/System 2 paradigm, we formulate this principle as a two-loop mechanism serving a common inference goal. A fast, System 1-like loop resolves the residual addressable by the available evidence; the remaining epistemic residual triggers a medium speed, System 2-like loop that actively acquires additional evidence and measures its informational value through residual reduction. Over nested solution spaces, the medium-loop optimum is provably no worse than the fast-loop optimum. Experiments show that the resulting two-loop model consistently improves upon the fast loop at approximately half the computation of the medium loop, including under unseen corruptions, and, when provided a cleaner observation, outperforms staged classifiers and learning-to-defer methods at equal computational cost.

AlphaFold 3 predicts protein structures with remarkable accuracy, yet how structural information emerges within the model remains poorly understood. Here, through causal interventions on internal representations and direct probing of every Pairformer block, we trace the formation of global protein geometry and identify the multiple sequence alignment (MSA) as a structural shortcut to the fold. Removing the MSA largely preserves local secondary structure while disrupting the long-range relationships that define global topology. Restoring the MSA-enriched pair representation at only forty residues recovers most of this lost organization, including at pairs never directly modified. This contribution depends on the detailed direction of the MSA module's output rather than its magnitude. The Pairformer rapidly converts this signal into global geometry: the final fold becomes recoverable by approximately block 9 of 48 for a majority of proteins, roughly twenty-seven blocks before the model's decoder can render it, whereas without the MSA it remains inaccessible for most proteins throughout the pass. Which homologs are supplied shapes this trajectory more strongly than which query is supplied; it persists for a designed query that never evolved but collapses for a shuffled sequence. Most importantly, an alignment built for a different protein that shares the fold, supplied only at the structurally corresponding columns, raises the median TM-score against experiment from 0.44 to 0.72, while the same alignment shifted a few residues along the chain performs worse than supplying no alignment at all. What AlphaFold 3 reads from an alignment is therefore a description of the fold itself, transferable between proteins that share one, rather than the query's own evolutionary history. This explains both its accuracy and the limits of what it has solved.

We determine the 4-point correlation function and amplitude in planar, maximally supersymmetric Yang-Mills theory to 12 loops. We find that the recently-introduced 'double-triangle' rule in fact implies the previously described square and pentagon rules; and when applied to 12 loops, it fully determines the 11-loop correlator and fixes all but 3 of the (22,024,902) 12-loop coefficients; these remaining coefficients can be subsequently fixed using the '(single-)triangle' rule. Not only do we confirm the Catalan conjecture for anti-prism graphs, but we discover evidence for a greatly generalized Catalan conjecture for the coefficients of all polygon-framed fishnet graphs. We provide all contributions through 12 loops as ancillary files to this work.

Repeating a small block of middle layers increases a language model's effective inference depth without adding parameters or generating extra tokens, and recent work shows that this latent recurrence improves reasoning. However, two design choices limit these gains. Each iteration sees only the previous output and cannot directly access earlier computations. Moreover, a fixed loop count wastes depth on easy inputs while leaving hard ones with too little computation. We introduce RecurTrace, which addresses both limitations using the loop's own trajectory. Specifically, Loop Memory Attention lets each looped layer attend to its own states from previous iterations along the loop-time axis, so the model can revisit earlier computations instead of relying on the latest state alone. A halting head then reads the loop state and predicts whether to continue, with supervision from an oracle that identifies when additional depth still reduces loss. In a controlled MathQA comparison on the same looped backbone, RecurTrace achieves 56.9% accuracy with an average of 2.0 loops, exceeding the best fixed loop depth by 2.2 points at matched compute. By comparison, ACT and PonderNet collapse to one loop, and CALM reaches only 54.1% with 5.6 loops, while the stronger LoopUS-Conf and TaH-Mismatch baselines reach 55.3% at 3.2 loops and 55.7% at 2.1 loops. Finally, RecurTrace improves generation accuracy over same-budget fine-tuned baselines at 0.6B, 1.7B, 4B, and 8B, with the gain growing with model size from 0.6 to 3.4 points.

We study auto research as a closed empirical loop driven by external measurement. Each submitted trial carries a hypothesis, an executable code edit, an evaluator-owned outcome, and feedback that shapes the next proposal. The output is not a generated paper or a single model checkpoint, but an auditable trajectory of proposals, code diffs, experiments, scores, and failure labels. We instantiate this loop with specialist agents that partition recipe surfaces and share measured lineage across trials. The central empirical finding is that lineage feedback lets agents turn evaluator outcomes, including crashes, budget overruns, size failures, and accuracy-gate misses, into later program-level recipe edits rather than one-shot suggestions. Across 1,197 headline-run trials plus 600 Parameter Golf control trials after one-time setup and launch, humans did not choose proposals, edit recipes, override scores, or repair failed trials during the search. In the three headline runs, the same submitted-trial loop reduces Parameter Golf validation bpb by 0.81%, raises NanoChat-D12 CORE by 38.7%, and reduces CIFAR-10 Airbench96 wallclock by 4.59%, with each task measured by its own external evaluator and legality checks. The trace includes a strict architecture-domain audit of 157 headline-run submissions and program rewrites such as a NanoChat attention-kernel path change. Within this scope the loop autonomously writes code, submits experiments, absorbs feedback, applies and combines known techniques inside each environment, and improves public starting recipes.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

We consider the problem of antibody sequence design given 3D structural information. Building on previous work, we propose a fine-tuned inverse folding model that is specifically optimised for antibody structures and outperforms generic protein models on sequence recovery and structure robustness when applied on antibodies, with notable improvement on the hypervariable CDR-H3 loop. We study the canonical conformations of complementarity-determining regions and find improved encoding of these loops into known clusters. Finally, we consider the applications of our model to drug discovery and binder design and evaluate the quality of proposed sequences using physics-based methods.

With the advent of neural language models, the performance of code generation has been significantly boosted. However, the problem of repetitions during the generation process continues to linger. Previous work has primarily focused on content repetition, which is merely a fraction of the broader repetition problem in code generation. A more prevalent and challenging problem is structural repetition. In structural repetition, the repeated code appears in various patterns but possesses a fixed structure, which can be inherently reflected in grammar. In this paper, we formally define structural repetition and propose an efficient decoding approach called RPG, which stands for Repetition Penalization based on Grammar, to alleviate the repetition problems in code generation for LLMs. Specifically, RPG first leverages grammar rules to identify repetition problems during code generation, and then strategically decays the likelihood of critical tokens that contribute to repetitions, thereby mitigating them in code generation. To facilitate this study, we construct a new dataset CodeRepetEval to comprehensively evaluate approaches for mitigating the repetition problems in code generation. Extensive experimental results demonstrate that RPG substantially outperforms the best-performing baselines on CodeRepetEval dataset as well as HumanEval and MBPP benchmarks, effectively reducing repetitions and enhancing the quality of generated code.

Looped Transformers repeatedly apply the same set of Transformer layers, giving them a recurrent architecture for latent computation. Their strong performance on iterative reasoning and length-generalization tasks suggests an appealing explanation: recurrence may provide an inductive bias that lets the model reuse a learned algorithm across loops. However, weight sharing alone does not imply that every loop performs the same operation. This raises a basic question: is each loop actually repeating the same computation, and if not, what routes the shared parameters to different operations? We study this question using graph walks as a test case. In the model's native trajectories, decoded predictions can advance by different numbers of graph steps or remain at a reached target, showing that recurrent progress need not follow a fixed one-loop-one-step pattern. We then show that a frozen loop can be steered toward different transitions by modifying its entering hidden state: a learned linear layer J selects the desired transition without changing the shared Transformer layers. To test how this steering works, we use activation patching and find that attention patterns can recover its effects and switch the selected transition. Across five matched pairs of graph models, changing intermediate supervision during backbone training changes which transitions J can induce. This suggests that J selects computations learned by the backbone rather than creating new algorithms. Together, these results show that the hidden state can control shared computation, with attention routing as a causal pathway.

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the underlying discrete representations are not well understood. In this work, we first demonstrate that the successful utilization of structural tokens in a language model for structure prediction depends on using rich, pre-trained sequence embeddings to bridge the semantic gap between the sequence and structural "language". The analysis of the structural vocabulary itself then reveals significant semantic redundancy, where multiple distinct tokens correspond to nearly identical local geometries, acting as "structural synonyms". This redundancy, rather than being a flaw, can be exploited with a simple "synonym swap" strategy to generate diverse conformational ensembles by perturbing a predicted structure with its structural synonyms. This computationally lightweight method accurately recapitulates protein flexibility, performing competitively with state-of-the-art models. Our study provides fundamental insights into the nature of discrete protein structure representations and introduces a powerful, near-instantaneous method for modeling protein dynamics. Source code is available in https://github.com/IDEA-XL/TokenMD.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

If autoresearch is itself a form of research, then autoresearch can be applied to research itself. We present Bilevel Autoresearch, a bilevel framework in which an outer autoresearch loop improves an inner autoresearch loop by reading its code and traces, identifying bottlenecks, and generating injectable Python search mechanisms at runtime. The inner loop optimizes task performance; the outer loop optimizes how the inner loop searches. Both loops use the same LLM, so improvements come from the bilevel architecture rather than a stronger meta-level model, although the outer loop consumes additional inference and wall-clock budget. On Karpathy's GPT pretraining benchmark, the meta-autoresearch outer loop achieves a 5x improvement over the standard inner loop alone (-0.045 vs. -0.009 val_bpb), while parameter-level adjustment without mechanism change yields no reliable gain. The outer loop instantiates mechanisms from adjacent search domains, including combinatorial optimization, multi-armed bandits, and design of experiments, without human specification of the final mechanism design. Trace analysis suggests that these mechanisms break deterministic search patterns and force exploration of directions the LLM's priors avoid. The experiments demonstrate, on this benchmark, a first bilevel step: an outer loop improves the search behavior of an inner loop. Code is the mechanism carrier in this implementation, but skills, prompts, workflows, evaluators, domain principles, world-model assumptions, and memory schemas can also encode mechanisms that shape future agent behavior. This suggests a path toward recursive bootstrapping, where mechanisms discovered for the inner loop can be fed back to improve the meta-level loop itself.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Recursive self-improvement (RSI) lets a system improve the model-building machinery from its own failures, so every later model inherits the gain. Yet RSI has been validated almost exclusively on coding and formal benchmarks such as science QA and mathematics. This format bound limits RSI to improvement within a machine-checkable slice, not general capability where questions are open and correctness is settled by argument, replication, or measurement. We argue RSI must next operate across real, diverse scientific, engineering, and meta-scientific domains, not where formal evaluation is merely tractable. To that end we present MetaRSI-v1, where improvement is the scheduled composition of three typed operators over one unified paradigm. Data-RSI amplifies existing competence and marks its boundary; Harness-RSI edits a five-slot scaffold without touching weights; Model-RSI internalizes capability into parameters through bounded training. Sharing one loop kernel and artifact vocabulary, they make data, scaffold, and model changes composable rather than exclusive. A two-axis optimizer jointly decides operator order and each operator's proposal policy, while a meta-level policy revises the schedule across terms. We validate MetaRSI-v1 under the field's standard evaluations, on code and closed-form science, with no external teacher: the target model plays every role in its own loop. MetaRSI-v1 reframes self-improvement from a single-surface edit to a composition across the full model-production pipeline, opening two paths: a model route internalizing capability through training, and a harness route leaving weights untouched and thus extending self-improvement to any model reachable through an interface, with Data-RSI redefined as the shared substrate feeding both. The framework further yields refutable laws on where loops exist, how operators compose, and what supervision buys.

