John Yang

Talor Abramovich, Meet Udeshi, Minghao Shao et al. · princeton, uw

Although language model (LM) agents have demonstrated increased performance in multiple domains, including coding and web-browsing, their success in cybersecurity has been limited. We present EnIGMA, an LM agent for autonomously solving Capture The Flag (CTF) challenges. We introduce new tools and interfaces to improve the agent's ability to find and exploit security vulnerabilities, focusing on interactive terminal programs. These novel Interactive Agent Tools enable LM agents, for the first time, to run interactive utilities, such as a debugger and a server connection tool, which are essential for solving these challenges. Empirical analysis on 390 CTF challenges across four benchmarks demonstrate that these new tools and interfaces substantially improve our agent's performance, achieving state-of-the-art results on NYU CTF, Intercode-CTF, and CyBench. Finally, we analyze data leakage, developing new methods to quantify it and identifying a new phenomenon we term soliloquizing, where the model self-generates hallucinated observations without interacting with the environment. Our code and development dataset are available at https://github.com/SWE-agent/SWE-agent/tree/v0.7 and https://github.com/NYU-LLM-CTF/NYU_CTF_Bench/tree/main/development respectively.

Carlos E. Jimenez, John Yang, Alexander Wettig et al. · princeton, uw

Language models have outpaced our ability to evaluate them effectively, but for their future development it is essential to study the frontier of their capabilities. We find real-world software engineering to be a rich, sustainable, and challenging testbed for evaluating the next generation of language models. To this end, we introduce SWE-bench, an evaluation framework consisting of $2,294$ software engineering problems drawn from real GitHub issues and corresponding pull requests across $12$ popular Python repositories. Given a codebase along with a description of an issue to be resolved, a language model is tasked with editing the codebase to address the issue. Resolving issues in SWE-bench frequently requires understanding and coordinating changes across multiple functions, classes, and even files simultaneously, calling for models to interact with execution environments, process extremely long contexts and perform complex reasoning that goes far beyond traditional code generation tasks. Our evaluations show that both state-of-the-art proprietary models and our fine-tuned model SWE-Llama can resolve only the simplest issues. The best-performing model, Claude 2, is able to solve a mere $1.96$% of the issues. Advances on SWE-bench represent steps towards LMs that are more practical, intelligent, and autonomous.

Shunyu Yao, Howard Chen, John Yang et al.

Existing benchmarks for grounding language in interactive environments either lack real-world linguistic elements, or prove difficult to scale up due to substantial human involvement in the collection of data or feedback signals. To bridge this gap, we develop WebShop -- a simulated e-commerce website environment with $1.18$ million real-world products and $12,087$ crowd-sourced text instructions. Given a text instruction specifying a product requirement, an agent needs to navigate multiple types of webpages and issue diverse actions to find, customize, and purchase an item. WebShop provides several challenges for language grounding including understanding compositional instructions, query (re-)formulation, comprehending and acting on noisy text in webpages, and performing strategic exploration. We collect over $1,600$ human demonstrations for the task, and train and evaluate a diverse range of agents using reinforcement learning, imitation learning, and pre-trained image and language models. Our best model achieves a task success rate of $29\%$, which outperforms rule-based heuristics ($9.6\%$) but is far lower than human expert performance ($59\%$). We also analyze agent and human trajectories and ablate various model components to provide insights for developing future agents with stronger language understanding and decision making abilities. Finally, we show that agents trained on WebShop exhibit non-trivial sim-to-real transfer when evaluated on amazon.com and ebay.com, indicating the potential value of WebShop in developing practical web-based agents that can operate in the wild.

