Daily Papers

Medical coding translates clinical documentation into standardized codes for billing, research, and public health, but manual coding is time-consuming and error-prone. Existing automation efforts rely on small datasets that poorly represent real-world patient heterogeneity. We trained a language model on 5.8 million electronic health records from 1.8 million patients across nearly all specialties in Eastern Denmark (2006--2016) to predict ICD-10 codes from clinical notes, medications, and laboratory results. Evaluated on 270,000 held-out patients, the model achieved a micro F1 of 71.8% and a top-10 recall of 95.5%. Performance varied by specialty (F1: 53--91%), with higher scores in specialties with well-defined diagnostic criteria. Codes appearing predominantly as secondary diagnoses had markedly lower F1 scores. For three such codes (suicide-related behaviors, weight disorders, and hypertension), the model identified thousands of uncoded cases, of which 76-86% were confirmed valid upon manual review, suggesting systematic under-coding rather than model error. These findings suggest under-coding of secondary diagnoses in Eastern Denmark during this period, with potential implications for epidemiological research, public health surveillance, and understanding of multimorbidity. Similar time constraints and reimbursement structures in other healthcare systems suggest this may not be isolated to this dataset. The model can automate coding for approximately 50% of cases and provide accurate suggestions for most others, and may offer a practical solution to help capture missed secondary conditions.

Test-Driven Development (TDD) is a widely adopted software engineering practice that requires developers to create and execute tests alongside code implementation, ensuring that software behavior is continuously validated and refined. In the era of vibe coding, where developers increasingly delegate code writing to large language models (LLMs) by specifying high-level intentions, TDD becomes even more crucial, as test cases serve as executable specifications that explicitly define and verify intended functionality beyond what natural-language descriptions and code context can convey. While vibe coding under TDD is promising, there are three main challenges: (1) selecting a small yet effective test suite to improve the generation accuracy and control the execution workload, (2) retrieving context such as relevant code effectively, and (3) systematically using test feedback for effective code refinement. To address these challenges, we introduce TENET, an LLM agent for generating functions in complex real-world repositories under the TDD setting. TENET features three components: (1) a novel test harness mechanism that selects a concise test suite to maximize diversity of target usage scenarios; (2) a tailored agent toolset that performs efficient retrieval of relevant code with interactive debugging; and (3) a reflection-based refinement workflow that iteratively analyzes failures, replenishes context, and applies code refinement. TENET achieves 69.08% and 81.77% Pass@1 on RepoCod and RepoEval benchmarks, outperforming the best agentic baselines by 9.49 and 2.17 percentage points, respectively. In addition, this is the first study of test-driven code generation with repository-level context, examining how different aspects of test suites affect the performance of LLM agents under the TDD setting.

Recent advances in large language models have improved the capabilities of coding agents, yet systematic evaluation of complex, end-to-end website development remains limited. To address this gap, we introduce Vision2Web, a hierarchical benchmark for visual website development, spanning from static UI-to-code generation, interactive multi-page frontend reproduction, to long-horizon full-stack website development. The benchmark is constructed from real-world websites and comprises a total of 193 tasks across 16 categories, with 918 prototype images and 1,255 test cases. To support flexible, thorough and reliable evaluation, we propose workflow-based agent verification paradigm based on two complementary components: a GUI agent verifier and a VLM-based judge. We evaluate multiple visual language models instantiated under different coding-agent frameworks, revealing substantial performance gaps at all task levels, with state-of-the-art models still struggling on full-stack development.

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

Frontier coding agents are increasingly used in workflows where users supervise progress primarily through repeated improvement of a public score, namely the reported score on a public evaluation file with labels in the workspace, rather than through direct inspection of the agent's intermediate outputs. We study whether multi-round user pressure to improve that score induces public score exploitation: behavior that raises the public score through shortcuts without improving hidden private evaluation. We begin with a preliminary single-script tabular classification task, where GPT-5.4 and Claude Opus 4.6 both exploit label information within 10 rounds of user-agent interaction. We then build AgentPressureBench, a 34-task machine-learning repository benchmark spanning three input modalities, and collect 1326 multi-round trajectories from 13 coding agents. On our benchmark, we observe 403 exploitative runs, spanning across all tasks. We also find that stronger models have higher exploitation rates, supported by a significant Spearman rank correlation of 0.77. Our ablation experiments show that higher user pressure leads to earlier exploitation, reducing the average first exploit round by 15.6 rounds (i.e., 19.67 to 4.08). As a mitigation, adding explicit anti-exploit wordings in prompt mostly eliminates exploitation (100% to 8.3%). We hope that our work can bring attention to more careful use of coding agents workflow, and developing more robust coding agents under user pressure. Our project page is at https://ucsc-vlaa.github.io/AgentPressureBench .

This study investigates the feasibility and performance of federated learning (FL) for multi-label ICD code classification using clinical notes from the MIMIC-IV dataset. Unlike previous approaches that rely on centralized training or fine-tuned large language models, we propose a lightweight and scalable pipeline combining frozen text embeddings with simple multilayer perceptron (MLP) classifiers. This design offers a privacy-preserving and deployment-efficient alternative for clinical NLP applications, particularly suited to distributed healthcare settings. Extensive experiments across both centralized and federated configurations were conducted, testing six publicly available embedding models from Massive Text Embedding Benchmark leaderboard and three MLP classifier architectures under two medical coding (ICD-9 and ICD-10). Additionally, ablation studies over ten random stratified splits assess performance stability. Results show that embedding quality substantially outweighs classifier complexity in determining predictive performance, and that federated learning can closely match centralized results in idealized conditions. While the models are orders of magnitude smaller than state-of-the-art architectures and achieved competitive micro and macro F1 scores, limitations remain including the lack of end-to-end training and the simplified FL assumptions. Nevertheless, this work demonstrates a viable way toward scalable, privacy-conscious medical coding systems and offers a step toward for future research into federated, domain-adaptive clinical AI.

For a language model (LM) to faithfully model human language, it must compress vast, potentially infinite information into relatively few dimensions. We propose analyzing compression in (pre-trained) LMs from two points of view: geometric and information-theoretic. We demonstrate that the two views are highly correlated, such that the intrinsic geometric dimension of linguistic data predicts their coding length under the LM. We then show that, in turn, high compression of a linguistic dataset predicts rapid adaptation to that dataset, confirming that being able to compress linguistic information is an important part of successful LM performance. As a practical byproduct of our analysis, we evaluate a battery of intrinsic dimension estimators for the first time on linguistic data, showing that only some encapsulate the relationship between information-theoretic compression, geometric compression, and ease-of-adaptation.

Humans view the world through many sensory channels, e.g., the long-wavelength light channel, viewed by the left eye, or the high-frequency vibrations channel, heard by the right ear. Each view is noisy and incomplete, but important factors, such as physics, geometry, and semantics, tend to be shared between all views (e.g., a "dog" can be seen, heard, and felt). We investigate the classic hypothesis that a powerful representation is one that models view-invariant factors. We study this hypothesis under the framework of multiview contrastive learning, where we learn a representation that aims to maximize mutual information between different views of the same scene but is otherwise compact. Our approach scales to any number of views, and is view-agnostic. We analyze key properties of the approach that make it work, finding that the contrastive loss outperforms a popular alternative based on cross-view prediction, and that the more views we learn from, the better the resulting representation captures underlying scene semantics. Our approach achieves state-of-the-art results on image and video unsupervised learning benchmarks. Code is released at: http://github.com/HobbitLong/CMC/.