Predicting how genetic perturbations change cellular state is a core problem for building controllable models of gene regulation. Perturbations targeting the same gene can produce different transcriptional responses depending on their genomic locus, including different transcription start sites and regulatory elements. Gene-level perturbation models collapse these distinct interventions into the same representation. We introduce STRAND, a generative model that predicts single-cell transcriptional responses by conditioning on regulatory DNA sequence. STRAND represents a perturbation by encoding the sequence at its genomic locus and uses this representation to parameterize a conditional transport process from control to perturbed cell states. Representing perturbations by sequence, rather than by a fixed set of gene identifiers, supports zero-shot inference at loci not seen during training and expands inference-time genomic coverage from ~1.5% for gene-level single-cell foundation models to ~95% of the genome. We evaluate STRAND on CRISPR perturbation datasets in K562, Jurkat, and RPE1 cells. STRAND improves discrimination scores by up to 33% in low-sample regimes, achieves the best average rank on unseen gene perturbation benchmarks, and improves transfer to novel cell lines by up to 0.14 in Pearson correlation. Ablations isolate the gains to sequence conditioning and transport, and case studies show that STRAND resolves functionally alternative transcription start sites missed by gene-level models.

Autonomous improvement loops are hard to trust because the improvement process is usually external scaffolding bolted onto the agent: failures go unlogged, diagnoses cannot be replayed, and promote-or-discard decisions land in a side database rather than the agent's own history. We show that an event-sourced agent runtime removes that friction and turns controlled improvement into a first-class workflow. When the agent's state is a deterministic projection of an append-only event log, failures are recorded, a run replays exactly from its log, candidate patches scope to typed pipeline seams, gates are auditable, and every promotion or discard is itself an event. We demonstrate this with Regimes, a loop on the ActiveGraph runtime that diagnoses failed evaluations, proposes a repair at a pipeline point, and promotes it only after static checks, sandbox execution, in-sample evaluation, and held-out validation. The loop is target-agnostic: the same control flow runs against different tasks through a common interface. On LongMemEval-S the dominant failure is not retrieval but reconciliation: the evidence is already in the assembled context, yet the reader answers incorrectly. Across five seeded held-out splits, Regimes discovers reader-prompt repairs that improve final held-out accuracy by +0.05 to +0.10 in four splits and +0.01 in one over-promotion split; two splits are individually significant (seed 5 unadjusted for its sequential promotion structure), and the pooled count is descriptive only, since the splits share one 500-question pool. The durable contributions are ActiveGraph as an auditable substrate that makes controlled improvement loops tractable, the held-out-gated loop it supports, the failure-regime taxonomy routing each failure to a pipeline location (whose marginal value over an unrouted baseline is the primary open question), and the prompt-as-discovery-probe hypothesis.

Looped, weight-tied Transformers reduce parameters by reusing a single block, but decoding still stores a separate K/V cache for every recurrence step. We show that this loop-indexed cache is highly structured. For a fixed token, layer and head, K/V vectors trace a short low-rank trajectory across loops, while the head and layer axes remain much flatter. We introduce Looped Latent Attention (), a post-training cache codec that stores compact K and V latents and reconstructs loop-specific K/V vectors only when attention reads them. The default per-head codec compresses recurrence, while -2D also folds heads into one latent for the extreme-compression regime. The codec is initialized from the SVD of teacher activations and refined with logit and attention-output distillation. At matched cache budget, per-head outperforms head-axis MLA, cross-layer sharing, KV quantization and final-loop reuse, showing that the recurrent cache is low-rank but not safely collapsible to a single state. The same axis advantage holds on Ouro-2.6B-Thinking and transfers to Huginn-3.5B, where an SVD codec remains near-lossless to 32times compression in decoder-independent evaluation. The cache reduction is exact. On one H200, the latent-store path increases measured Ouro-1.4B batch capacity at 4k context from 32 to 768 sequences at 21.3times compression. Lastly, for long reasoning rollouts such as in MATH-500, on-policy refinement on student-generated prefixes raises accuracy at 4times compression from 0.43 to 0.66 and reduces no-answer generations when compared to token-level off-policy distillation.

Looped language models (LoopLMs) improve parameter efficiency by recursively reusing Transformer blocks, enabling deeper computation under a fixed model size. However, this reuse makes LoopLMs more fragile under post-training quantization (PTQ). We present the first systematic study of quantization in LoopLMs and identify three challenges: distribution shift across roles, state reuse across loop transitions, and recursive error accumulation. To address these challenges, we propose LoopQ, a loop-aware PTQ framework that preserves a shared quantized backbone while introducing lightweight adaptations. LoopQ combines activation scaling, selective transformation, cross-loop state alignment, and trajectory-aware optimization to reduce distributional mismatch within loops and error accumulation across loops. Experiments across seven benchmarks show that, under W4A4 quantization, LoopQ improves average downstream accuracy by 68.8% and reduces average perplexity by 87.7% compared with the strongest static PTQ baseline.

Starting from the Mellin-Barnes integral representation of a Feynman integral depending on set of kinematic variables z_i, we derive a system of partial differential equations w.r.t.\ new variables x_j, which parameterize the differentiable constraints z_i=y_i(x_j). In our algorithm, the powers of propagators can be considered as arbitrary parameters. Our algorithm can also be used for the reduction of multiple hypergeometric sums to sums of lower dimension, finding special values and reduction equations of hypergeometric functions in a singular locus of continuous variables, or finding systems of partial differential equations for master integrals with arbitrary powers of propagators. As an illustration, we produce a differential equation of fourth order in one variable for the one-loop two-point Feynman diagram with two different masses and arbitrary propagator powers.

Loop Engineering is emerging as a practice for organizing development work around coding agents. Instead of writing each prompt by hand, practitioners design loops that monitor progress, assign work, run checks, and decide what the agent should do next. Even with a capable coding agent, a loop may trust a stale progress note, skip needed verification, spend its budget in the wrong direction, or stop before the task is safe to submit. Yet the final outcome of one end-to-end run cannot tell whether success or failure reflects the loop's guidance or the coding agent's ability to carry out the task. We introduce LoopArena, a benchmark for evaluating how well one model can guide a separate coding agent through a long-running task. The model under evaluation is the Controller: after each coding round, it receives a structured summary of the run and instructs a separate, fixed coding agent, the Worker, on what to do or verify next, or decides whether to stop. LoopArena evaluates this ability in three complementary settings that differ in execution scope and cost. Type I scores next-step Loop Contract selection through execution-validated questions without running the Worker at evaluation time. Type II executes repeated control over a selected slice of a full task, while Type III evaluates the paired full task from its original state. On full tasks, the best observed Strict Success Rate is 24.69\%, leaving substantial room for improvement in long-horizon loop control. Across Controllers, the paired reduction in estimated inference cost averages 64.4\%, and Type II produces a similar ordering under the main Core criterion (Spearman's \(ρ=0.9747\)). We release the benchmark data and evaluation code at https://github.com/AMAP-ML/LoopArena .

We introduce the category of information structures, whose objects are suitable diagrams of measurable sets that encode the possible outputs of a given family of observables and their mutual relationships of refinement; they serve as mathematical models of contextuality in classical and quantum settings. Each information structure can be regarded as a ringed site with trivial topology; the structure ring is generated by the observables themselves and its multiplication corresponds to joint measurement. We extend Baudot and Bennequin's definition of information cohomology to this setting, as a derived functor in the category of modules over the structure ring, and show explicitly that the bar construction gives a projective resolution in that category, recovering in this way the cochain complexes previously considered in the literature. Finally, we study the particular case of a one-parameter family of coefficients made of functions of probability distributions. The only 1-cocycles are Shannon entropy or Tsallis alpha-entropy, depending on the value of the parameter.

Self-driving laboratories couple a learned design surrogate to an instrument, and on every new target domain it must answer four questions: when it can be trusted, how many target measurements it needs, which to make first, and when to stop adapting, switch models or escalate. We state a framework making each measurable (a competence ratio, a budget k^*(varepsilon), a time-to-target and a priced decision) and instantiate it without wet experiments on six public droplet-microfluidic and liposome tables as offline laboratories: 107 leave-one-group tiers whose rows are hidden labels. A sealed, pre-registered programme (two sealed negative validations and a pre-registered test on three more tables) and seven frozen closed-loop protocols, each run twice, yield 23 findings. Shift cost is stratified by shift type; no label-free statistic certifies individual candidates; random-split model-family rankings predicted neither the sealed nor the loop rankings. Warm-start residual boosting returns a surrogate to 1.25times its development reference within 20 target rows in 94% of chemistry tiers (27% under a strict noise-floor reading), 90% of laboratory and 40% of device tiers, and a budget planned from the shift type on other tables is not measurably worse on a new one. In the loop, one gain survives drift and shuffled-label controls on all tiers, carried by the sparsely sampled ones: proposing at once and warm-starting on every measurement reaches a 10% target in 2.80 measurements against 3.31 for the reference, and in 5.72 against 11.35 for random proposals on 301 hard units at a 3% tolerance. No label-free acquisition rule survives the shuffled-label control, no interval-aware proposal or other model family does better, and no threshold rule on the tested diagnostics beats always continuing once escalation is priced. No wet-lab validation is claimed.