John Yang, Akshara Prabhakar, Karthik Narasimhan et al. · princeton

Humans write code in a fundamentally interactive manner and rely on constant execution feedback to correct errors, resolve ambiguities, and decompose tasks. While LLMs have recently exhibited promising coding capabilities, current coding benchmarks mostly consider a static instruction-to-code sequence transduction process, which has the potential for error propagation and a disconnect between the generated code and its final execution environment. To address this gap, we introduce InterCode, a lightweight, flexible, and easy-to-use framework of interactive coding as a standard reinforcement learning (RL) environment, with code as actions and execution feedback as observations. Our framework is language and platform agnostic, uses self-contained Docker environments to provide safe and reproducible execution, and is compatible out-of-the-box with traditional seq2seq coding methods, while enabling the development of new methods for interactive code generation. We use InterCode to create three interactive code environments with Bash, SQL, and Python as action spaces, leveraging data from the static NL2Bash, Spider, and MBPP datasets. We demonstrate InterCode's viability as a testbed by evaluating multiple state-of-the-art LLMs configured with different prompting strategies such as ReAct and Plan & Solve. Our results showcase the benefits of interactive code generation and demonstrate that InterCode can serve as a challenging benchmark for advancing code understanding and generation capabilities. InterCode is designed to be easily extensible and can even be used to create new tasks such as Capture the Flag, a popular coding puzzle that is inherently multi-step and involves multiple programming languages. Project site with code and data: https://intercode-benchmark.github.io

John Yang, Kilian Lieret, Joyce Yang et al.

Current benchmarks for coding evaluate language models (LMs) on concrete, well-specified tasks such as fixing specific bugs or writing targeted tests. However, human programmers do not spend all day incessantly addressing isolated tasks. Instead, real-world software development is grounded in the pursuit of high-level goals, like improving user retention or reducing costs. Evaluating whether LMs can also iteratively develop code to better accomplish open-ended objectives without any explicit guidance remains an open challenge. To address this, we introduce CodeClash, a benchmark where LMs compete in multi-round tournaments to build the best codebase for achieving a competitive objective. Each round proceeds in two phases: agents edit their code, then their codebases compete head-to-head in a code arena that determines winners based on objectives like score maximization, resource acquisition, or survival. Whether it's writing notes, scrutinizing documentation, analyzing competition logs, or creating test suites, models must decide for themselves how to improve their codebases both absolutely and against their opponents. We run 1680 tournaments (25,200 rounds total) to evaluate 8 LMs across 6 arenas. Our results reveal that while models exhibit diverse development styles, they share fundamental limitations in strategic reasoning. Models also struggle with long-term codebase maintenance, as repositories become progressively messy and redundant. These limitations are stark: top models lose every round against expert human programmers. We open-source CodeClash to advance the study of autonomous, goal-oriented code development.

John Yang, Le An, Anurag Dixit et al.

Transformer and its variants have shown state-of-the-art results in many vision tasks recently, ranging from image classification to dense prediction. Despite of their success, limited work has been reported on improving the model efficiency for deployment in latency-critical applications, such as autonomous driving and robotic navigation. In this paper, we aim at improving upon the existing transformers in vision, and propose a method for self-supervised monocular Depth Estimation with Simplified Transformer (DEST), which is efficient and particularly suitable for deployment on GPU-based platforms. Through strategic design choices, our model leads to significant reduction in model size, complexity, as well as inference latency, while achieving superior accuracy as compared to state-of-the-art. We also show that our design generalize well to other dense prediction task without bells and whistles.

Etash Guha, Ryan Marten, Sedrick Keh et al. · cmu

Reasoning models have made rapid progress on many benchmarks involving math, code, and science. Yet, there are still many open questions about the best training recipes for reasoning since state-of-the-art models often rely on proprietary datasets with little to no public information available. To address this, the goal of the OpenThoughts project is to create open-source datasets for training reasoning models. After initial explorations, our OpenThoughts2-1M dataset led to OpenThinker2-32B, the first model trained on public reasoning data to match DeepSeek-R1-Distill-32B on standard reasoning benchmarks such as AIME and LiveCodeBench. We then improve our dataset further by systematically investigating each step of our data generation pipeline with 1,000+ controlled experiments, which led to OpenThoughts3. Scaling the pipeline to 1.2M examples and using QwQ-32B as teacher yields our OpenThoughts3-7B model, which achieves state-of-the-art results: 53% on AIME 2025, 51% on LiveCodeBench 06/24-01/25, and 54% on GPQA Diamond - improvements of 15.3, 17.2, and 20.5 percentage points compared to the DeepSeek-R1-Distill-Qwen-7B. All of our datasets and models are available on https://openthoughts.ai.