Large language model (LLM) powered code agents are rapidly transforming software engineering by automating tasks such as testing, debugging, and repairing, yet the security risks of their generated code have become a critical concern. Existing benchmarks have offered valuable insights but remain insufficient: they often overlook the genuine context in which vulnerabilities were introduced or adopt narrow evaluation protocols that fail to capture either functional correctness or newly introduced vulnerabilities. We therefore introduce SecureAgentBench, a benchmark of 105 coding tasks designed to rigorously evaluate code agents' capabilities in secure code generation. Each task includes (i) realistic task settings that require multi-file edits in large repositories, (ii) aligned contexts based on real-world open-source vulnerabilities with precisely identified introduction points, and (iii) comprehensive evaluation that combines functionality testing, vulnerability checking through proof-of-concept exploits, and detection of newly introduced vulnerabilities using static analysis. We evaluate three representative agents (SWE-agent, OpenHands, and Aider) with three state-of-the-art LLMs (Claude 3.7 Sonnet, GPT-4.1, and DeepSeek-V3.1). Results show that (i) current agents struggle to produce secure code, as even the best-performing one, SWE-agent supported by DeepSeek-V3.1, achieves merely 15.2% correct-and-secure solutions, (ii) some agents produce functionally correct code but still introduce vulnerabilities, including new ones not previously recorded, and (iii) adding explicit security instructions for agents does not significantly improve secure coding, underscoring the need for further research. These findings establish SecureAgentBench as a rigorous benchmark for secure code generation and a step toward more reliable software development with LLMs.

AI coding agents are reshaping software development through both autonomous and human-mediated pull requests (PRs). When developers use AI agents to generate code under their own accounts, code authorship attribution becomes critical for repository governance, research validity, and understanding modern development practices. We present the first study on fingerprinting AI coding agents, analyzing 33,580 PRs from five major agents (OpenAI Codex, GitHub Copilot, Devin, Cursor, Claude Code) to identify behavioral signatures. With 41 features spanning commit messages, PR structure, and code characteristics, we achieve 97.2% F1-score in multi-class agent identification. We uncover distinct fingerprints: Codex shows unique multiline commit patterns (67.5% feature importance), and Claude Code exhibits distinctive code structure (27.2% importance of conditional statements). These signatures reveal that AI coding tools produce detectable behavioral patterns, suggesting potential for identifying AI contributions in software repositories.

Large models have achieved remarkable performance across various tasks, yet they incur significant computational costs and privacy concerns during both training and inference. Distributed deployment has emerged as a potential solution, but it necessitates the exchange of intermediate information between model segments, with feature representations serving as crucial information carriers. To optimize information exchange, feature coding methods are applied to reduce transmission and storage overhead. Despite its importance, feature coding for large models remains an under-explored area. In this paper, we draw attention to large model feature coding and make three contributions to this field. First, we introduce a comprehensive dataset encompassing diverse features generated by three representative types of large models. Second, we establish unified test conditions, enabling standardized evaluation pipelines and fair comparisons across future feature coding studies. Third, we introduce two baseline methods derived from widely used image coding techniques and benchmark their performance on the proposed dataset. These contributions aim to advance the field of feature coding, facilitating more efficient large model deployment. All source code and the dataset are now available at https://github.com/chansongoal/FCM-LM/tree/master{https://github.com/chansongoal/FCM-LM/tree/master}.

Agents based on Large Language Models (LLMs) have shown promise for performing sophisticated software engineering tasks autonomously. In addition, there has been progress towards developing agents that can perform parts of the research pipeline in machine learning and the natural sciences. We argue that research extension and its implementation is a critical capability for such systems, and introduce RExBench to support the evaluation of this capability. RExBench is a benchmark consisting of 12 realistic research experiment implementation tasks that aim to investigate research hypotheses that have not previously been implemented. Each task is set up as an extension to an existing research paper and codebase, accompanied by domain expert-written instructions. RExBench is robust to data contamination, and supports an automatic evaluation infrastructure that executes agent outputs to determine whether the success criteria are met. We use this benchmark to evaluate nine LLM agents implemented using three different frameworks: aider, Claude Code, and OpenHands. We find that all agents evaluated fail to autonomously implement the majority of the extensions. Although the success rate improves with additional human-written hints, the best performance under this setting remains below 40%. This indicates that current agents are still short of being able to handle realistic research extension tasks without substantial human guidance.

Evaluating large language models (LLMs) for software engineering has been limited by narrow task coverage, language bias, and insufficient alignment with real-world developer workflows. Existing benchmarks often focus on algorithmic problems or Python-centric bug fixing, leaving critical dimensions of software engineering underexplored. To address these gaps, we introduce SWE-Compass1, a comprehensive benchmark that unifies heterogeneous code-related evaluations into a structured and production-aligned framework. SWE-Compass spans 8 task types, 8 programming scenarios, and 10 programming languages, with 2000 high-quality instances curated from authentic GitHub pull requests and refined through systematic filtering and validation. We benchmark ten state-of-the-art LLMs under two agentic frameworks, SWE-Agent and Claude Code, revealing a clear hierarchy of difficulty across task types, languages, and scenarios. Moreover, by aligning evaluation with real-world developer practices, SWE-Compass provides a rigorous and reproducible foundation for diagnosing and advancing agentic coding capabilities in large language models.

Modern coding scaffolds turn LLMs into capable software agents, but their ability to follow scaffold-specified instructions remains under-examined, especially when constraints are heterogeneous and persist across interactions. To fill this gap, we introduce OctoBench, which benchmarks scaffold-aware instruction following in repository-grounded agentic coding. OctoBench includes 34 environments and 217 tasks instantiated under three scaffold types, and is paired with 7,098 objective checklist items. To disentangle solving the task from following the rules, we provide an automated observation-and-scoring toolkit that captures full trajectories and performs fine-grained checks. Experiments on eight representative models reveal a systematic gap between task-solving and scaffold-aware compliance, underscoring the need for training and evaluation that explicitly targets heterogeneous instruction following. We release the benchmark to support reproducible benchmarking and to accelerate the development of more scaffold-aware coding agents.

Auto-regressive Large Language Models (LLMs) achieve strong performance on coding tasks, but incur high memory and inference costs. Diffusion-based language models (d-LLMs) offer bounded inference cost via iterative denoising, but their behavior under post-training quantization (PTQ) has been sparsely explored. We investigate the application and robustness of PTQ techniques, specifically GPTQ and a modified Hessian-Aware Quantization (HAWQ) algorithm, on a diffusion-based coding LLM (CoDA) and observe that these methods applied to CoDA exhibit greater robustness at low bitwidths compared to Qwen3-1.7B, its auto-regressive counterpart, under a standardized evaluation pipeline. We find that in our setup, CoDA exhibits greater robustness at low bitwidths (2-4 bits), with smaller accuracy degradation across HumanEval and MBPP benchmarks. Additionally, mixed-precision configurations derived from HAWQ provide smooth trade-offs across accuracy, latency, and memory. The results suggest that diffusion LLMs may offer advantages for efficient deployment due to more quantization-resilience.

In this paper, we propose KnowCoder, a Large Language Model (LLM) to conduct Universal Information Extraction (UIE) via code generation. KnowCoder aims to develop a kind of unified schema representation that LLMs can easily understand and an effective learning framework that encourages LLMs to follow schemas and extract structured knowledge accurately. To achieve these, KnowCoder introduces a code-style schema representation method to uniformly transform different schemas into Python classes, with which complex schema information, such as constraints among tasks in UIE, can be captured in an LLM-friendly manner. We further construct a code-style schema library covering over 30,000 types of knowledge, which is the largest one for UIE, to the best of our knowledge. To ease the learning process of LLMs, KnowCoder contains a two-phase learning framework that enhances its schema understanding ability via code pretraining and its schema following ability via instruction tuning. After code pretraining on around 1.5B automatically constructed data, KnowCoder already attains remarkable generalization ability and achieves relative improvements by 49.8% F1, compared to LLaMA2, under the few-shot setting. After instruction tuning, KnowCoder further exhibits strong generalization ability on unseen schemas and achieves up to 12.5% and 21.9%, compared to sota baselines, under the zero-shot setting and the low resource setting, respectively. Additionally, based on our unified schema representations, various human-annotated datasets can simultaneously be utilized to refine KnowCoder, which achieves significant improvements up to 7.5% under the supervised setting.

