arXiv subjects

James Zou

Publications and source records attributed to James Zou.

At least 163 records · Page 9Linked to original sources

arXiv2025

Protein Large Language Models: A Comprehensive Survey

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art Protein LLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning Protein LLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.

q-bio.BM↗

arXiv2025

Locality Alignment Improves Vision-Language Models

Vision language models (VLMs) have seen growing adoption in recent years, but many still struggle with basic spatial reasoning errors. We hypothesize that this is due to VLMs adopting pre-trained vision backbones, specifically vision transformers (ViTs) trained with image-level supervision and minimal inductive biases. Such models may fail to encode the class contents at each position in the image, and our goal is to resolve this with a vision backbone that effectively captures both local and global image semantics. Our main insight is that we do not require new supervision to learn this capability - pre-trained models contain significant knowledge of local semantics that we can extract and use for scalable self-supervision. We propose a new efficient post-training stage for ViTs called locality alignment and a novel fine-tuning procedure called MaskEmbed that uses a masked reconstruction loss to learn semantic contributions for each image patch. We first evaluate locality alignment with a vision-only benchmark, finding that it improves a model's performance at patch-level semantic segmentation, especially for strong backbones trained with image-caption pairs (e.g., CLIP and SigLIP). We then train a series of VLMs with and without locality alignment, and show that locality-aligned backbones improve performance across a range of benchmarks, particularly ones that involve spatial understanding (e.g., RefCOCO, OCID-Ref, TallyQA, VSR, AI2D). Overall, we demonstrate that we can efficiently learn local semantic extraction via a locality alignment stage, and that this procedure benefits VLM training recipes that use off-the-shelf vision backbones.

cs.CV↗

arXiv2025

MMed-RAG: Versatile Multimodal RAG System for Medical Vision Language Models

Artificial Intelligence (AI) has demonstrated significant potential in healthcare, particularly in disease diagnosis and treatment planning. Recent progress in Medical Large Vision-Language Models (Med-LVLMs) has opened up new possibilities for interactive diagnostic tools. However, these models often suffer from factual hallucination, which can lead to incorrect diagnoses. Fine-tuning and retrieval-augmented generation (RAG) have emerged as methods to address these issues. However, the amount of high-quality data and distribution shifts between training data and deployment data limit the application of fine-tuning methods. Although RAG is lightweight and effective, existing RAG-based approaches are not sufficiently general to different medical domains and can potentially cause misalignment issues, both between modalities and between the model and the ground truth. In this paper, we propose a versatile multimodal RAG system, MMed-RAG, designed to enhance the factuality of Med-LVLMs. Our approach introduces a domain-aware retrieval mechanism, an adaptive retrieved contexts selection method, and a provable RAG-based preference fine-tuning strategy. These innovations make the RAG process sufficiently general and reliable, significantly improving alignment when introducing retrieved contexts. Experimental results across five medical datasets (involving radiology, ophthalmology, pathology) on medical VQA and report generation demonstrate that MMed-RAG can achieve an average improvement of 43.8% in the factual accuracy of Med-LVLMs. Our data and code are available in https://github.com/richard-peng-xia/MMed-RAG.

cs.LG↗

arXiv2025

Minions: Cost-efficient Collaboration Between On-device and Cloud Language Models

We investigate an emerging setup in which a small, on-device language model (LM) with access to local data communicates with a frontier, cloud-hosted LM to solve real-world tasks involving financial, medical, and scientific reasoning over long documents. Can a local-remote collaboration reduce cloud inference costs while preserving quality? First, we consider a naive collaboration protocol where the local and remote models simply chat back and forth. Because only the local model reads the full context, this protocol achieves a 30.4x reduction in remote costs, but recovers only 87% of the performance of the frontier model. We identify two key limitations of this protocol: the local model struggles to (1) follow the remote model's multi-step instructions and (2) reason over long contexts. Motivated by these observations, we study an extension of this protocol, coined MinionS, in which the remote model decomposes the task into easier subtasks over shorter chunks of the document, that are executed locally in parallel. MinionS reduces costs by 5.7x on average while recovering 97.9% of the performance of the remote model alone. Our analysis reveals several key design choices that influence the trade-off between cost and performance in local-remote systems.

cs.LG↗

arXiv2025

Optimizing Model Selection for Compound AI Systems

Compound AI systems that combine multiple LLM calls, such as self-refine and multi-agent-debate, achieve strong performance on many AI tasks. We address a core question in optimizing compound systems: for each LLM call or module in the system, how should one decide which LLM to use? We show that these LLM choices have a large effect on quality, but the search space is exponential. We propose LLMSelector, an efficient framework for model selection in compound systems, which leverages two key empirical insights: (i) end-to-end performance is often monotonic in how well each module performs, with all other modules held fixed, and (ii) per-module performance can be estimated accurately by an LLM. Building upon these insights, LLMSelector iteratively selects one module and allocates to it the model with the highest module-wise performance, as estimated by an LLM, until no further gain is possible. LLMSelector is applicable to any compound system with a bounded number of modules, and its number of API calls scales linearly with the number of modules, achieving high-quality model allocation both empirically and theoretically. Experiments with popular compound systems such as multi-agent debate and self-refine using LLMs such as GPT-4o, Claude 3.5 Sonnet and Gemini 1.5 show that LLMSelector confers 5%-70% accuracy gains compared to using the same LLM for all modules.