John Yang, Kilian Lieret, Carlos E. Jimenez et al. · gatech, princeton

Despite recent progress in Language Models (LMs) for software engineering, collecting training data remains a significant pain point. Existing datasets are small, with at most 1,000s of training instances from 11 or fewer GitHub repositories. The procedures to curate such datasets are often complex, necessitating hundreds of hours of human labor; companion execution environments also take up several terabytes of storage, severely limiting their scalability and usability. To address this pain point, we introduce SWE-smith, a novel pipeline for generating software engineering training data at scale. Given any Python codebase, SWE-smith constructs a corresponding execution environment, then automatically synthesizes 100s to 1,000s of task instances that break existing test(s) in the codebase. Using SWE-smith, we create a dataset of 50k instances sourced from 128 GitHub repositories, an order of magnitude larger than all previous works. We train SWE-agent-LM-32B, achieving 40.2% Pass@1 resolve rate on the SWE-bench Verified benchmark, state of the art among open source models. We open source SWE-smith (collection procedure, task instances, trajectories, models) to lower the barrier of entry for research in LM systems for automated software engineering. All assets available at https://swesmith.com.

Jinkyu Koo, John Yang, Le An et al.

Transformer models have shown great potential in computer vision, following their success in language tasks. Swin Transformer is one of them that outperforms convolution-based architectures in terms of accuracy, while improving efficiency when compared to Vision Transformer (ViT) and its variants, which have quadratic complexity with respect to the input size. Swin Transformer features shifting windows that allows cross-window connection while limiting self-attention computation to non-overlapping local windows. However, shifting windows introduces memory copy operations, which account for a significant portion of its runtime. To mitigate this issue, we propose Swin-Free in which we apply size-varying windows across stages, instead of shifting windows, to achieve cross-connection among local windows. With this simple design change, Swin-Free runs faster than the Swin Transformer at inference with better accuracy. Furthermore, we also propose a few of Swin-Free variants that are faster than their Swin Transformer counterparts.

Nithin Parsan, David J. Yang, John J. Yang

Protein language models have revolutionized structure prediction, but their nonlinear nature obscures how sequence representations inform structure prediction. While sparse autoencoders (SAEs) offer a path to interpretability here by learning linear representations in high-dimensional space, their application has been limited to smaller protein language models unable to perform structure prediction. In this work, we make two key advances: (1) we scale SAEs to ESM2-3B, the base model for ESMFold, enabling mechanistic interpretability of protein structure prediction for the first time, and (2) we adapt Matryoshka SAEs for protein language models, which learn hierarchically organized features by forcing nested groups of latents to reconstruct inputs independently. We demonstrate that our Matryoshka SAEs achieve comparable or better performance than standard architectures. Through comprehensive evaluations, we show that SAEs trained on ESM2-3B significantly outperform those trained on smaller models for both biological concept discovery and contact map prediction. Finally, we present an initial case study demonstrating how our approach enables targeted steering of ESMFold predictions, increasing structure solvent accessibility while fixing the input sequence. To facilitate further investigation by the broader community, we open-source our code, dataset, pretrained models https://github.com/johnyang101/reticular-sae , and visualizer https://sae.reticular.ai .

Patrick Tser Jern Kon, Archana Pradeep, Ang Chen et al.