The advancement of large language models (LLMs) has catalyzed a paradigm shift from code generation assistance to autonomous coding agents, enabling a novel development methodology termed "Vibe Coding" where developers validate AI-generated implementations through outcome observation rather than line-by-line code comprehension. Despite its transformative potential, the effectiveness of this emergent paradigm remains under-explored, with empirical evidence revealing unexpected productivity losses and fundamental challenges in human-AI collaboration. To address this gap, this survey provides the first comprehensive and systematic review of Vibe Coding with large language models, establishing both theoretical foundations and practical frameworks for this transformative development approach. Drawing from systematic analysis of over 1000 research papers, we survey the entire vibe coding ecosystem, examining critical infrastructure components including LLMs for coding, LLM-based coding agent, development environment of coding agent, and feedback mechanisms. We first introduce Vibe Coding as a formal discipline by formalizing it through a Constrained Markov Decision Process that captures the dynamic triadic relationship among human developers, software projects, and coding agents. Building upon this theoretical foundation, we then synthesize existing practices into five distinct development models: Unconstrained Automation, Iterative Conversational Collaboration, Planning-Driven, Test-Driven, and Context-Enhanced Models, thus providing the first comprehensive taxonomy in this domain. Critically, our analysis reveals that successful Vibe Coding depends not merely on agent capabilities but on systematic context engineering, well-established development environments, and human-agent collaborative development models.

Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources pair problems with solutions, but omit the intermediate thought process that guides coding. To close this gap, we present a scalable synthetic data generation pipeline that produces nearly 800k instruction-reasoning-code-test quadruplets. Each sample combines a task, a step-by-step reasoning trace, a working solution, and executable tests, enabling models to learn not just the what but also the how of problem solving. Our pipeline combines four key components: curated contest problems, web-mined content filtered by relevance classifiers, data expansion guided by reasoning patterns, and multi-stage execution-based validation. A genetic mutation algorithm further increases task diversity while maintaining consistency between reasoning traces and code implementations. Our key finding is that fine-tuning LLMs on this dataset yields consistent improvements on coding benchmarks. Beyond raw accuracy, reasoning-aware data can substitute for model scaling, generalize across architectures, and outperform leading open-source alternatives under identical sample budgets. Our work establishes reasoning-centered synthetic data generation as an efficient approach for advancing coding capabilities in LLMs. We publish our dataset and generation pipeline to facilitate further research.

Coding problems are problems that require a solution in the form of a computer program. Coding problems are popular among students and professionals as it enhances their skills and career opportunities. An AI system that would help those who practice coding problems would be highly useful and there is a huge potential for such a system. In this work, we propose a model which uses stacking of hyperparameter tuned boosting models to achieve impressive metric scores of 77.8% accuracy and 0.815 PR-AUC on the dataset that was scraped from Codeforces and Leetcode. We open source the dataset and the models developed for this work.

Conventional communication systems, including both separation-based coding and AI-driven joint source-channel coding (JSCC), are largely guided by Shannon's rate-distortion theory. However, relying on generic distortion metrics fails to capture complex human visual perception, often resulting in blurred or unrealistic reconstructions. In this paper, we propose Joint Source-Channel-Generation Coding (JSCGC), a novel paradigm that shifts the focus from deterministic reconstruction to probabilistic generation. JSCGC leverages a generative model at the receiver as a generator rather than a conventional decoder to parameterize the data distribution, enabling direct maximization of mutual information under channel constraints while controlling stochastic sampling to produce outputs residing on the authentic data manifold with high fidelity. We further derive a theoretical lower bound on the maximum semantic inconsistency with given transmitted mutual information, elucidating the fundamental limits of communication in controlling the generative process. Extensive experiments on image transmission demonstrate that JSCGC substantially improves perceptual quality and semantic fidelity, significantly outperforming conventional distortion-oriented JSCC methods.

Recent advances in video generation techniques have given rise to an emerging paradigm of generative video coding for Ultra-Low Bitrate (ULB) scenarios by leveraging powerful generative priors. However, most existing methods are limited by domain specificity (e.g., facial or human videos) or excessive dependence on high-level text guidance, which tend to inadequately capture fine-grained motion details, leading to unrealistic or incoherent reconstructions. To address these challenges, we propose Trajectory-Guided Generative Video Coding (dubbed T-GVC), a novel framework that bridges low-level motion tracking with high-level semantic understanding. T-GVC features a semantic-aware sparse motion sampling pipeline that extracts pixel-wise motion as sparse trajectory points based on their semantic importance, significantly reducing the bitrate while preserving critical temporal semantic information. In addition, by integrating trajectory-aligned loss constraints into diffusion processes, we introduce a training-free guidance mechanism in latent space to ensure physically plausible motion patterns without sacrificing the inherent capabilities of generative models. Experimental results demonstrate that T-GVC outperforms both traditional and neural video codecs under ULB conditions. Furthermore, additional experiments confirm that our framework achieves more precise motion control than existing text-guided methods, paving the way for a novel direction of generative video coding guided by geometric motion modeling.

Game development sits at the intersection of creative design and intricate software engineering, demanding the joint orchestration of game engines, real-time loops, and tightly coupled state across many files. While Large Language Models (LLMs) and code agents now solve isolated programming tasks with ease, they consistently stumble when asked to produce a fully playable game from a high-level design, collapsing under cross-file inconsistencies, broken scene wiring, and logical incoherence. We bridge this gap with OpenGame, the first open-source agentic framework explicitly designed for end-to-end web game creation. At its core lies Game Skill, a reusable, evolving capability composed of a Template Skill that grows a library of project skeletons from experience and a Debug Skill that maintains a living protocol of verified fixes - together enabling the agent to scaffold stable architectures and systematically repair integration errors rather than patch isolated syntax bugs. Powering this framework is GameCoder-27B, a code LLM specialized for game engine mastery through a three-stage pipeline of continual pre-training, supervised fine-tuning, and execution-grounded reinforcement learning. Since verifying interactive playability is fundamentally harder than checking static code, we further introduce OpenGame-Bench, an evaluation pipeline that scores agentic game generation along Build Health, Visual Usability, and Intent Alignment via headless browser execution and VLM judging. Across 150 diverse game prompts, OpenGame establishes a new state-of-the-art. We hope OpenGame pushes code agents beyond discrete software engineering problems and toward building complex, interactive real-world applications. Our framework will be fully open-sourced.

Recent advances in large language models (LLMs) have given rise to powerful coding agents, making it possible for code assistants to evolve into code engineers. However, existing methods still face significant challenges in achieving high-fidelity document-to-codebase synthesis--such as scientific papers to code--primarily due to a fundamental conflict between information overload and the context bottlenecks of LLMs. In this work, we introduce DeepCode, a fully autonomous framework that fundamentally addresses this challenge through principled information-flow management. By treating repository synthesis as a channel optimization problem, DeepCode seamlessly orchestrates four information operations to maximize task-relevant signals under finite context budgets: source compression via blueprint distillation, structured indexing using stateful code memory, conditional knowledge injection via retrieval-augmented generation, and closed-loop error correction. Extensive evaluations on the PaperBench benchmark demonstrate that DeepCode achieves state-of-the-art performance, decisively outperforming leading commercial agents such as Cursor and Claude Code, and crucially, surpassing PhD-level human experts from top institutes on key reproduction metrics. By systematically transforming paper specifications into production-grade implementations comparable to human expert quality, this work establishes new foundations for autonomous scientific reproduction that can accelerate research evaluation and discovery.