How do protein structure prediction models fold proteins? We investigate this question through causal interventions on the folding trunks of ESMFold, OpenFold, and Boltz-1. Across all three models, we find a shared two-stage computational structure. In the first stage, early blocks initialize pairwise biochemical signals: features like charge propagate from sequence into pairwise representations through architecture-specific pathways. In the second stage, late blocks develop pairwise spatial features: distance and contact information accumulate in the pairwise representation. We verify these mechanisms causally by showing that steering charge and distance features induces predictable structural changes. Furthermore, these representations are functionally interchangeable: pairwise states can be linearly aligned and substituted across models. Together, these results suggest that folding trunks with different architectures, inputs, and training procedures converge on a shared representational organization for mapping sequence chemistry into spatial geometry.

Yes. Can it cure doom loops? Probably not. The Gemma 4 instruction-tuned models share a reproducible failure: on long factual enumeration prompts, such as listing every episode of a TV series, the 88 IAU constellations, or the 151 original Pokemon, they collapse into repetition, either a tight verbatim loop or a list whose entries decay onto a single answer. These loops occur at rates as high as 95% and survive prompt rewording, inference-engine changes, and most sampling adjustments. In this paper we explore whether this behavior is localized enough to remove by weight edits. To localize the cause, we use per-layer ablation and per-neuron attribution, then confirm the strongest candidates with full-generation sweeps. The loops trace to a small set of MLP neurons (or, in the 26B-A4B Mixture-of-Experts model, a few routed experts) which we suppress with static weight edits. These "surgeries" can be as small as a single sign-inverted neuron (in the E2B model). The size of the effective edits grows with model scale, but in all cases, the loop patterns can be addressed at normal generation budgets while preserving general-purpose benchmark scores. However, the edits do not solve everything: we also study longer thinking budgets, where the two larger models most visibly enter doom looping, i.e. a non-convergent regime in which the model self-corrects in circles over a fact it cannot recall, exhausting the budget without committing to a final answer. We show this residual failure is reduced but not eliminated by the same edits, and argue it is fundamentally a knowledge-precision problem rather than a removable circuit; weight surgery can delete a loop, but it cannot supply a missing fact. Our results are both a feasibility demonstration, that is, evidence that a concrete generation pathology can be localized to a few parameters and edited out, and a delineation of where that approach stops.

A single two-input gate suffices for all of Boolean logic in digital hardware. No comparable primitive has been known for continuous mathematics: computing elementary functions such as sin, cos, sqrt, and log has always required multiple distinct operations. Here I show that a single binary operator, eml(x,y)=exp(x)-ln(y), together with the constant 1, generates the standard repertoire of a scientific calculator. This includes constants such as e, pi, and i; arithmetic operations including addition, subtraction, multiplication, division, and exponentiation as well as the usual transcendental and algebraic functions. For example, exp(x)=eml(x,1), ln(x)=eml(1,eml(eml(1,x),1)), and likewise for all other operations. That such an operator exists was not anticipated; I found it by systematic exhaustive search and established constructively that it suffices for the concrete scientific-calculator basis. In EML (Exp-Minus-Log) form, every such expression becomes a binary tree of identical nodes, yielding a grammar as simple as S -> 1 | eml(S,S). This uniform structure also enables gradient-based symbolic regression: using EML trees as trainable circuits with standard optimizers (Adam), I demonstrate the feasibility of exact recovery of closed-form elementary functions from numerical data at shallow tree depths up to 4. The same architecture can fit arbitrary data, but when the generating law is elementary, it may recover the exact formula.

State Space Models (SSMs) are inherently recurrent along the sequence dimension, yet depth-recurrence - reusing the same block repeatedly across layers, as recently applied in looped transformers - has not been explored in this model family. We show that a looped SSM with k parameters iterated L times consistently closely matches or outperforms a standard SSM with k cdot L independent parameters across four architectures (LRU, S5, LinOSS, LrcSSM) and six time series classification benchmarks, despite operating within a strictly smaller hypothesis space, as we formally establish. Since the larger model contains the looped model as a special case, this dominance cannot be explained by expressivity and instead points to parameter sharing across depth as a beneficial inductive bias that simplifies optimization. These results demonstrate that depth-recurrence is orthogonal to sequence-recurrence and independently beneficial. We further show that input reshaping is an equally neglected design axis: concatenating timesteps for low-dimensional inputs, or flattening and rechunking the joint feature-time dimension for high-dimensional ones, yields accuracy gains of 1-6% across all models, confirmed over 5 random seeds. Both techniques provide standalone improvements that compound when combined, suggesting that depth and input reshaping are two independent and underexplored design axes for SSMs on time series.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

Long-sequence memory tracking places two opposing demands on a recurrent state: near-lossless retention of stored bindings over long horizons, and active overwriting of stale ones. In our diagnostic suite, the strongest efficient baselines tend to solve only one side well. Continuous-time-parameterized state-space models (SSMs) such as Mamba obtain their discrete recurrence by zero-order-hold discretization of a continuous-time system; we argue that this detour is unnecessary for memory tracking and parameterize the discrete transition directly. Naju (Native Adaptive Junction Unit) factorizes the recurrent update, schematically x_n = f_nodot x_{n-1} + i_nodot(B_n u_n), into an explicit discrete pole (a learned forget gate f_n), an independent write gain i_n, and input-dependent write/read maps. Since the sigmoid pole satisfies 0<f_n<1, each frozen local coordinate is Schur-stable by construction, and the full time-varying recurrence satisfies a fading-memory/BIBO bound under uniform boundedness assumptions, with no stability regularizer. We formalize the key structural limitation of coupled designs: any non-expansive complementary single-gate recurrence ties the effective retention r and write gain w through |r|+wle 1, so near-complete retention forces weak writing; decoupling f_n from i_n removes this constraint. Empirically, Naju is the only evaluated model that remains strong on both retention and overwriting at 4x the training length. Beyond the diagnostic suite, we evaluate Naju on WikiText-103 language modeling, Long Range Arena, and multi-query associative recall. Across these settings, Naju consistently combines strong long-range memory with competitive or superior performance, outperforming the Mamba baselines in the principal comparisons while remaining competitive with the Transformer and preserving linear-time, linear-memory scaling.

Reverse-mode differentiation is used for optimization, but it introduces references, which break the purity of the underlying programs, making them notoriously harder to optimize. We present a reverse-mode differentiation on a purely functional language with array operations. It is the first one to deliver a provably efficient, purely functional, and denotationally correct reverse-mode differentiation. We show that our transformation is semantically correct and verifies the cheap gradient principle. Inspired by PROPs and compilation to categories, we introduce a novel intermediate representation that we call 'unary form'. Our reverse-mode transformation is factored as a compilation scheme through this intermediate representation. We obtain provably efficient gradients by performing general partial evaluation optimizations after our reverse-mode transformation, as opposed to manually derived ones. For simple first-order programs, the obtained output programs resemble static-single-assignment (SSA) code. We emphasize the modularity of our approach and show how our language can easily be enriched with more optimized primitives, as required for some speed-ups in practice.

Turning a frontier vision-language model into a robot policy usually means fine-tuning it to emit an action representation it never saw in pretraining, which throws away much of the reasoning that made the model worth reaching for. We go the other way and keep the VLM frozen. It writes the policy as a short Python control function, with no demonstrations and no fine-tuning. Writing that code once is open-loop, though. Existing closed-loop methods react at the wrong level: they retry a fixed policy or pick a different subtask, but never rewrite the code that failed. VLCP closes the loop where the failure actually lives, on the control code, within a single episode. Every K steps the VLM re-observes the scene from multi-view RGB, proprioceptive state, and a state delta, then rewrites the control function from what it just saw, so a failure is caught before it compounds. We evaluate on a 57-task MuJoCo/RoboVerse sweep. This training-free policy reaches 35.1% pooled success, against 3.5% for the identical system queried once per episode. That tenfold gap holds with non-overlapping confidence intervals in every scene family. The gain traces to a 27.3% within-episode recovery rate on failed grasps: a miss an open-loop controller would carry to the end of the episode gets re-observed and fixed at the next replan. And the loop stays cheap. A median 84% of input tokens hit cache, an episode needs only about 10 compact queries, and control blocks written during any replan persist to a cross-episode skill library reused in later prompts.

Looped architectures provide an inductive bias toward learning step-by-step procedures for tasks that require compositional reasoning. The number of effective layers reached by looping determines the quality of the solution these models find. Like deep architectures, looped architectures are prone to a signal propagation problem induced by depth as the halting decision is postponed. In this paper, we address this signal propagation issue using pre-norm layers and residual scaling. Building on these architectural modifications, we propose FPRM, a Transformer-based Fixed-Point Reasoning Model that uses fixed-point convergence as an end-to-end halting mechanism in a looped architecture. We show that fixed-point halting allows FPRM to adapt its compute to task difficulty. FPRM is effective on common reasoning benchmarks, namely Sudoku, Maze, state-tracking, and ARC-AGI.

Intrinsically disordered protein regions (IDRs) play central roles in cellular processes such as transcriptional regulation, signal transduction, and subcellular localization, yet their functional design remains challenging. Structure-based design methods do not readily apply to IDRs, and existing protein language models are trained on full-length protein sequences, thus learning a prior that is biased towards folded domains. Here, we present IDiom, an autoregressive protein language model trained on IDiom-DB, a dataset of 54 million predicted IDRs curated from the AlphaFold Database. IDiom generates diverse sequences that recapitulate the composition, patterning, motifs, and predicted disorder of natural IDRs. To control function-associated sequence patterns, we also introduce reinforcement learning with sparse autoencoder features (RL-SAE), a post-training method that rewards the generation of sequences that activate specified feature sets. Across eight IDR design tasks, RL-SAE sequences activate, on average, 90% of 30 targeted features, compared to 24% for activation steering. We demonstrate that RL-SAE improves the predicted subcellular localization and transcriptional activity of generated IDRs compared to steering and supervised fine-tuning, and enables features associated with distinct biological functions to be combined within individual sequences. Thus, IDiom and RL-SAE enable interpretable and composable IDR design through explicit control of function-associated sequence features. More broadly, RL-SAE could extend to other protein design settings where interpretable features provide useful design targets. Code is available at https://github.com/rotskoff-group/idiom.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

Large Language Models (LLMs) are powerful but often too slow and costly for real-world use during inference. Looped transformers save on parameters by reusing the same weights for multiple computational steps, or "loops." However, this approach has a major flaw: the loops run one after another, causing inference latency and memory requirements to increase with each added loop. This makes them impractical for fast applications. To solve this problem, we introduce the Parallel Loop Transformer (PLT). PLT is a new architecture that delivers the performance benefits of a deep, looped model but with the low latency of a standard, non-looped model. PLT works using two key techniques. First, Cross-Loop Parallelism (CLP) breaks the sequential dependency by computing different loops for different tokens at the same time, all within a single pass. Second, to prevent memory costs from growing, we use an Efficient Representation Enhancement strategy. This method shares the memory (KV cache) from the first loop with all other loops. It then uses a Gated Sliding-Window Attention (G-SWA) to combine this shared global information with local information, maintaining high accuracy. Our experiments show that PLT achieves the high accuracy of a traditional looped model but with almost no extra latency or memory cost compared to a standard transformer.