Small language models (SLMs) offer compelling advantages in cost, latency, and adaptability, but have so far lagged behind larger models on long-horizon software engineering tasks such as SWE-bench, where they suffer from pervasive action looping and low resolution rates. We introduce SWE-Protégé, a post-training framework that reframes software repair as an expert-protégé collaboration problem. In SWE-Protégé, an SLM remains the sole decision-maker while learning to selectively seek guidance from a strong expert model, recognize stalled states, and follow through on expert feedback. Our approach combines supervised fine-tuning on expert-augmented trajectories with agentic reinforcement learning that explicitly discourages degenerative looping and unproductive expert collaboration. We lightly post-train Qwen2.5-Coder-7B-Instruct to achieve 42.4% Pass@1 on SWE-bench Verified, a +25.4% improvement over the prior SLM state of the art, while using expert assistance sparsely (~4 calls per task and 11% of total tokens).

Kenneth Enevoldsen, Isaac Chung, Imene Kerboua et al. · cambridge, meta-ai

Text embeddings are typically evaluated on a limited set of tasks, which are constrained by language, domain, and task diversity. To address these limitations and provide a more comprehensive evaluation, we introduce the Massive Multilingual Text Embedding Benchmark (MMTEB) - a large-scale, community-driven expansion of MTEB, covering over 500 quality-controlled evaluation tasks across 250+ languages. MMTEB includes a diverse set of challenging, novel tasks such as instruction following, long-document retrieval, and code retrieval, representing the largest multilingual collection of evaluation tasks for embedding models to date. Using this collection, we develop several highly multilingual benchmarks, which we use to evaluate a representative set of models. We find that while large language models (LLMs) with billions of parameters can achieve state-of-the-art performance on certain language subsets and task categories, the best-performing publicly available model is multilingual-e5-large-instruct with only 560 million parameters. To facilitate accessibility and reduce computational cost, we introduce a novel downsampling method based on inter-task correlation, ensuring a diverse selection while preserving relative model rankings. Furthermore, we optimize tasks such as retrieval by sampling hard negatives, creating smaller but effective splits. These optimizations allow us to introduce benchmarks that drastically reduce computational demands. For instance, our newly introduced zero-shot English benchmark maintains a ranking order similar to the full-scale version but at a fraction of the computational cost.

Yijia Shao, Vinay Samuel, Yucheng Jiang et al. · stanford

Recent advancements in language models (LMs) have sparked growing interest in developing LM agents. While fully autonomous agents could excel in many scenarios, numerous use cases inherently require them to collaborate with humans due to humans' latent preferences, domain expertise, or need for control. To facilitate the study of human-agent collaboration, we present Collaborative Gym (Co-Gym), a general framework enabling asynchronous, tripartite interaction among agents, humans, and task environments. We instantiate Co-Gym with three representative tasks in both simulated and real-world conditions, and propose an evaluation framework that assesses both the collaboration outcomes and processes. Our findings reveal that collaborative agents consistently outperform their fully autonomous counterparts in task performance within those delivered cases, achieving win rates of 86% in Travel Planning, 74% in Tabular Analysis, and 66% in Related Work when evaluated by real users. However, our study also highlights significant challenges in developing collaborative agents, requiring advancements in core aspects of intelligence -- communication capabilities, situational awareness, and balancing autonomy and human control.

Sophie L. Wang, Alex Quach, Nithin Parsan et al.

Sparse autoencoders (SAEs) have been widely used for interpretability of neural networks, but their learned features often vary across seeds and hyperparameter settings. We introduce Ordered Sparse Autoencoders (OSAE), which extend Matryoshka SAEs by (1) establishing a strict ordering of latent features and (2) deterministically using every feature dimension, avoiding the sampling-based approximations of prior nested SAE methods. Theoretically, we show that OSAEs resolve permutation non-identifiability in settings of sparse dictionary learning where solutions are unique (up to natural symmetries). Empirically on Gemma2-2B and Pythia-70M, we show that OSAEs can help improve consistency compared to Matryoshka baselines.

Bowen Li, Wenhan Wu, Ziwei Tang et al.