Software development is iterative, yet agentic coding benchmarks overwhelmingly evaluate single-shot solutions against complete specifications. Code can pass the test suite but become progressively harder to extend. Recent iterative benchmarks attempt to close this gap, but constrain the agent's design decisions too tightly to faithfully measure how code quality shapes future extensions. We introduce SlopCodeBench, a language-agnostic benchmark comprising 20 problems and 93 checkpoints, in which agents repeatedly extend their own prior solutions under evolving specifications that force architectural decisions without prescribing internal structure. We track two trajectory-level quality signals: verbosity, the fraction of redundant or duplicated code, and structural erosion, the share of complexity mass concentrated in high-complexity functions. No agent solves any problem end-to-end across 11 models; the highest checkpoint solve rate is 17.2%. Quality degrades steadily: erosion rises in 80% of trajectories and verbosity in 89.8%. Against 48 open-source Python repositories, agent code is 2.2x more verbose and markedly more eroded. Tracking 20 of those repositories over time shows that human code stays flat, while agent code deteriorates with each iteration. A prompt-intervention study shows that initial quality can be improved, but it does not halt degradation. These results demonstrate that pass-rate benchmarks systematically undermeasure extension robustness, and that current agents lack the design discipline iterative software development demands.

Recent studies operationalize self-improvement through coding agents that edit their own codebases. They grow a tree of self-modifications through expansion strategies that favor higher software engineering benchmark performance, assuming that this implies more promising subsequent self-modifications. However, we identify a mismatch between the agent's self-improvement potential (metaproductivity) and its coding benchmark performance, namely the Metaproductivity-Performance Mismatch. Inspired by Huxley's concept of clade, we propose a metric (CMP) that aggregates the benchmark performances of the descendants of an agent as an indicator of its potential for self-improvement. We show that, in our self-improving coding agent development setting, access to the true CMP is sufficient to simulate how the G\"odel Machine would behave under certain assumptions. We introduce the Huxley-G\"odel Machine (HGM), which, by estimating CMP and using it as guidance, searches the tree of self-modifications. On SWE-bench Verified and Polyglot, HGM outperforms prior self-improving coding agent development methods while using less wall-clock time. Last but not least, HGM demonstrates strong transfer to other coding datasets and large language models. The agent optimized by HGM on SWE-bench Verified with GPT-5-mini and evaluated on SWE-bench Lite with GPT-5 achieves human-level performance, matching the best officially checked results of human-engineered coding agents. Our code is available at https://github.com/metauto-ai/HGM.

Training next-generation code generation models requires high-quality datasets, yet existing datasets face difficulty imbalance, format inconsistency, and data quality problems. We address these challenges through systematic data processing and difficulty scaling. We introduce a four-stage Data Processing Framework encompassing collection, processing, filtering, and verification, incorporating Automatic Difficulty Filtering via an LLM-based predict-calibrate-select framework that leverages multi-dimensional difficulty metrics across five weighted dimensions to retain challenging problems while removing simplistic ones. The resulting MicroCoder dataset comprises tens of thousands of curated real competitive programming problems from diverse platforms, emphasizing recency and difficulty. Evaluations on strictly unseen LiveCodeBench demonstrate that MicroCoder achieves 3x larger performance gains within 300 training steps compared to widely-used baseline datasets of comparable size, with consistent advantages under both GRPO and its variant training algorithms. The MicroCoder dataset delivers obvious improvements on medium and hard problems across different model sizes, achieving up to 17.2% relative gains in overall performance where model capabilities are most stretched. These results validate that difficulty-aware data curation improves model performance on challenging tasks, providing multiple insights for dataset creation in code generation.

The rapid progress of Large Multimodal Models (LMMs) and cloud-based AI agents is transforming human-AI collaboration into bidirectional, multimodal interaction. However, existing codecs remain optimized for unimodal, one-way communication, resulting in repeated degradation under conventional compress-transmit-reconstruct pipelines. To address this limitation, we propose UniMIC, a Unified token-based Multimodal Interactive Coding framework that bridges edge devices and cloud AI agents. Instead of transmitting raw pixels or plain text, UniMIC employs compact tokenized representations as the communication medium, enabling efficient low-bitrate transmission while maintaining compatibility with LMMs. To further enhance compression, lightweight Transformer-based entropy models with scenario-specific designs-generic, masked, and text-conditioned-effectively minimize inter-token redundancy. Extensive experiments on text-to-image generation, text-guided inpainting, outpainting, and visual question answering show that UniMIC achieves substantial bitrate savings and remains robust even at ultra-low bitrates (<0.05bpp), without compromising downstream task performance. These results establish UniMIC as a practical and forward-looking paradigm for next-generation multimodal interactive communication.

AI coding agents select frameworks, scaffold infrastructure, and wire integrations, often in seconds. These are architectural decisions, yet almost no one reviews them as such. We identify five mechanisms by which agents make implicit architectural choices and propose six prompt-architecture coupling patterns that map natural-language prompt features to the infrastructure they require. The patterns range from contingent couplings (structured output validation) that may weaken as models improve to fundamental ones (tool-call orchestration) that persist regardless of model capability. An illustrative demonstration confirms that prompt wording alone produces structurally different systems for the same task. We term the phenomenon vibe architecting, architecture shaped by prompts rather than deliberate design, and outline review practices, decision records, and tooling to bring these hidden decisions under governance.

Image coding for multi-task applications, catering to both human perception and machine vision, has been extensively investigated. Existing methods often rely on multiple task-specific encoder-decoder pairs, leading to high overhead of parameter and bitrate usage, or face challenges in multi-objective optimization under a unified representation, failing to achieve both performance and efficiency. To this end, we propose Multi-Path Aggregation (MPA) integrated into existing coding models for joint human-machine vision, unifying the feature representation with an all-in-one architecture. MPA employs a predictor to allocate latent features among task-specific paths based on feature importance varied across tasks, maximizing the utility of shared features while preserving task-specific features for subsequent refinement. Leveraging feature correlations, we develop a two-stage optimization strategy to alleviate multi-task performance degradation. Upon the reuse of shared features, as low as 1.89% parameters are further augmented and fine-tuned for a specific task, which completely avoids extensive optimization of the entire model. Experimental results show that MPA achieves performance comparable to state-of-the-art methods in both task-specific and multi-objective optimization across human viewing and machine analysis tasks. Moreover, our all-in-one design supports seamless transitions between human- and machine-oriented reconstruction, enabling task-controllable interpretation without altering the unified model. Code is available at https://github.com/NJUVISION/MPA.

Autoregressive Predictive Coding (APC), as a self-supervised objective, has enjoyed success in learning representations from large amounts of unlabeled data, and the learned representations are rich for many downstream tasks. However, the connection between low self-supervised loss and strong performance in downstream tasks remains unclear. In this work, we propose Vector-Quantized Autoregressive Predictive Coding (VQ-APC), a novel model that produces quantized representations, allowing us to explicitly control the amount of information encoded in the representations. By studying a sequence of increasingly limited models, we reveal the constituents of the learned representations. In particular, we confirm the presence of information with probing tasks, while showing the absence of information with mutual information, uncovering the model's preference in preserving speech information as its capacity becomes constrained. We find that there exists a point where phonetic and speaker information are amplified to maximize a self-supervised objective. As a byproduct, the learned codes for a particular model capacity correspond well to English phones.

Neural audio codecs are a fundamental component of modern generative audio pipelines. Although recent codecs achieve strong low-bitrate reconstruction and provide powerful representations for downstream tasks, most are non-streamable, limiting their use in real-time applications. We present FocalCodec-Stream, a hybrid codec based on focal modulation that compresses speech into a single binary codebook at 0.55 - 0.80 kbps with a theoretical latency of 80 ms. Our approach combines multi-stage causal distillation of WavLM with targeted architectural improvements, including a lightweight refiner module that enhances quality under latency constraints. Experiments show that FocalCodec-Stream outperforms existing streamable codecs at comparable bitrates, while preserving both semantic and acoustic information. The result is a favorable trade-off between reconstruction quality, downstream task performance, latency, and efficiency. Code and checkpoints will be released at https://github.com/lucadellalib/focalcodec.