We introduce training-free looped transformers, in which a lightweight inference-time wrapper loops a contiguous mid-stack block of layers of a frozen checkpoint without additional fine-tuning, continued training, or architectural changes. Unlike prior looped transformer methods that train with the looped structure end-to-end, we retrofit recurrence onto pretrained models at test time. We show that naive block reapplication usually degrades performance, highlighting the importance of the loop application strategy. Motivated by viewing a pre-norm transformer block as a forward Euler step on an ODE, we instead treat looping as a refinement of the same approximation, replacing one large update with smaller damped sub-steps. Across seven dense, sparse MoE, and MLA+MoE model families, our method improves Qwen3-4B-Instruct by +2.64 pp on MMLU-Pro, Qwen3-30B-A3B-Instruct by +1.14 pp on CommonsenseQA, and Moonlight-16B-A3B-Instruct by +1.20 pp on OpenBookQA.

Mixture-of-Experts (MoE) and looped architectures scale models along two orthogonal axes, namely parameter capacity and effective depth. However, mainstream looped architectures rely on dense backbones that couple parameter count with per-token FLOPs, which makes it impossible to isolate the effect of iterative computation under matched budgets. To this end, we present LoopMoE, a looped MoE language model that integrates sparse routing with iterative weight-shared computation through two designs. The first is IterAdaLN, which resolves weight-sharing symmetry via a modulation signal jointly conditioned on the iteration index and the per-token hidden state. The second is a capacity-balancing strategy that recovers the attention-to-FFN active parameter ratio of well-tuned non-looped references. Together, these designs enable the first strictly controlled, head-to-head evaluation of a looped MoE against a Vanilla MoE under identical total parameters, per-token FLOPs, and active sublayer ratios. At the 3B scale, LoopMoE outperforms the Vanilla MoE on 8 of 9 downstream benchmarks with an average improvement exceeding 1 point. At the 9B scale, LoopMoE continues to outperform the matched Vanilla MoE, indicating that the architectural gain persists at larger scale. Our work establishes a controlled synthesis of sparsity and recurrence, and suggests a promising direction for looped language models.

Multi-controlled single-target (MC) gates are some of the most crucial building blocks for varied quantum algorithms. How to implement them optimally is thus a pivotal question. To answer this question in an architecture-independent manner, and to get a worst-case estimate, we should look at a linear nearest-neighbor (LNN) architecture, as this can be embedded in almost any qubit connectivity. Motivated by the above, here we describe a method which implements MC gates using no more than sim 4k+8n CNOT gates -- up-to 60% reduction over state-of-the-art -- while allowing for complete flexibility to choose the locations of n controls, the target, and a dirty ancilla out of k qubits. More strikingly, in case k approx n, our upper bound is sim 12n -- the best known for unrestricted connectivity -- and if n = 1, our upper bound is sim 4k -- the best known for a single long-range CNOT gate over k qubits -- therefore, if our upper bound can be reduced, then the cost of one or both of these simpler versions of MC gates will be immediately reduced accordingly. In practice, our method provides circuits that tend to require fewer CNOT gates than our upper bound for almost any given instance of MC gates.

Looped transformers have emerged as a parameter-efficient alternative to scaling depth for strong reasoning. By reusing one stack of layers across T iterations, they attain the effective depth and reasoning capabilities of larger models at a fixed parameter count. Yet existing approaches suffer from latent overthinking and undifferentiated computation, largely because intermediate representations receive no guidance across loops. Multi-token prediction (MTP) supplies exactly the dense, forward-looking supervision the loop is missing. We propose LoopMTP, which links the two through a structural correspondence in latent space: a model that loops T times can anticipate T future tokens. LoopMTP realizes this by softly aligning the hidden state of loop t with the embedding of the token t steps ahead, while a lightweight gate preserves useful information across iterations. LoopMTP improves average accuracy by up to 8.1\% (relative) over the non-looped baseline, with training remaining stable for up to 15 loops.

Looped Language Models (LoopLMs) offer a parameter efficient approach to scaling reasoning by reusing shared parameters across recurrent computation steps. Despite their promise, effective post-training of LoopLMs remains challenging. Existing approaches either provide reward based supervision that is sparse or costly to extend across loops, or rely on external teachers or privileged information, leading to limited teacher availability or teacher-student context mismatch. To address these limitations, we introduce LoopOPD, a cross-loop on-policy distillation framework that uses additional recurrent computation within a LoopLM as its own source of supervision. LoopOPD uses a frozen terminal loop policy as a compute privileged teacher for an intermediate loop student on student generated rollouts, providing dense supervision without an external teacher or privileged information. We further propose Dynamic LoopOPD (D-LoopOPD), which continually refreshes the terminal loop teacher as the shared model parameters are updated, enabling recurrent self-improvement. We characterize how distillation updates propagate across loop depths and derive sufficient conditions under which a single update yields simultaneous local improvement at both loop depths. Experiments on Ouro-Thinking models show that LoopOPD improves mathematical reasoning, while D-LoopOPD yields further gains through dynamic teacher updates. Despite being trained only on mathematical data, the resulting models also improve on general reasoning and code generation benchmarks, demonstrating that recurrent computation can serve as an effective source of supervision for LoopLMs. Our code and model checkpoints will be released upon acceptance.

Iterative repair loops have become a core design pattern in LLM-based software engineering systems. These workflows repeatedly generate, validate, and repair artifacts using feedback such as compiler errors or test failures. Despite their widespread use, the impact of repair-loop iteration limits remains poorly understood, as most prior work adopts fixed, often arbitrary, repair budgets. We study repair-loop effectiveness across multiple software engineering tasks, including code generation, test generation, and code translation. Across several representative workflows, datasets, and contemporary low-cost LLMs, we observe a consistent pattern of diminishing returns: the first three to four repair iterations account for most achievable gains, while later iterations contribute only marginal improvements. We further find that repair behavior is influenced more strongly by workflow orchestration and feedback design than by the underlying model itself. These results suggest that repair budgets should be treated as an explicit experimental variable, as they directly affect evaluation outcomes, computational cost, runtime, and reproducibility in LLM-based software engineering research.

Large language models exhibit sophisticated capabilities, yet understanding how they work internally remains a central challenge. A fundamental obstacle is that training selects for behavior, not circuitry, so many weight configurations can implement the same function. Which internal structures reflect the computation, and which are accidents of a particular training run? This work extracts algorithmic cores: compact subspaces necessary and sufficient for task performance. Independently trained transformers learn different weights but converge to the same cores. Markov-chain transformers embed 3D cores in nearly orthogonal subspaces yet recover identical transition spectra. Modular-addition transformers discover compact cyclic operators at grokking that later inflate, yielding a predictive model of the memorization-to-generalization transition. GPT-2 language models govern subject-verb agreement through a single axis that, when flipped, inverts grammatical number throughout generation across scales. These results reveal low-dimensional invariants that persist across training runs and scales, suggesting that transformer computations are organized around compact, shared algorithmic structures. Mechanistic interpretability could benefit from targeting such invariants -- the computational essence -- rather than implementation-specific details.

We advocate a strategy of bootstrapping Feynman integrals from just knowledge of their singular behavior. This approach is complementary to other bootstrap programs, which exploit non-perturbative constraints such as unitarity, or amplitude-level constraints such as gauge invariance. We begin by studying where a Feynman integral can become singular, and the behavior it exhibits near these singularities. We then characterize the space of functions that we expect the integral to evaluate to, in order to formulate an appropriate ansatz. Finally, we derive constraints on where each singularity can appear in this ansatz, and use information about the expansion of the integral around singular points in order to determine the value of all remaining free coefficients. Throughout, we highlight how constraints that have previously only been derived for integrals with generic masses can be extended to integrals involving particles of equal or vanishing mass. We illustrate the effectiveness of this approach by bootstrapping a number of examples, including the four-point double box with a massive internal loop.

Unified vision-language models (VLMs) that tokenize images through a vector-quantized (VQ) codebook routinely hallucinate objects on grounded yes/no benchmarks, yet existing decoding-time fixes treat this as generic miscalibration without an architectural account. Using activation patching across twenty-five models spanning eight LLM families, we identify an early-layer (L_0) attention routing circuit shared across VQ-tokenized VLMs and propose a three-gate diagnostic that distinguishes the models carrying it from those that do not. The diagnostic isolates ten positive models (five natural unified-VQ VLMs across three LLM families and five induced variants) and rejects the remaining fifteen. A single-variable architectural swap (LLaVA-1.6 CLIP+MLP rightarrow VQ+Linear) installs the circuit, while a matched-compute MLP control on identical data does not, isolating vector quantization as the source of the pathological signal; the routing pathway that carries it is one that the backbone already provides. Against tuned VCD and DoLA baselines, tuned DoLA wins on binary calibration, but only L_0 ablation reduces object hallucination in open-ended generation (CHAIR_i reduces by 31,% relatively, whereas tuned DoLA and VCD leave it unchanged or worsen it). These results recast object hallucination in unified VQ VLMs as a property of architecture and pretraining, and yield a targeted intervention that mechanism-agnostic decoding cannot replicate.