Recent advancements in large language models (LLMs) have significantly enhanced their coding capabilities. However, existing benchmarks predominantly focused on simplified or isolated aspects of coding, such as single-file code generation or repository issue debugging, falling short of measuring the full spectrum of challenges raised by real-world programming activities. In this case study, we explore the performance of LLMs across the entire software development lifecycle with DevEval, encompassing stages including software design, environment setup, implementation, acceptance testing, and unit testing. DevEval features four programming languages, multiple domains, high-quality data collection, and carefully designed and verified metrics for each task. Empirical studies show that current LLMs, including GPT-4, fail to solve the challenges presented within DevEval. Our findings offer actionable insights for the future development of LLMs toward real-world programming applications.

Rebonto Haque, Oliver M. Turnbull, Anisha Parsan et al.

Sparse autoencoders (SAEs) are a mechanistic interpretability technique that have been used to provide insight into learned concepts within large protein language models. Here, we employ TopK and Ordered SAEs to investigate an autoregressive antibody language model, p-IgGen, and steer its generation. We show that TopK SAEs can reveal biologically meaningful latent features, but high feature concept correlation does not guarantee causal control over generation. In contrast, Ordered SAEs impose an hierarchical structure that reliably identifies steerable features, but at the expense of more complex and less interpretable activation patterns. These findings advance the mechanistic interpretability of domain-specific protein language models and suggest that, while TopK SAEs are sufficient for mapping latent features to concepts, Ordered SAEs are preferable when precise generative steering is required.

John Yang, Carlos E. Jimenez, Alexander Wettig et al.

Language model (LM) agents are increasingly being used to automate complicated tasks in digital environments. Just as humans benefit from powerful software applications, such as integrated development environments, for complex tasks like software engineering, we posit that LM agents represent a new category of end users with their own needs and abilities, and would benefit from specially-built interfaces to the software they use. We investigate how interface design affects the performance of language model agents. As a result of this exploration, we introduce SWE-agent: a system that facilitates LM agents to autonomously use computers to solve software engineering tasks. SWE-agent's custom agent-computer interface (ACI) significantly enhances an agent's ability to create and edit code files, navigate entire repositories, and execute tests and other programs. We evaluate SWE-agent on SWE-bench and HumanEvalFix, achieving state-of-the-art performance on both with a pass@1 rate of 12.5% and 87.7%, respectively, far exceeding the previous state-of-the-art achieved with non-interactive LMs. Finally, we provide insight on how the design of the ACI can impact agents' behavior and performance.

Michael Tang, Shunyu Yao, John Yang et al.

We propose Referral-Augmented Retrieval (RAR), a simple technique that concatenates document indices with referrals, i.e. text from other documents that cite or link to the given document, to provide significant performance gains for zero-shot information retrieval. The key insight behind our method is that referrals provide a more complete, multi-view representation of a document, much like incoming page links in algorithms like PageRank provide a comprehensive idea of a webpage's importance. RAR works with both sparse and dense retrievers, and outperforms generative text expansion techniques such as DocT5Query and Query2Doc a 37% and 21% absolute improvement on ACL paper retrieval Recall@10 -- while also eliminating expensive model training and inference. We also analyze different methods for multi-referral aggregation and show that RAR enables up-to-date information retrieval without re-training.

John Yang, Yash Bhalgat, Simyung Chang et al.

While hand pose estimation is a critical component of most interactive extended reality and gesture recognition systems, contemporary approaches are not optimized for computational and memory efficiency. In this paper, we propose a tiny deep neural network of which partial layers are recursively exploited for refining its previous estimations. During its iterative refinements, we employ learned gating criteria to decide whether to exit from the weight-sharing loop, allowing per-sample adaptation in our model. Our network is trained to be aware of the uncertainty in its current predictions to efficiently gate at each iteration, estimating variances after each loop for its keypoint estimates. Additionally, we investigate the effectiveness of end-to-end and progressive training protocols for our recursive structure on maximizing the model capacity. With the proposed setting, our method consistently outperforms state-of-the-art 2D/3D hand pose estimation approaches in terms of both accuracy and efficiency for widely used benchmarks.