LLM-based coding agents extend their capabilities via third-party agent skills distributed through open marketplaces without mandatory security review. Unlike traditional packages, these skills are executed as operational directives with system-level privileges, so a single malicious skill can compromise the host. Prior work has not examined whether supply-chain attacks can directly hijack an agent's action space, such as file writes, shell commands, and network requests, despite existing safeguards. We introduce Document-Driven Implicit Payload Execution (DDIPE), which embeds malicious logic in code examples and configuration templates within skill documentation. Because agents reuse these examples during normal tasks, the payload executes without explicit prompts. Using an LLM-driven pipeline, we generate 1,070 adversarial skills from 81 seeds across 15 MITRE ATTACK categories. Across four frameworks and five models, DDIPE achieves 11.6% to 33.5% bypass rates, while explicit instruction attacks achieve 0% under strong defenses. Static analysis detects most cases, but 2.5% evade both detection and alignment. Responsible disclosure led to four confirmed vulnerabilities and two fixes.

Large language models (LLMs) have shown impressive performance in general programming tasks. However, in Machine Learning Engineering (MLE) scenarios such as AutoML and Kaggle competitions, achieving high performance depends heavily on expert intervention and repeated adjustments rather than simply generating correct code. When applied directly to these tasks, LLMs often lack fine-grained domain priors, and existing MLE approaches that use linear or tree-structured searches limit knowledge transfer to adjacent hierarchical links. As a result, they cannot leverage past full trajectories or share information across branches, limiting self-evolving ability and search space diversity. To address these limitations, we introduce AutoMLGen, an LLM-based coding agent that integrates a domain knowledge base for high-quality prior guidance and Monte Carlo Graph Search (MCGS) for efficient exploration. MCGS retains the tree-guided exploration of MCTS while embedding a graph structure into the expansion stage to enable dynamic path reorganization, historical trajectory reuse, and multi-solution fusion to support both self-evolution and collaborative learning. Combined with fine-grained operator sets, this design improves stability and accelerates convergence. Evaluation on the MLE-Bench shows that AutoMLGen achieves state-of-the-art performance in numerous dimensions, such as the average medal rate and the valid submission rate, under a 12-hour budget (half the standard runtime). The code is available at https://github.com/Alpha-Innovator/InternAgent.

Recent advancements in Large Language Models (LLMs) have significantly enhanced their code generation capabilities. However, their robustness against adversarial misuse, particularly through multi-turn malicious coding prompts, remains underexplored. In this work, we introduce code decomposition attacks, where a malicious coding task is broken down into a series of seemingly benign subtasks across multiple conversational turns to evade safety filters. To facilitate systematic evaluation, we introduce , a large-scale benchmark designed to evaluate the robustness of code LLMs against both single-turn and multi-turn malicious prompts. Empirical results across open- and closed-source models reveal persistent vulnerabilities, especially under multi-turn scenarios. Fine-tuning on MOCHA improves rejection rates while preserving coding ability, and importantly, enhances robustness on external adversarial datasets with up to 32.4% increase in rejection rates without any additional supervision.

Modern code generation models exhibit longer outputs, accelerated capability growth, and changed training dynamics, rendering traditional training methodologies, algorithms, and datasets ineffective for improving their performance. To address these training bottlenecks, we propose MicroCoder-GRPO, an improved Group Relative Policy Optimization approach with three innovations: conditional truncation masking to improve long output potential while maintaining training stability, diversity-determined temperature selection to maintain and encourage output diversity, and removal of KL loss with high clipping ratios to facilitate solution diversity. MicroCoder-GRPO achieves up to 17.6% relative improvement over strong baselines on LiveCodeBench v6, with more pronounced gains under extended context evaluation. Additionally, we release MicroCoder-Dataset, a more challenging training corpus that achieves 3x larger performance gains than mainstream datasets on LiveCodeBench v6 within 300 training steps, and MicroCoder-Evaluator, a robust framework with approximately 25% improved evaluation accuracy and around 40% faster execution. Through comprehensive analysis across more than thirty controlled experiments, we reveal 34 training insights across seven main aspects, demonstrating that properly trained models can achieve competitive performance with larger counterparts.

While AI shows promise for enhancing the efficiency of qualitative analysis, the unique human-AI interaction resulting from varied coding strategies makes it challenging to develop a trustworthy AI-assisted qualitative coding system (AIQCs) that supports coding tasks effectively. We bridge this gap by exploring the impact of varying coding strategies on user trust and reliance on AI. We conducted a mixed-methods split-plot 3x3 study, involving 30 participants, and a follow-up study with 6 participants, exploring varying text selection and code length in the use of our AIQCs system for qualitative analysis. Our results indicate that qualitative open coding should be conceptualized as a series of distinct subtasks, each with differing levels of complexity, and therefore, should be given tailored design considerations. We further observed a discrepancy between perceived and behavioral measures, and emphasized the potential challenges of under- and over-reliance on AIQCs systems. Additional design implications were also proposed for consideration.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

We introduce KodCode, a synthetic dataset that addresses the persistent challenge of acquiring high-quality, verifiable training data across diverse difficulties and domains for training Large Language Models for coding. Existing code-focused resources typically fail to ensure either the breadth of coverage (e.g., spanning simple coding tasks to advanced algorithmic problems) or verifiable correctness (e.g., unit tests). In contrast, KodCode comprises question-solution-test triplets that are systematically validated via a self-verification procedure. Our pipeline begins by synthesizing a broad range of coding questions, then generates solutions and test cases with additional attempts allocated to challenging problems. Finally, post-training data synthesis is done by rewriting questions into diverse formats and generating responses under a test-based reject sampling procedure from a reasoning model (DeepSeek R1). This pipeline yields a large-scale, robust and diverse coding dataset. KodCode is suitable for supervised fine-tuning and the paired unit tests also provide great potential for RL tuning. Fine-tuning experiments on coding benchmarks (HumanEval(+), MBPP(+), BigCodeBench, and LiveCodeBench) demonstrate that KodCode-tuned models achieve state-of-the-art performance, surpassing models like Qwen2.5-Coder-32B-Instruct and DeepSeek-R1-Distill-Llama-70B.

Existing LMs struggle with proof-oriented programming due to data scarcity, which manifest in two key ways: (1) a lack of sufficient corpora for proof-oriented programming languages such as F*, and (2) the absence of large-scale, project-level proof-oriented implementations that can teach the model the intricate reasoning process when performing proof-oriented programming. We present the first on synthetic data augmentation for project level proof oriented programming for both generation and repair. Our method addresses data scarcity by synthesizing basic proof-oriented programming problems for proficiency in that language; incorporating diverse coding data for reasoning capability elicitation and creating new proofs and repair data within existing repositories. This approach enables language models to both synthesize and repair proofs for function- and repository-level code. We show that our fine-tuned 14B parameter model, PoPilot, can exceed the performance of the models that outperforms GPT-4o in project-level proof-oriented programming by 64% relative margin, and can improve GPT-4o's performance by 54% by repairing its outputs over GPT-4o's self-repair.

Competition-level code generation tasks pose significant challenges for current state-of-the-art large language models (LLMs). For example, on the LiveCodeBench-Hard dataset, models such as O1-Mini and O1-Preview achieve pass@1 rates of only 0.366 and 0.143, respectively. While tree search techniques have proven effective in domains like mathematics and general coding, their potential in competition-level code generation remains under-explored. In this work, we propose a novel token-level tree search method specifically designed for code generation. Leveraging Qwen2.5-Coder-32B-Instruct, our approach achieves a pass rate of 0.305 on LiveCodeBench-Hard, surpassing the pass@100 performance of GPT4o-0513 (0.245). Furthermore, by integrating Chain-of-Thought (CoT) prompting, we improve our method's performance to 0.351, approaching O1-Mini's pass@1 rate. To ensure reproducibility, we report the average number of generations required per problem by our tree search method on the test set. Our findings underscore the potential of tree search to significantly enhance performance on competition-level code generation tasks. This opens up new possibilities for large-scale synthesis of challenging code problems supervised fine-tuning (SFT) data, advancing competition-level code generation tasks.