Training a model to predict the next step in a concurrent program is harder than it looks: two runs of the same program from the same trace prefix can produce different next events, both valid, because the scheduler is nondeterministic. A model trained against a single label is learning to guess one outcome of a random process. We turn this around and use the nondeterminism as a training signal. We run each program many times, aggregate the observed next events into an empirical distribution, and fine-tune a 7B model to match that distribution with a KL objective. On 798 held-out predictions drawn from real production Go bugs (CockroachDB, Kubernetes, gRPC, etcd), fine-tuning on fewer than a thousand traces reaches 36.2% accuracy, ahead of Gemini 3.5 Flash used zero-shot (34.8%) and the same model without fine-tuning (28.6%). Distribution training matches cross-entropy on accuracy (35.8% vs. 36.2%) while reducing Expected Calibration Error from 0.205 to 0.169. We also derive a formal goroutine-leak signature for a class of select-blocked goroutines where P(GoUnblock)=0 holds by scheduler semantics, not by learning. We release the dataset, trained adapters, and all tooling.

Language models are increasingly used in scientific discovery to generate hypotheses, propose candidate solutions, implement systems, and iteratively refine them. At the core of these trial-and-error loops lies evaluation: the process of obtaining feedback on candidate solutions via verifiers, simulators, or task-specific scoring functions. While prior work has highlighted the importance of evaluation, it has not explicitly formulated the problem of how evaluation-driven discovery loops can be scaled up in a principled and effective manner to push the boundaries of scientific discovery, a problem this paper seeks to address. We introduce Simple Test-time Evaluation-driven Scaling (SimpleTES), a general framework that strategically combines parallel exploration, feedback-driven refinement, and local selection, revealing substantial gains unlocked by scaling evaluation-driven discovery loops along the right dimensions. Across 21 scientific problems spanning six domains, SimpleTES discovers state-of-the-art solutions using gpt-oss models, consistently outperforming both frontier-model baselines and sophisticated optimization pipelines. Particularly, we sped up the widely used LASSO algorithm by over 2x, designed quantum circuit routing policies that reduce gate overhead by 24.5%, and discovered new Erdos minimum overlap constructions that surpass the best-known results. Beyond novel discoveries, SimpleTES produces trajectory-level histories that naturally supervise feedback-driven learning. When post-trained on successful trajectories, models not only improve efficiency on seen problems but also generalize to unseen problems, discovering solutions that base models fail to uncover. Together, our results establish effective evaluation-driven loop scaling as a central axis for advancing LLM-driven scientific discovery, and provide a simple yet practical framework for realizing these gains.

In this work we demonstrate that a single transformer-based generative model can capture Standard Model structure spanning five decades of invariant mass, from the sub-GeV regime to the TeV continuum, a range that no single Monte Carlo sample covers. To achieve this we design ShellFlow, a Riemannian conditional flow matching model that, given the recorded event composition, generates each particle on its on-shell manifold. Its only physics priors are the on-shell condition and the invariant-mass formula. The model is trained on sim 10^{9} real pp collision events from the ATLAS Open Data 13~TeV release and told nothing else. From a single training run, the model learns to reproduce all of the following: intra-particle kinematics, the dilepton resonances (J/ψ, Υ, Z) at their PDG positions, the leptonic Weinberg angle, the W and top-quark masses, and inter-particle correlations that enter no training objective. A substantial fraction of the Standard Model is thus learnable directly from recorded collision data.

This monograph develops a unified account of training and inference in Power Law Decoder Representation language models (PLDR-LLMs). Exact finite work identities decompose changes in the absolute energy of the row-centered learned map into parameter contributions, signed interactions, and numerical observation defects. Positive affine blocking retains restarts at the row-constant face, while the augmented AdamW state supplies the complete dynamical description. Predictive renormalization acts on the complete conditional training law for a single pass over distinct corpus target blocks, retaining optimizer memory, remaining data, schedule, and numerical policy. Autonomous reductions require closure; approximate reductions carry successor and emission errors. Finite-population covariance, matched physical clocks, matrix fluxes, and signed temporal energy connect row dynamics to model-wide observations. Absolute row collapse, relative row concentration, operator stabilization, and predictive accuracy are distinguished. Experiments reveal observer and optimizer dependence, reject the tested autonomous row-state candidates, and support finite conditional prediction and state-specific operator reduction. Independent single-pass families exhibit moving finite fluctuation regions without establishing a thermodynamic critical class. Conditional symmetry, head limits, covariance flows, and readout error budgets specify assumptions needed to transfer scaling laws to inference. The theory separates exact identities, conditional dynamical claims, and finite empirical findings, with proofs, selected formal checks, and compact numerical evidence.

Looped transformers are a parameter-efficient alternative to standard transformers for language modeling. By reapplying the same layers across multiple loop steps, recent looped language models match the performance of non-looped models several times their size. While this architecture effectively reduces parameter memory, each loop step still stores its own keys and values, so the key-value (KV) cache grows linearly with the number of loop steps and becomes the main memory bottleneck. We observe that the KV cache of looped models is highly redundant along the loop axis and that the loop steps differ substantially in their sensitivity to quantization. Based on these observations, we propose LoopVQ, a KV cache vector quantization method for looped transformers that codes channels of multiple loop steps jointly, and fine-tunes the codebooks to match the output of the full-precision model. At 0.5 bits per element, LoopVQ outperforms existing KV cache vector quantization methods for standard LLMs on general, long chain-of-thought reasoning, and long-context retrieval tasks with Ouro and Huginn models. Its design is orthogonal to these methods, and combined with TaSQ, it retains much of the BF16 accuracy even at 0.25 bits per element. We also implement LoopVQ in SGLang, where it nearly halves the decode latency at a 32K-token context and raises the peak serving throughput by up to 4.3times and 6.1times on the 1.4B and 2.6B Ouro models compared to the BF16 baseline.

The success of deep learning is due in large part to our ability to solve certain massive non-convex optimization problems with relative ease. Though non-convex optimization is NP-hard, simple algorithms -- often variants of stochastic gradient descent -- exhibit surprising effectiveness in fitting large neural networks in practice. We argue that neural network loss landscapes often contain (nearly) a single basin after accounting for all possible permutation symmetries of hidden units a la Entezari et al. 2021. We introduce three algorithms to permute the units of one model to bring them into alignment with a reference model in order to merge the two models in weight space. This transformation produces a functionally equivalent set of weights that lie in an approximately convex basin near the reference model. Experimentally, we demonstrate the single basin phenomenon across a variety of model architectures and datasets, including the first (to our knowledge) demonstration of zero-barrier linear mode connectivity between independently trained ResNet models on CIFAR-10. Additionally, we identify intriguing phenomena relating model width and training time to mode connectivity. Finally, we discuss shortcomings of the linear mode connectivity hypothesis, including a counterexample to the single basin theory.

Traditional fixed-depth architectures scale quality by increasing training FLOPs, typically through increased parameterization, at the expense of a higher memory footprint, or data. A potential alternative is looped architectures, which instead increase FLOPs by sending activations through a block of layers in a loop. While promising, existing recipes for training looped architectures can be unstable, suffering from residual explosion and loss spikes. We address these challenges by recasting looping as a nonlinear time-variant dynamical system over the residual stream. Via a linear approximation to this system, we find that instability occurs in existing looped architectures as a result of large spectral norms in their injection parameters. To address these instability issues, we propose Parcae, a novel stable, looped architecture that constrains the spectral norm of the injection parameters via discretization of a negative diagonal parameterization. As a result, Parcae achieves up to 6.3% lower validation perplexity over prior large-scale looped models. Using our stable looped architecture, we investigate the scaling properties of looping as a medium to improve quality by increasing FLOPs in training and test-time. For training, we derive predictable power laws to scale FLOPs while keeping parameter count fixed. Our initial scaling laws suggest that looping and data should be increased in tandem, given a fixed FLOP budget. At test-time, we find that Parcae can use looping to scale compute, following a predictable, saturating exponential decay. When scaled up to 1.3B parameters, we find that Parcae improves CORE and Core-Extended quality by 2.99 and 1.18 points when compared to strong Transformer baselines under a fixed parameter and data budget, achieving a relative quality of up to 87.5% a Transformer twice the size.

Predicting single-cell responses to genetic and chemical perturbations is important for understanding regulatory mechanisms and prioritizing therapeutic interventions. Existing methods have made progress by modeling perturbation-conditioned expression shifts with neural networks, graph priors, foundation-model representations, or distributional generative models. However, combinatorial perturbation prediction remains challenging because much of the response can be explained by additive single-perturbation effects, while the biologically informative signal often lies in a smaller non-additive residual induced by perturbation interactions. Directly generating the full post-perturbation expression profile may therefore allocate substantial capacity to the dominant additive component and underemphasize synergy-specific structure. To address this issue, we propose SynGeneFlow, a synergy-aware flow matching framework that anchors the source distribution at an additive prior and learns a residual flow toward the true perturbed state. SynGeneFlow further incorporates perturbation-conditioned gene interaction modeling, where a static gene-gene mask provides biological structure and a perturbation-dependent deformation bias dynamically modulates gene-gene coupling. To preserve population-level response structure, we align both endpoint distributions and biological residual distributions with MMD-based regularization. We evaluate SynGeneFlow on genetic and drug perturbation benchmarks under observed-single, held-out, and cross-modality settings. The results demonstrate that residualizing flow matching around additive perturbation effects provides a biologically grounded and robust framework for single-cell perturbation response prediction.

Efficient quantum compiling tactics greatly enhance the capability of quantum computers to execute complicated quantum algorithms. Due to its fundamental importance, a plethora of quantum compilers has been designed in past years. However, there are several caveats to current protocols, which are low optimality, high inference time, limited scalability, and lack of universality. To compensate for these defects, here we devise an efficient and practical quantum compiler assisted by advanced deep reinforcement learning (RL) techniques, i.e., data generation, deep Q-learning, and AQ* search. In this way, our protocol is compatible with various quantum machines and can be used to compile multi-qubit operators. We systematically evaluate the performance of our proposal in compiling quantum operators with both inverse-closed and inverse-free universal basis sets. In the task of single-qubit operator compiling, our proposal outperforms other RL-based quantum compilers in the measure of compiling sequence length and inference time. Meanwhile, the output solution is near-optimal, guaranteed by the Solovay-Kitaev theorem. Notably, for the inverse-free universal basis set, the achieved sequence length complexity is comparable with the inverse-based setting and dramatically advances previous methods. These empirical results contribute to improving the inverse-free Solovay-Kitaev theorem. In addition, for the first time, we demonstrate how to leverage RL-based quantum compilers to accomplish two-qubit operator compiling. The achieved results open an avenue for integrating RL with quantum compiling to unify efficiency and practicality and thus facilitate the exploration of quantum advantages.

Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence. A student network infers each target-block representation from the remaining genes in a cell, while a slowly updated teacher supplies the corresponding target from the full observed gene set. Under the reported extraction procedure, block-level prediction produced embeddings with higher effective rank and weaker association with detected-gene depth in the tested diagnostics than token-prediction, random-block and reconstruction controls. Across CellBench tasks, frozen BioM-JEPA embeddings retained expression, pathway and neighbourhood information and achieved the lowest aggregate perturbation-response error among the evaluated models. Representation diagnostics were also consistent with canonical pancreatic programmes and compositional relationships between genetic perturbations. Linear attention avoids constructing a quadratic gene-by-gene attention matrix; in a matched one-epoch hPancreas experiment at batch size 8, BioM-JEPA provided 5.75-fold higher fine-tuning throughput and 3.76-fold higher held-out embedding throughput than scFoundation. Together, these results support graph-connected gene blocks as useful prediction units for JEPA-style representation learning in single-cell biology.

Experimental materials-science labs routinely accumulate synthesis and characterization data across spreadsheets, instrument export files, and ad-hoc folders, with no durable link between a sample's recipe, its measured properties, and whether a similar composition has been reported elsewhere. We present Stage 1 of an open-source data infrastructure closing this loop for a single working alloy-synthesis lab: a relational schema for composition and synthesis records, a strict composition/mass calculator, three empirical alloy-design screening metrics (VEC, atomic-size mismatch, mixing enthalpy) plus a melt/boil-point synthesis-feasibility check, an automated cross-referencing layer against three public materials databases (Materials Project, OQMD, Alexandria) with deduplication and adjustable relevance filtering, and a desktop GUI unifying the workflow behind a single "new entry" action. Built and used by a practicing researcher rather than a software team, we report it as a systems/methodology contribution - the architecture, the concrete engineering failures encountered while building it, and how each was diagnosed and fixed - rather than new materials-science results. We argue the specific defects found - a parser ambiguity that produced silent wrong answers, a partial code edit that broke a dependency chain invisibly, a database-metadata bug traceable to an un-cast numeric type, and a credential-hygiene gap that .gitignore alone did not close - generalize to any small scientific-software project built by a domain expert without formal software-engineering training. Both the system and the lessons from building it are reported here; two follow-on papers cover the validated characterization pipelines (Stage 2) and the retrieval-augmented synthesis advisor and CALPHAD thermodynamics module (Stage 3) built on this foundation.

Language-model agents that run long tasks often redo work they have already done: they re-issue a tool call they made earlier and get back exactly the same observation, a step that adds no new information. We identify this failure as a loop. Loops appear natively in Qwen, Llama, and Gemini agents and become far more common once the agent's history is compressed to fit its context window. To reduce these loops, we propose DeLoop, a self-supervised training method. DeLoop builds on a simple observation: the agent's own rollout can provide the supervision needed to learn from its loops. We use a looping action as a negative example and the first later non-looping action in the same rollout as a positive example. DeLoop learns from these pairs through direct preference optimization and does not require task rewards, gold answers, or LLM judges. On CodeGym under compression, DeLoop reduces the share of Qwen3-8B tasks containing loops from 57.3% to 6.1%. It also uses about one third as many steps per task, with similar task success. On Qwen3-32B, DeLoop reduces loops and steps while raising task success from 37.7% to 44.8%.

Protein motif scaffolding benchmarks assess whether generative models can build scaffolds around functionally important residues. Their conclusions depend on which motifs are tested and which criteria define success. Existing benchmarks typically use small hand-curated motif sets and static refolding criteria, but protein function often depends on conformational ensembles and transitions. Here, we address both benchmark scope and success criteria. We introduce BILBY-PRO, a systematically derived benchmark of structurally conserved functional motifs from PROSITE-linked experimental structures, comprising 220 cases from 174 PROSITE motif-pattern entries. Evaluating six recent scaffold-generation models reveals distinct patterns in target coverage and unique-solution yield: RFDiffusion and Proteina solve more targets, whereas ESM3 produces more unique successful scaffolds on the targets it solves. We further introduce BILBY-MD, a reference-based all-atom molecular dynamics evaluation framework. Applied to statically solved designs from the original MotifBench benchmark, it compares motif drift, scaffold drift, motif-contact preservation, and motif-dihedral free-energy landscapes against reference simulations. Of 55 statically solved model-problem pairs, 31 satisfy our MD-supported criterion and only 8 pass all checks. Compact, self-contained motifs are often MD-supported, whereas interface-like or context-dependent motifs fail more frequently. Static refolding success therefore provides useful evidence of local motif recovery but does not establish dynamical fidelity of the full scaffold. BILBY highlights three complementary axes of motif-scaffolding evaluation: target coverage, unique-solution yield, and MD-supported dynamical fidelity.

The synthesis of inductive loop invariants remains a critical bottleneck in automated program verification. While Large Language Models (LLMs) show promise in mitigating this issue, they often fail on complex programs, producing invariants that are invalid or computationally ineffective. Although fine-tuning is a natural strategy to address these limitations, obtaining high-quality training data remains an open challenge. We first formalize the properties required for a high-quality training invariant, and then present Wonda, a rigorous data curation pipeline that extracts such invariants from raw verifier output via AST-based normalization followed by LLM-driven semantic rewriting and augmentation with provable quality guarantees. Fine-tuning Small Language Models (SLMs) on Wonda-curated data yields consistent gains across the Qwen3, Llama-3.1, and Mistral families: the 4B and 8B Qwen3 models nearly double invariant correctness and double speedup rates, while Llama-3.1-8B triples both. On the challenging InvBench suite, the same 4B model outperforms an off-the-shelf model 20x its size and matches the end-to-end verification time of GPT-OSS-120B, while a 14B Qwen3 model matches that of the frontier model GPT-5.2, all without test-time compute overhead. Our code is publicly available on GitHub.

Coding agent infrastructure is shifting from harness engineering toward loop engineering as coding agents are deployed for sustained long-horizon software development. Existing benchmarks often center on localized tasks or end-state outcomes, offering limited insight into sustained execution. We introduce LOOPSBENCH, a long-horizon benchmark for loop engineering in coding agent evaluation. Each task is a dependency DAG over separately testable development units with source-evidenced prerequisite edges. LOOPSBENCH comprises 112 tasks from authentic sources spanning 8 programming languages and 9 domains. Its flow-aware runtime releases tests along the ready frontier and retains completed nodes as regression obligations. We evaluate frontier coding agents paired with widely used loop implementations. The strongest configuration, Opus-4.7 with Claude Code and outer continuation, resolves 25.00% of tasks. Recorded plans recover only part of the source-recovered prerequisite DAG, and regression events remain visible across the evaluated loop profiles. We open source the benchmark data and code, including all tasks, more than 5,300 development units, and executable tests, at microsoft/Loopsbench.

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

AI systems increasingly participate in their own improvement: revising their outputs, adapting their own harnesses during deployment, training on data they generate, and, increasingly, conducting AI research itself. This literature is described under a vocabulary ("self-refine," "self-reward," "self-play," "self-evolve") that conflates fundamentally different ambitions. We survey 1,250 arXiv papers (2024-2026) along two axes: what the system improves -- its behavior in deployment, its policy through training, its evaluator, or the research process itself -- and the degree of loop closure (human-in-the-loop to fully closed). The taxonomy separates bounded self-refinement -- convergent, evaluable, and already industrial practice -- from open-ended recursive self-improvement (RSI), which remains bounded by grounding requirements, collapse dynamics, and compute constraints on every measured axis. Its distinctive feature is a dedicated category for self-evaluation: every improvement loop is a claim that some signal can substitute for human judgment. We survey the evaluator design space -- judges, process reward models, verifiers, rubrics, meta-evaluation -- order the signals into a verification hierarchy from formal verifiers (strongest) to intrinsic self-assessment (weakest), and observe that demonstrated self-improvement strength tracks this hierarchy, that its failure modes (self-confirming loops, model collapse, diversity collapse) follow from its violations, and that the "research direction-setting" bottleneck keeping humans in the loop sits at the top of that hierarchy. We connect the technical literature to the theory of RSI limits and to the safety and governance questions raised by frontier-lab accounts of closing the loop, and identify governance-grade measurement of self-improvement as the field's most underpopulated niche.

Calculating the action and the interaction Hamiltonian at higher orders in cosmological perturbation theory is a cumbersome task. We employ the formalism of EFT of inflation in models of single field ultra slow-roll inflation and obtain a non-perturbative result for the Hamiltonian in terms of the Goldstone field pi. To complete the dictionary, a non-linear relation between the curvature perturbations and pi is presented. Equipped with these non-linear results, we calculate the higher order loop corrections in USR models which are employed for PBHs formation. It is shown that the loop corrections on long CMB scales increase rapidly with the number of loop L and the setup will go out of perturbative control at the four-loop level.

High-Level Synthesis leverages loop unrolling and array partitioning, but scheduling concurrent accesses is challenging when indices contain non-affine arithmetic. Conventional polyhedral frameworks systematically over-approximate these non-linear transformations, forcing conservative serialization that degrades performance. To minimize this bottleneck, we present a spatial verification framework operating at the LLVM Intermediate Representation (IR) level. By extracting flat arithmetic expressions from "getelementptr" instructions, it models memory banks as polymorphic spatial predicates to handle non-affine terms. Structural safety is enforced via a Conflict-Free Unrolling condition using Separation Logic's separating conjunction; concurrent operations targeting the same bank trigger an automatic spatial contradiction. This disjointness requirement is reduced to a matrix of pairwise inequalities over immutable Static Single Assignment (SSA) variables for a Satisfiability Modulo Theories (SMT) oracle. To guarantee safety against undecidable non-linear arithmetic, we implement a deterministic sequential fallback. Finally, a theorem of soundness bridges algebraic SMT verification with Register Transfer Level trace safety, ensuring physical hardware immune to structural memory collisions.