Decentralized Finance (DeFi) has turned blockchains into financial infrastructure, allowing anyone to trade, lend, and build protocols without intermediaries, but this openness exposes pools of value controlled by code. Within five years, the DeFi ecosystem has lost over 15.75B USD to reported exploits. Many exploits arise from permissionless opportunities that any participant can trigger using only public state and standard interfaces, which we call Anyone-Can-Take (ACT) opportunities. Despite on-chain transparency, postmortem analysis remains slow and manual: investigations start from limited evidence, sometimes only a single transaction hash, and must reconstruct the exploit lifecycle by recovering related transactions, contract code, and state dependencies. We present TxRay, a Large Language Model (LLM) agentic postmortem system that uses tool calls to reconstruct live ACT attacks from limited evidence. Starting from one or more seed transactions, TxRay recovers the exploit lifecycle, derives an evidence-backed root cause, and generates a runnable, self-contained Proof of Concept (PoC) that deterministically reproduces the incident. TxRay self-checks postmortems by encoding incident-specific semantic oracles as executable assertions. To evaluate PoC correctness and quality, we develop PoCEvaluator, an independent agentic execution-and-review evaluator. On 114 incidents from DeFiHackLabs, TxRay produces an expert-aligned root cause and an executable PoC for 105 incidents, achieving 92.11% end-to-end reproduction. Under PoCEvaluator, 98.1% of TxRay PoCs avoid hard-coding attacker addresses, a +22.9pp lift over DeFiHackLabs. In a live deployment, TxRay delivers validated root causes in 40 minutes and PoCs in 59 minutes at median latency. TxRay's oracle-validated PoCs enable attack imitation, improving coverage by 15.6% and 65.5% over STING and APE.

As coding agents are increasingly deployed in large codebases, the need to automatically design challenging, codebase-level evaluation is central. We propose Gistify, a task where a coding LLM must create a single, minimal, self-contained file that can reproduce a specific functionality of a codebase. The coding LLM is given full access to a codebase along with a specific entrypoint (e.g., a python command), and the generated file must replicate the output of the same command ran under the full codebase, while containing only the essential components necessary to execute the provided command. Success on Gistify requires both structural understanding of the codebase, accurate modeling of its execution flow as well as the ability to produce potentially large code patches. Our findings show that current state-of-the-art models struggle to reliably solve Gistify tasks, especially ones with long executions traces.

User interface (UI) programming is a core yet highly complex part of modern software development. Recent advances in visual language models (VLMs) highlight the potential of automatic UI coding, but current approaches face two key limitations: multimodal coding capabilities remain underdeveloped, and single-turn paradigms make little use of iterative visual feedback. We address these challenges with an interactive UI-to-code paradigm that better reflects real-world workflows and raises the upper bound of achievable performance. Under this paradigm, we present UI2Code^N, a visual language model trained through staged pretraining, fine-tuning, and reinforcement learning to achieve foundational improvements in multimodal coding. The model unifies three key capabilities: UI-to-code generation, UI editing, and UI polishing. We further explore test-time scaling for interactive generation, enabling systematic use of multi-turn feedback. Experiments on UI-to-code and UI polishing benchmarks show that UI2Code^N establishes a new state of the art among open-source models and achieves performance comparable to leading closed-source models such as Claude-4-Sonnet and GPT-5. Our code and models are available at https://github.com/zai-org/UI2Code_N.

We introduce SWE-Bench Pro, a substantially more challenging benchmark that builds upon the best practices of SWE-BENCH [25], but is explicitly designed to capture realistic, complex, enterprise-level problems beyond the scope of SWE-BENCH. SWE-BENCH PRO contains 1,865 problems sourced from a diverse set of 41 actively maintained repositories spanning business applications, B2B services, and developer tools. The benchmark is partitioned into a public set with open access to problems sourced from 11 repositories, a held-out set of 12 repositories and a commercial set of 18 proprietary repositories where we have formal partnership agreements with early-stage startups. Problems in the held-out and the commercial set are not publicly accessible, but we release results on the commercial set. Our benchmark features long-horizon tasks that may require hours to days for a professional software engineer to complete, often involving patches across multiple files and substantial code modifications. All tasks are human-verified and augmented with sufficient context to ensure resolvability. In our evaluation of widely used coding models, under a unified scaffold, we observe that their performance on SWE-Bench PRO remains below 25% (Pass@1), with GPT-5 achieving the highest score to date at 23.3%. To better understand these limitations, we cluster the failure modes observed in the collected agent trajectories for a clearer characterization of the error patterns exhibited by current models. Overall, SWE-BENCH PRO provides a contamination-resistant testbed that more faithfully captures the complexity and diversity of real-world software development, advancing the pursuit of truly autonomous software engineering agents at a professional level.

This paper introduces a multi-agent framework guided by Large Language Models (LLMs) to assist in the early stages of engineering design, a phase often characterized by vast parameter spaces and inherent uncertainty. Operating under a human-in-the-loop paradigm and demonstrated on the canonical problem of aerodynamic airfoil design, the framework employs a team of specialized agents: a Coding Assistant, a Design Agent, a Systems Engineering Agent, and an Analyst Agent - all coordinated by a human Manager. Integrated within a set-based design philosophy, the process begins with a collaborative phase where the Manager and Coding Assistant develop a suite of validated tools, after which the agents execute a structured workflow to systematically explore and prune a large set of initial design candidates. A key contribution of this work is the explicit integration of formal risk management, employing the Conditional Value-at-Risk (CVaR) as a quantitative metric to filter designs that exhibit a high probability of failing to meet performance requirements, specifically the target coefficient of lift. The framework automates labor-intensive initial exploration through a global sensitivity analysis conducted by the Analyst agent, which generates actionable heuristics to guide the other agents. The process culminates by presenting the human Manager with a curated final set of promising design candidates, augmented with high-fidelity Computational Fluid Dynamics (CFD) simulations. This approach effectively leverages AI to handle high-volume analytical tasks, thereby enhancing the decision-making capability of the human expert in selecting the final, risk-assessed design.

Multi-token generation has emerged as a promising paradigm for accelerating transformer-based large model inference. Recent efforts primarily explore diffusion Large Language Models (dLLMs) for parallel decoding to reduce inference latency. To achieve AR-level generation quality, many techniques adapt AR models into dLLMs to enable parallel decoding. However, they suffer from limited speedup compared to AR models due to a pretrain-to-posttrain mismatch. Specifically, the masked data distribution in post-training deviates significantly from the real-world data distribution seen during pretraining, and dLLMs rely on bidirectional attention, which conflicts with the causal prior learned during pretraining and hinders the integration of exact KV cache reuse. To address this, we introduce Jacobi Forcing, a progressive distillation paradigm where models are trained on their own generated parallel decoding trajectories, smoothly shifting AR models into efficient parallel decoders while preserving their pretrained causal inference property. The models trained under this paradigm, Jacobi Forcing Model, achieves 3.8x wall-clock speedup on coding and math benchmarks with minimal loss in performance. Based on Jacobi Forcing Models' trajectory characteristics, we introduce multi-block decoding with rejection recycling, which enables up to 4.5x higher token acceptance count per iteration and nearly 4.0x wall-clock speedup, effectively trading additional compute for lower inference latency. Our code is available at https://github.com/hao-ai-lab/JacobiForcing.

Large language model (LLM) coding agents increasingly operate at the repository level, motivating benchmarks that evaluate their ability to optimize entire codebases under realistic constraints. Existing code benchmarks largely rely on synthetic tasks, binary correctness signals, or single-objective evaluation, limiting their ability to assess holistic optimization behavior. We introduce FormulaCode, a benchmark for evaluating agentic optimization on large, real-world codebases with fine-grained, multi-objective performance metrics. FormulaCode comprises 957 performance bottlenecks mined from scientific Python repositories on GitHub, each paired with expert-authored patches and, on average, 264.6 community-maintained performance workloads per task, enabling the holistic ability of LLM agents to optimize codebases under realistic correctness and performance constraints. Our evaluations reveal that repository-scale, multi-objective optimization remains a major challenge for frontier LLM agents. Project website at: https://formula-code.github.io

Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged far behind. Here we have applied ribosome profiling - which measures both global mRNA levels and their translation rates - to two species of Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis and trans-acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority of translational divergence acts to buffer changes in mRNA abundance, suggesting a widespread role for stabilizing selection acting across regulatory levels. Nevertheless, we observe evidence of lineage-specific selection acting on a number of yeast functional modules, including instances of reinforcing selection acting at both levels of regulation. Finally, we also uncover multiple instances of stop-codon readthrough that are conserved between species. Our analysis reveals the under-appreciated complexity of post-transcriptional regulatory divergence and indicates that partitioning the search for the locus of selection into the binary categories of 'coding' vs. 'regulatory' may overlook a significant source of selection, acting at multiple regulatory levels along the path from genotype to phenotype.