We introduce Loop Flow Transformers (LiFT), a family of looped generative models that scales computation by repeatedly applying a shared Diffusion Transformer (DiT) core, with only light changes to the standard architecture. Rather than asking every recurrent step for the final prediction, LiFT trains each step with a single regression target: a point on a straight path from the model's initial estimate to the flow-matching target. Because we index these targets by a continuous depth coordinate, a trained model can loop far beyond its training depth with no retraining, early exits, or other modifications. In our experiments, these longer rollouts improve generation, so inference computation can grow without adding parameters. On ImageNet at 256x256, LiFT-L/2 achieves an FID 3.34 points lower than our dense DiT-XL/2 baseline while using approximately 60% fewer parameters, 32% fewer training FLOPs, and 52% fewer inference FLOPs.

We study the realizability of simplicial complexes with a given pair of integer sequences, representing the node degree distribution and the facet size distribution, respectively. While the s-uniform variant of the problem is NP-complete when s geq 3, we identify two populations of input sequences, most of which can be solved in polynomial time using a recursive algorithm that we contribute. Combining with a sampler for the simplicial configuration model [J.-G. Young et al., Phys. Rev. E 96, 032312 (2017)], we facilitate the efficient sampling of simplicial ensembles from arbitrary degree and size distributions. We find that, contrary to expectations based on dyadic networks, increasing the nodes' degrees reduces the number of loops in simplicial complexes. Our work unveils a fundamental constraint on the degree-size sequences and sheds light on further analysis of higher-order phenomena based on local structures.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

We propose an evolution strategies-based algorithm for estimating gradients in unrolled computation graphs, called ES-Single. Similarly to the recently-proposed Persistent Evolution Strategies (PES), ES-Single is unbiased, and overcomes chaos arising from recursive function applications by smoothing the meta-loss landscape. ES-Single samples a single perturbation per particle, that is kept fixed over the course of an inner problem (e.g., perturbations are not re-sampled for each partial unroll). Compared to PES, ES-Single is simpler to implement and has lower variance: the variance of ES-Single is constant with respect to the number of truncated unrolls, removing a key barrier in applying ES to long inner problems using short truncations. We show that ES-Single is unbiased for quadratic inner problems, and demonstrate empirically that its variance can be substantially lower than that of PES. ES-Single consistently outperforms PES on a variety of tasks, including a synthetic benchmark task, hyperparameter optimization, training recurrent neural networks, and training learned optimizers.

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.

Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Nonetheless, given the success of generative models across different but related problems, it is natural to question whether these architectural designs are a necessary condition to build performant models. In this paper, we introduce SimpleFold, the first flow-matching based protein folding model that solely uses general purpose transformer blocks. Protein folding models typically employ computationally expensive modules involving triangular updates, explicit pair representations or multiple training objectives curated for this specific domain. Instead, SimpleFold employs standard transformer blocks with adaptive layers and is trained via a generative flow-matching objective with an additional structural term. We scale SimpleFold to 3B parameters and train it on approximately 9M distilled protein structures together with experimental PDB data. On standard folding benchmarks, SimpleFold-3B achieves competitive performance compared to state-of-the-art baselines, in addition SimpleFold demonstrates strong performance in ensemble prediction which is typically difficult for models trained via deterministic reconstruction objectives. Due to its general-purpose architecture, SimpleFold shows efficiency in deployment and inference on consumer-level hardware. SimpleFold challenges the reliance on complex domain-specific architectures designs in protein folding, opening up an alternative design space for future progress.

We present a deterministic framework for preparing an arbitrary three-qubit pure state. To leverage entanglement structure in the state-preparation task, we classify three-qubit pure states into five types with respect to a 1|2 bipartition. Given a target state specified by its amplitudes, we provide concrete criteria and concurrence-based tests that determine its type. For each type, we derive an explicit circuit template composed of elementary single-qubit rotations and CNOT gates, with gate parameters determined systematically from the Schmidt decomposition. The full construction is described step by step from the target amplitudes, with no procedural ambiguity. As an application, we further group frequently encountered three-qubit pure states in quantum information into four classes and provide an explicit circuit for each class. Compared with prior approaches, our circuits are designed for practical use: they admit a direct algorithmic instantiation, use only CNOT gates between adjacent qubits, and for certain classes achieve smaller gate counts and circuit depth.

This article provides an introduction to surface code quantum computing. We first estimate the size and speed of a surface code quantum computer. We then introduce the concept of the stabilizer, using two qubits, and extend this concept to stabilizers acting on a two-dimensional array of physical qubits, on which we implement the surface code. We next describe how logical qubits are formed in the surface code array and give numerical estimates of their fault-tolerance. We outline how logical qubits are physically moved on the array, how qubit braid transformations are constructed, and how a braid between two logical qubits is equivalent to a controlled-NOT. We then describe the single-qubit Hadamard, S and T operators, completing the set of required gates for a universal quantum computer. We conclude by briefly discussing physical implementations of the surface code. We include a number of appendices in which we provide supplementary information to the main text.

Synthesizing inductive loop invariants is fundamental to automating program verification. In this work, we observe that Large Language Models (such as gpt-3.5 or gpt-4) are capable of synthesizing loop invariants for a class of programs in a 0-shot setting, yet require several samples to generate the correct invariants. This can lead to a large number of calls to a program verifier to establish an invariant. To address this issue, we propose a {\it re-ranking} approach for the generated results of LLMs. We have designed a ranker that can distinguish between correct inductive invariants and incorrect attempts based on the problem definition. The ranker is optimized as a contrastive ranker. Experimental results demonstrate that this re-ranking mechanism significantly improves the ranking of correct invariants among the generated candidates, leading to a notable reduction in the number of calls to a verifier.

LLM-based agents execute multi-step tasks, but their behavioral structure remains opaque: long unstructured traces resist the safety auditing and runtime monitoring that deployment requires. Existing approaches operate per-trace or success-only, so they miss the cross-run topology that links next-step and failure prediction. To recover that shared structure, we collapse an entire trace corpus into a single, compact finite-state machine (FSM) that serves as a structural substrate for the otherwise unpredictable behavior of LLM agents. Across twelve public datasets, the FSMs are compact (7-43 states), replay held-out data at >=0.997 fitness with near-identical topology across splits, and build in milliseconds. This substrate addresses both prediction goals. For next-step prediction, FSM-state context outperforms Agent Workflow Memory on every ground-truth-matched dataset. For failure prediction, per-state behavioral features reach held-out AUROC up to 0.94, and an online monitor ranks failing runs above passing ones from a partial trace, triggering early stopping well before completion. Behavioral topology thus appears shaped more by the deployment harness than by the LLM, providing a model-agnostic structural primitive for safety auditing and runtime monitoring.

We apply the positivity bootstrap approach to SU(3) lattice Yang-Mills (YM) theory, extending previous studies of large N and SU(2) theories by incorporating multiple-trace Wilson loop operators. By utilizing Hermitian and reflection positivity conditions, alongside Schwinger-Dyson (SD) loop equations, we compute rigorous bounds for the expectation values of plaquette Wilson loops in 2D, 3D, and 4D YM theories. Our results exhibit clear convergence and are consistent with known analytic or numerical results. To enhance the approach, we introduce a novel twist-reflection positivity condition, which we prove to be exact in 2D YM theory. Additionally, we propose a dimensional-reduction truncation, where Wilson loop operators are effectively restricted to a lower-dimensional subplane, significantly simplifying computations. SD equations for double-trace Wilson loops are also derived in detail. Our findings suggest that the positivity bootstrap method is broadly applicable to higher-rank gauge theories beyond single-trace cases, providing a solid foundation for further non-perturbative investigations of gauge theories using positivity-based methods.

We measure how much one extra recurrence is worth to a looped (depth-recurrent) language model, in equivalent unique parameters. From an iso-depth sweep of 116 pretraining runs across recurrence counts r in {1, 2, 4, 8} spanning {sim}50times in training compute, we fit a joint scaling law L = E + A,(N_once + r^φ N_rec)^{-α} + B,D^{-β} and recover a new recurrence-equivalence exponent φ= 0.46. Intuitively, φ tells us whether looping a block r times is equivalent in validation loss to r unique blocks of a non-looped model (full equivalence, φ{=}1) or to a single block run repeatedly with no capacity gain (φ{=}0). Our φ= 0.46 sits in between, so each additional recurrence predictably increases validation loss at matched training compute. For example, at r{=}4 a 410M looped model performs on par with a 580M non-looped model, but incurs the training cost of a 1B non-looped one. We demonstrate the utility of φ as a measurement tool on two probes. Truncated backpropagation lowers φ to 0.38, indicating that the loop mechanism is poorly trained under truncation, even though validation loss decreases. Conversely, hyperconnections raise φ to 0.65, a genuine capacity gain. Our method applies to any looped LM and separates true loop improvements from token-budget gains.

We introduce Dory1.0-4B, a 4-billion-parameter looped (latent-recurrent) language model with elastic depth: a single checkpoint serves different inference compute budgets. Dory1.0-4B is built on a normalized Transformer (nGPT) backbone with interleaved sliding-window and full-attention layers, organized into an input block, a shared recurrent block, and an output block. At inference, the recurrent block can be applied a variable number of times. We pre-trained Dory1.0-4B on 6 trillion tokens. The first 4.5 trillion tokens were trained in NVFP4, and additional pre-training then extended the context length to 256K tokens. Next, we post-trained the model using Supervised Fine-Tuning (SFT) and Reinforcement Learning with Verifiable Rewards (RLVR), with a difficulty-aware loop curriculum that routes harder prompts to deeper loops. Increasing the loop count improves accuracy, with the largest gains on coding, agentic, and long-context benchmarks. With two or more loops, Dory1.0-4B outperforms larger models such as Qwen3.5-9B, Gemma 4 12B, and Gemma 4 26B-A4B on average across 12 benchmarks. Looping also makes Dory1.0-4B more token-efficient on agentic benchmarks: with four loops, it generates 1.3-2.5x fewer tokens than with one loop, as the extra computation is spent in latent space rather than on longer outputs. To reduce memory during looping, Dory1.0-4B caches keys and values only from the last loop, keeping its KV-cache footprint equal to that of a non-looped model at any loop count while retaining most of the accuracy gains. We open-source the BF16, MXFP8, NVFP4, and GGUF quantized checkpoints.

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

We present a reproducible, parameter-driven software workflow for optimizing approximate mutually unbiased basis (AMUB) configurations in arbitrary dimensions d using a Lie-algebra unitary parameterization. The workflow is designed for portable execution across CPU, Apple MPS, CUDA-capable GPU, and HPC backends, using a Taylor-series matrix exponential layer as an accelerator compatibility pathway. As a dimension-six case study, we optimize unanchored configurations across 100 random seeds for basis counts n = 3, 4, 5, 6 in complex128 and complex64 arithmetic. The workflow recovers exact three-basis configurations, identifies a recurrent four-basis partial-exact hub-and-triangle structure, and finds no near-exact pairs for n = 5 or n = 6 in the reported campaigns under the primary tolerance. As a hardware-execution check, we embed the representative d = 6, n = 4 transition unitaries into three-qubit 8x8 unitaries and execute the resulting circuits on the 156-qubit Heron processor ibm-marrakesh using subspace post-selection. The measured QPU pairwise losses are dominated by a hardware and compilation noise floor of approximately 0.02-0.08, associated with compiled circuits averaging 37 native CZ gates, which obscures the distinction between classically near-exact and defective pairs. The results provide a reproducible computational framework for exploring AMUB landscapes, together with an initial assessment of the challenges involved in executing optimized dimension-six unitaries on current quantum hardware.

Effective instruction tuning is indispensable for optimizing code LLMs, aligning model behavior with user expectations and enhancing model performance in real-world applications. However, most existing methods focus on code snippets, which are limited to specific functionalities and rigid structures, restricting the complexity and diversity of the synthesized data. To address these limitations, we introduce a novel feature tree-based synthesis framework inspired by Abstract Syntax Trees (AST). Unlike AST, which captures syntactic structure of code, our framework models semantic relationships between code elements, enabling the generation of more nuanced and diverse data. The feature tree is constructed from raw data and refined iteratively to increase the quantity and diversity of the extracted features. This process enables the identification of more complex patterns and relationships within the code. By sampling subtrees with controlled depth and breadth, our framework allows precise adjustments to the complexity of the generated code, supporting a wide range of tasks from simple function-level operations to intricate multi-file scenarios. We fine-tuned widely-used base models to create the EpiCoder series, achieving state-of-the-art performance at both the function and file levels across multiple benchmarks. Notably, empirical evidence indicates that our approach shows significant potential in synthesizing highly complex repository-level code data. Further analysis elucidates the merits of this approach by rigorously assessing data complexity and diversity through software engineering principles and LLM-as-a-judge method.

We propose LGGPT, an LLM-based model tailored for unified layout generation. First, we propose Arbitrary Layout Instruction (ALI) and Universal Layout Response (ULR) as the uniform I/O template. ALI accommodates arbitrary layout generation task inputs across multiple layout domains, enabling LGGPT to unify both task-generic and domain-generic layout generation hitherto unexplored. Collectively, ALI and ULR boast a succinct structure that forgoes superfluous tokens typically found in existing HTML-based formats, facilitating efficient instruction tuning and boosting unified generation performance. In addition, we propose an Interval Quantization Encoding (IQE) strategy that compresses ALI into a more condensed structure. IQE precisely preserves valid layout clues while eliminating the less informative placeholders, facilitating LGGPT to capture complex and variable layout generation conditions during the unified training process. Experimental results demonstrate that LGGPT achieves superior or on par performance compared to existing methods. Notably, LGGPT strikes a prominent balance between proficiency and efficiency with a compact 1.5B parameter LLM, which beats prior 7B or 175B models even in the most extensive and challenging unified scenario. Furthermore, we underscore the necessity of employing LLMs for unified layout generation and suggest that 1.5B could be an optimal parameter size by comparing LLMs of varying scales. Code is available at https://github.com/NiceRingNode/LGGPT.

We present the powerful module-intersection integration-by-parts (IBP) method, suitable for multi-loop and multi-scale Feynman integral reduction. Utilizing modern computational algebraic geometry techniques, this new method successfully trims traditional IBP systems dramatically to much simpler integral-relation systems on unitarity cuts. We demonstrate the power of this method by explicitly carrying out the complete analytic reduction of two-loop five-point non-planar hexagon-box integrals, with degree-four numerators, to a basis of 73 master integrals.

Antibodies are essential therapeutic molecules, and their complementarity-determining regions (CDRs) form the primary antigen-recognition interface. Recent protein generative models have demonstrated broad capabilities in biomolecular design, yet post-training strategies for downstream objectives remain limited. Standard denoising training operates on noisy states obtained by perturbing native structures, whereas recursive generation proceeds through model-generated intermediate states. For flexible antibody CDR loops such as CDR-H3, this mismatch can allow backbone deviations to accumulate along the denoising trajectory and compromise antigen-facing loop geometry. We introduce ABOPD, an antibody design framework based on on-policy distillation that leverages privileged native geometry during training to supervise states visited along the model's own denoising trajectories. With this fine-grained structural supervision, ABOPD substantially improves structural recovery on RAbD CDR-H3 generation, reducing RMSD by 0.42 Å (from 2.37 Å to 1.95 Å) and outperforming supervised fine-tuning and offline distillation controls, offering a path to higher-fidelity protein design.

Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing dataset offers comprehensive 3D structural information with detailed subcellular localization annotations, thus severely hindering the application of promising structure-based models on this task. To address this gap, we introduce a new benchmark called CAPSUL, a Comprehensive humAn Protein benchmark for SUbcellular Localization. It features a dataset that integrates diverse 3D structural representations with fine-grained subcellular localization annotations carefully curated by domain experts. We evaluate this benchmark using a variety of state-of-the-art sequence-based and structure-based models, showcasing the importance of involving structural features in this task. Furthermore, we explore reweighting and single-label classification strategies to facilitate future investigation on structure-based methods for this task. Lastly, we showcase the powerful interpretability of structure-based methods through a case study on the Golgi apparatus, where we discover a decisive localization pattern α-helix from attention mechanisms, demonstrating the potential for bridging the gap with intuitive biological interpretability and paving the way for data-driven discoveries in cell biology.

We present a decomposition technique that uses non-deterministic circuits to approximate an arbitrary single-qubit unitary to within distance ε and requires significantly fewer non-Clifford gates than existing techniques. We develop "Repeat-Until-Success" (RUS) circuits and characterize unitaries that can be exactly represented as an RUS circuit. Our RUS circuits operate by conditioning on a given measurement outcome and using only a small number of non-Clifford gates and ancilla qubits. We construct an algorithm based on RUS circuits that approximates an arbitrary single-qubit Z-axis rotation to within distance ε, where the number of T gates scales as 1.26log_2(1/ε) - 3.53, an improvement of roughly three-fold over state-of-the-art techniques. We then extend our algorithm and show that a scaling of 2.4log_2(1/ε) - 3.28 can be achieved for arbitrary unitaries and a small range of ε, which is roughly twice as good as optimal deterministic decomposition methods.

Self-evolving agents violate the assumption behind most learning-theoretic guarantees: the data, evaluator, components, and hypothesis space are produced by the policy being updated. We present SEA, an architecture that confines self-modification to a small steering adapter and a versioned harness around a frozen base model and admits each modification only through an anytime-valid gate that emits an auditable certificate against a fixed error budget. Five loop controllers compose published guarantees; because such gates can only select among behaviors the frozen base already produces, five verifier-in-the-loop mechanisms -- best-of-N, micro-step search, self-authored reproduction oracles, search-layer control, and self-repair -- supply the dense, grader-free signal the gates require, computed from the issue text alone. On a 52-instance SWE-bench Verified subset across four base models, base capability is the dominant, confound-free effect, and on two strong base models a deliberate no-op-composite control isolates the suite's contribution at +4 and +5 (Glm~5.2 24to28; Gpt 29to34, the 65% best), with event logs confirming that its mechanisms fire and prevent regressions. Results are single-run on expensive evaluations; confirming run-to-run variance and adapting the per-task algorithm mix are future work.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D geometry and conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. Under the hood, gRNAde is a multi-state Graph Neural Network that generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. [2010], gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Open source code: https://github.com/chaitjo/geometric-rna-design

The ground state search problem is central to quantum computing, with applications spanning quantum chemistry, condensed matter physics, and optimization. The Variational Quantum Eigensolver (VQE) has shown promise for small systems but faces significant limitations. These include barren plateaus, restricted ansatz expressivity, and reliance on domain-specific structure. We present SpinGQE, an extension of the Generative Quantum Eigensolver (GQE) framework to spin Hamiltonians. Our approach reframes circuit design as a generative modeling task. We employ a transformer-based decoder to learn distributions over quantum circuits that produce low-energy states. Training is guided by a weighted mean-squared error loss between model logits and circuit energies evaluated at each gate subsequence. We validate our method on the four-qubit Heisenberg model, demonstrating successfulconvergencetonear-groundstates. Throughsystematichyperparameterexploration, we identify optimal configurations: smaller model architectures (12 layers, 8 attention heads), longer sequence lengths (12 gates), and carefully chosen operator pools yield the most reliable convergence. Our results show that generative approaches can effectively navigate complex energy landscapes without relying on problem-specific symmetries or structure. This provides a scalable alternative to traditional variational methods for general quantum systems. An open-source implementation is available at https://github.com/Mindbeam-AI/SpinGQE.

We study a class of orbit recovery problems in which we observe independent copies of an unknown element of R^p, each linearly acted upon by a random element of some group (such as Z/p or SO(3)) and then corrupted by additive Gaussian noise. We prove matching upper and lower bounds on the number of samples required to approximately recover the group orbit of this unknown element with high probability. These bounds, based on quantitative techniques in invariant theory, give a precise correspondence between the statistical difficulty of the estimation problem and algebraic properties of the group. Furthermore, we give computer-assisted procedures to certify these properties that are computationally efficient in many cases of interest. The model is motivated by geometric problems in signal processing, computer vision, and structural biology, and applies to the reconstruction problem in cryo-electron microscopy (cryo-EM), a problem of significant practical interest. Our results allow us to verify (for a given problem size) that if cryo-EM images are corrupted by noise with variance σ^2, the number of images required to recover the molecule structure scales as σ^6. We match this bound with a novel (albeit computationally expensive) algorithm for ab initio reconstruction in cryo-EM, based on invariant features of degree at most 3. We further discuss how to recover multiple molecular structures from mixed (or heterogeneous) cryo-EM samples.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.