Large language models (LLMs) have made significant strides at code generation through improved model design, training, and chain-of-thought. However, prompt-level optimizations remain an important yet under-explored aspect of LLMs for coding. This work focuses on the few-shot examples present in most code generation prompts, offering a systematic study on whether few-shot examples improve LLM's coding capabilities, which few-shot examples have the largest impact, and how to select impactful examples. Our work offers 2 approaches for selecting few-shot examples, a model-free method, CODEEXEMPLAR-FREE, and a model-based method, CODEEXEMPLAR-BASED. The 2 methods offer a trade-off between improved performance and reliance on training data and interpretability. Both methods significantly improve CodeLlama's coding ability across the popular HumanEval+ coding benchmark. In summary, our work provides valuable insights into how to pick few-shot examples in code generation prompts to improve LLM code generation capabilities.

As large language models engage in extended reasoning tasks, they accumulate significant state -- architectural mappings, trade-off decisions, codebase conventions -- within the context window. This understanding is lost when sessions reach context limits and undergo lossy compaction. We propose Contextual Memory Virtualisation (CMV), a system that treats accumulated LLM understanding as version-controlled state. Borrowing from operating system virtual memory, CMV models session history as a Directed Acyclic Graph (DAG) with formally defined snapshot, branch, and trim primitives that enable context reuse across independent parallel sessions. We introduce a three-pass structurally lossless trimming algorithm that preserves every user message and assistant response verbatim while reducing token counts by a mean of 20% and up to 86% for sessions with significant overhead by stripping mechanical bloat such as raw tool outputs, base64 images, and metadata. A single-user case-study evaluation across 76 real-world coding sessions demonstrates that trimming remains economically viable under prompt caching, with the strongest gains in mixed tool-use sessions, which average 39% reduction and reach break-even within 10 turns. A reference implementation is available at https://github.com/CosmoNaught/claude-code-cmv.

We study whether an aperiodic hierarchy can provide a structural advantage for lossless compression over periodic alternatives. We show that Fibonacci quasicrystal tilings avoid the finite-depth collapse that affects periodic hierarchies: usable n-gram lookup positions remain non-zero at every level, while periodic tilings collapse after O(log p) levels for period p. This yields an aperiodic hierarchy advantage: dictionary reuse remains available across all scales instead of vanishing beyond a finite depth. Our analysis gives four main consequences. First, the Golden Compensation property shows that the exponential decay in the number of positions is exactly balanced by the exponential growth in phrase length, so potential coverage remains scale-invariant with asymptotic value Wvarphi/5. Second, using the Sturmian complexity law p(n)=n+1, we show that Fibonacci/Sturmian hierarchies maximize codebook coverage efficiency among binary aperiodic tilings. Third, under long-range dependence, the resulting hierarchy achieves lower coding entropy than comparable periodic hierarchies. Fourth, redundancy decays super-exponentially with depth, whereas periodic systems remain locked at the depth where collapse occurs. We validate these results with Quasicryth, a lossless text compressor built on a ten-level Fibonacci hierarchy with phrase lengths {2,3,5,8,13,21,34,55,89,144}. In controlled A/B experiments with identical codebooks, the aperiodic advantage over a Period-5 baseline grows from 36{,}243 B at 3 MB to 11{,}089{,}469 B at 1 GB, explained by the activation of deeper hierarchy levels. On enwik9, Quasicryth achieves 225{,}918{,}349 B (22.59%), with 20{,}735{,}733 B saved by the Fibonacci tiling relative to no tiling.

Mixture-of-Experts (MoE) architectures scale large language models (LLMs) by activating only a subset of experts per token, but the standard TopK routing assigns the same fixed number of experts to all tokens, ignoring their varying complexity. Prior adaptive routing methods introduce additional modules and hyperparameters, often requiring costly retraining from scratch. We propose Sequence-level TopK (SeqTopK), a minimal modification that shifts the expert budget from the token level to the sequence level. By selecting the top T cdot K experts across all T tokens, SeqTopK enables end-to-end learned dynamic allocation -- assigning more experts to difficult tokens and fewer to easy ones -- while preserving the same overall budget. SeqTopK requires only a few lines of code, adds less than 1% overhead, and remains fully compatible with pretrained MoE models. Experiments across math, coding, law, and writing show consistent improvements over TopK and prior parameter-free adaptive methods, with gains that become substantially larger under higher sparsity (up to 16.9%). These results highlight SeqTopK as a simple, efficient, and scalable routing strategy, particularly well-suited for the extreme sparsity regimes of next-generation LLMs. Code is available at https://github.com/Y-Research-SBU/SeqTopK.

Traditional and neural video codecs commonly encounter limitations in controllability and generality under ultra-low-bitrate coding scenarios. To overcome these challenges, we propose M3-CVC, a controllable video compression framework incorporating multimodal generative models. The framework utilizes a semantic-motion composite strategy for keyframe selection to retain critical information. For each keyframe and its corresponding video clip, a dialogue-based large multimodal model (LMM) approach extracts hierarchical spatiotemporal details, enabling both inter-frame and intra-frame representations for improved video fidelity while enhancing encoding interpretability. M3-CVC further employs a conditional diffusion-based, text-guided keyframe compression method, achieving high fidelity in frame reconstruction. During decoding, textual descriptions derived from LMMs guide the diffusion process to restore the original video's content accurately. Experimental results demonstrate that M3-CVC significantly outperforms the state-of-the-art VVC standard in ultra-low bitrate scenarios, particularly in preserving semantic and perceptual fidelity.

Diffusion large language models (dLLMs) are compelling alternatives to autoregressive (AR) models because their denoising models operate over the entire sequence. The global planning and iterative refinement features of dLLMs are particularly useful for code generation. However, current training and inference mechanisms for dLLMs in coding are still under-explored. To demystify the decoding behavior of dLLMs and unlock their potential for coding, we systematically investigate their denoising processes and reinforcement learning (RL) methods. We train a 7B dLLM, DiffuCoder, on 130B tokens of code. Using this model as a testbed, we analyze its decoding behavior, revealing how it differs from that of AR models: (1) dLLMs can decide how causal their generation should be without relying on semi-AR decoding, and (2) increasing the sampling temperature diversifies not only token choices but also their generation order. This diversity creates a rich search space for RL rollouts. For RL training, to reduce the variance of token log-likelihood estimates and maintain training efficiency, we propose coupled-GRPO, a novel sampling scheme that constructs complementary mask noise for completions used in training. In our experiments, coupled-GRPO significantly improves DiffuCoder's performance on code generation benchmarks (+4.4\% on EvalPlus) and reduces reliance on AR causal during decoding. Our work provides deeper insight into the machinery of dLLM generation and offers an effective, diffusion-native RL training framework. https://github.com/apple/ml-diffucoder.

LLMs are increasingly being used for complex problems which are not necessarily resolved in a single response, but require interacting with an environment to acquire information. In these scenarios, LLMs must reason about inherent cost-uncertainty tradeoffs in when to stop exploring and commit to an answer. For instance, on a programming task, an LLM should test a generated code snippet if it is uncertain about the correctness of that code; the cost of writing a test is nonzero, but typically lower than the cost of making a mistake. In this work, we show that we can induce LLMs to explicitly reason about balancing these cost-uncertainty tradeoffs, then perform more optimal environment exploration. We formalize multiple tasks, including information retrieval and coding, as sequential decision-making problems under uncertainty. Each problem has latent environment state that can be reasoned about via a prior which is passed to the LLM agent. We introduce a framework called Calibrate-Then-Act (CTA), where we feed the LLM this additional context to enable it to act more optimally. This improvement is preserved even under RL training of both the baseline and CTA. Our results on information-seeking QA and on a simplified coding task show that making cost-benefit tradeoffs explicit with CTA can help agents discover more optimal decision-making strategies.

This paper investigates a novel lossy compression framework operating under logarithmic loss, designed to handle situations where the reconstruction distribution diverges from the source distribution. This framework is especially relevant for applications that require joint compression and retrieval, and in scenarios involving distributional shifts due to processing. We show that the proposed formulation extends the classical minimum entropy coupling framework by integrating a bottleneck, allowing for a controlled degree of stochasticity in the coupling. We explore the decomposition of the Minimum Entropy Coupling with Bottleneck (MEC-B) into two distinct optimization problems: Entropy-Bounded Information Maximization (EBIM) for the encoder, and Minimum Entropy Coupling (MEC) for the decoder. Through extensive analysis, we provide a greedy algorithm for EBIM with guaranteed performance, and characterize the optimal solution near functional mappings, yielding significant theoretical insights into the structural complexity of this problem. Furthermore, we illustrate the practical application of MEC-B through experiments in Markov Coding Games (MCGs) under rate limits. These games simulate a communication scenario within a Markov Decision Process, where an agent must transmit a compressed message from a sender to a receiver through its actions. Our experiments highlight the trade-offs between MDP rewards and receiver accuracy across various compression rates, showcasing the efficacy of our method compared to conventional compression baseline.

Developing domain models is one of the few remaining places that require manual human labor in AI planning. Thus, in order to make planning more accessible, it is desirable to automate the process of domain model generation. To this end, we investigate if large language models (LLMs) can be used to generate planning domain models from simple textual descriptions. Specifically, we introduce a framework for automated evaluation of LLM-generated domains by comparing the sets of plans for domain instances. Finally, we perform an empirical analysis of 7 large language models, including coding and chat models across 9 different planning domains, and under three classes of natural language domain descriptions. Our results indicate that LLMs, particularly those with high parameter counts, exhibit a moderate level of proficiency in generating correct planning domains from natural language descriptions. Our code is available at https://github.com/IBM/NL2PDDL.

We introduce Motif-2-12.7B-Reasoning, a 12.7B parameter language model designed to bridge the gap between open-weight systems and proprietary frontier models in complex reasoning and long-context understanding. Addressing the common challenges of model collapse and training instability in reasoning adaptation, we propose a comprehensive, reproducible training recipe spanning system, data, and algorithmic optimizations. Our approach combines memory-efficient infrastructure for 64K-token contexts using hybrid parallelism and kernel-level optimizations with a two-stage Supervised Fine-Tuning (SFT) curriculum that mitigates distribution mismatch through verified, aligned synthetic data. Furthermore, we detail a robust Reinforcement Learning Fine-Tuning (RLFT) pipeline that stabilizes training via difficulty-aware data filtering and mixed-policy trajectory reuse. Empirical results demonstrate that Motif-2-12.7B-Reasoning achieves performance comparable to models with significantly larger parameter counts across mathematics, coding, and agentic benchmarks, offering the community a competitive open model and a practical blueprint for scaling reasoning capabilities under realistic compute constraints.

Existing foundation models typically process visual input as pixels and textual input as tokens, a paradigm that contrasts with human perception, where both modalities are processed in a unified manner. With the rise of embodied and agentic AI, where inputs primarily come from camera pixels, the need for a unified perception framework becomes increasingly evident. In this paper, we propose to unify all modalities (text, tables, code, diagrams, images, etc) as pixel inputs, i.e. "Perceive Everything as Pixels" (PEAP). We introduce PixelWorld, a novel evaluation suite that unifies all the mentioned modalities into pixel space to gauge the existing models' performance. Our findings show that (1) PEAP outperforms baseline with token-based input in multimodal datasets, benefiting from unified input for better disambiguation, (2) significant declines in reasoning and coding capabilities across all models when processing pixel-based input, underscoring the need to enhance foundation models' perceptual abilities, (3) larger models can maintain strong performance on non-reasoning tasks under PEAP, while smaller models like Phi-3.5-V suffer significant performance degradation, (4) the attention pattern of PEAP is highly aligned with text token input, (5) PEAP can be accelerated significantly by exploiting the spatial sparsity. We conclude that the existing frontier models are competent in pixel perception, however, there is still headroom for improvement. Our code, dataset will be released upon acceptance.

As Vision-Language Models (VLMs) grow in sophistication, their ability to perform reasoning is coming under increasing supervision. While they excel at many tasks, their grasp of fundamental scientific principles, such as physics, remains an underexplored frontier. To reflect the advancements in these capabilities, we introduce a novel and accessible framework designed to rigorously evaluate VLMs on their understanding of 2D physics. Our framework features a pragmatic scenario generator that creates a diverse testbed of over 400 problems across four core domains: Projectile Motion, Collision Dynamics, Mechanics, and Fluid Dynamics. Through comprehensive evaluation of four state-of-the-art VLMs, we demonstrate a strong correlation between model scale and reasoning ability, with our top-performing model, Qwen2.5-VL-7B, achieving an overall score of 0.815. We find that while models excel at formulaic problems, they struggle significantly with domains requiring abstract spatial reasoning. By designing this framework, we aim to democratize the study of scientific reasoning in VLMs and foster deeper insights into their capabilities and limitations.

Polymeric nano- and micro-scale particles have critical roles in tackling critical healthcare and energy challenges with their miniature characteristics. However, tailoring their synthesis process to meet specific design targets has traditionally depended on domain expertise and costly trial-and-errors. Recently, modeling strategies, particularly Bayesian optimization (BO), have been proposed to aid materials discovery for maximized/minimized properties. Coming from practical demands, this study for the first time integrates constrained and composite Bayesian optimization (CCBO) to perform efficient target value optimization under black-box feasibility constraints and limited data for laboratory experimentation. Using a synthetic problem that simulates electrospraying, a model nanomanufacturing process, CCBO strategically avoided infeasible conditions and efficiently optimized particle production towards predefined size targets, surpassing standard BO pipelines and providing decisions comparable to human experts. Further laboratory experiments validated CCBO capability to guide the rational synthesis of poly(lactic-co-glycolic acid) (PLGA) particles with diameters of 300 nm and 3.0 mum via electrospraying. With minimal initial data and unknown experiment constraints, CCBO reached the design targets within 4 iterations. Overall, the CCBO approach presents a versatile and holistic optimization paradigm for next-generation target-driven particle synthesis empowered by artificial intelligence (AI).

Selecting LLM-generated code candidates using LLM-generated tests is challenging because the tests themselves may be incorrect. Existing methods either treat all tests equally or rely on ad-hoc heuristics to filter unreliable tests. Yet determining test correctness requires knowing which codes are correct, creating a circular dependency. Our key insight is that we need not determine test correctness at all: test votes should rank, not merely count. What matters is not how many codes pass a test, but whether the test can distinguish correct from incorrect code. We break the circular dependency via leave-one-out evaluation: hold out one test, rank codes by their aggregate scores on all remaining tests, and measure whether the held-out test's pass/fail pattern agrees with this ranking. We formalize this agreement as the leave-one-out AUC~(LOO-AUC) and prove that the expected LOO-AUC is proportional to each test's ability to separate correct code from incorrect code. Building on this, we propose ACES~(AUC ConsistEncy Scoring) with two complementary variants: ACES-C provides closed-form weights that provably approximate the oracle in expectation under a mild assumption on average test quality; ACES-O drops this assumption and iteratively optimizes a differentiable LOO-AUC objective. Both operate solely on the binary pass matrix with negligible overhead, and achieve state-of-the-art Pass@k on multiple code generation benchmarks.