cs.AI↗

arXiv2025

The Widespread Adoption of Large Language Model-Assisted Writing Across Society

The recent advances in large language models (LLMs) attracted significant public and policymaker interest in its adoption patterns. In this paper, we systematically analyze LLM-assisted writing across four domains-consumer complaints, corporate communications, job postings, and international organization press releases-from January 2022 to September 2024. Our dataset includes 687,241 consumer complaints, 537,413 corporate press releases, 304.3 million job postings, and 15,919 United Nations (UN) press releases. Using a robust population-level statistical framework, we find that LLM usage surged following the release of ChatGPT in November 2022. By late 2024, roughly 18% of financial consumer complaint text appears to be LLM-assisted, with adoption patterns spread broadly across regions and slightly higher in urban areas. For corporate press releases, up to 24% of the text is attributable to LLMs. In job postings, LLM-assisted writing accounts for just below 10% in small firms, and is even more common among younger firms. UN press releases also reflect this trend, with nearly 14% of content being generated or modified by LLMs. Although adoption climbed rapidly post-ChatGPT, growth appears to have stabilized by 2024, reflecting either saturation in LLM adoption or increasing subtlety of more advanced models. Our study shows the emergence of a new reality in which firms, consumers and even international organizations substantially rely on generative AI for communications.

cs.CL↗

arXiv2025

SMIR: Efficient Synthetic Data Pipeline To Improve Multi-Image Reasoning

Vision-Language Models (VLMs) excel at understanding single images, aided by high-quality instruction datasets. However, multi-image reasoning remains underexplored in the open-source community due to two key challenges: (1) scaling datasets with correlated images and complex reasoning instructions is resource-intensive, and (2) robust evaluation benchmarks for multi-image tasks are lacking. To address this, we introduce SMiR, a synthetic data-generation pipeline for multi-image reasoning, along with a high-quality dataset generated using this pipeline. SMiR efficiently extracts correlated images via multimodal embeddings, integrates visual and descriptive information, and leverages open-source LLMs to generate quality instructions. Using this approach, we produce 160K synthetic training samples, offering a cost-effective alternative to closed-source solutions. Additionally, we present SMiR-Bench, a multi-image reasoning benchmark comprising 200 diverse examples across seven complex reasoning tasks. SMiR-Bench is multi-turn and employs a VLM judge to evaluate free-form responses, providing a comprehensive assessment of model expressiveness and reasoning capability across modalities. We demonstrate the effectiveness of SMiR by fine-tuning open-source VLMs and evaluating them on SMiR-Bench.

cs.CV↗

arXiv2025

Optimizing Calibration by Gaining Aware of Prediction Correctness

Model calibration aims to align confidence with prediction correctness. The Cross-Entropy (CE) loss is widely used for calibrator training, which enforces the model to increase confidence on the ground truth class. However, we find the CE loss has intrinsic limitations. For example, for a narrow misclassification (e.g., a test sample is wrongly classified and its softmax score on the ground truth class is 0.4), a calibrator trained by the CE loss often produces high confidence on the wrongly predicted class, which is undesirable. In this paper, we propose a new post-hoc calibration objective derived from the aim of calibration. Intuitively, the proposed objective function asks that the calibrator decrease model confidence on wrongly predicted samples and increase confidence on correctly predicted samples. Because a sample itself has insufficient ability to indicate correctness, we use its transformed versions (e.g., rotated, greyscaled, and color-jittered) during calibrator training. Trained on an in-distribution validation set and tested with isolated, individual test samples, our method achieves competitive calibration performance on both in-distribution and out-of-distribution test sets compared with the state of the art. Further, our analysis points out the difference between our method and commonly used objectives such as CE loss and Mean Square Error (MSE) loss, where the latters sometimes deviates from the calibration aim.

cs.CV↗

arXiv2025

MedAgentBench: A Realistic Virtual EHR Environment to Benchmark Medical LLM Agents

Recent large language models (LLMs) have demonstrated significant advancements, particularly in their ability to serve as agents thereby surpassing their traditional role as chatbots. These agents can leverage their planning and tool utilization capabilities to address tasks specified at a high level. However, a standardized dataset to benchmark the agent capabilities of LLMs in medical applications is currently lacking, making the evaluation of LLMs on complex tasks in interactive healthcare environments challenging. To address this gap, we introduce MedAgentBench, a broad evaluation suite designed to assess the agent capabilities of large language models within medical records contexts. MedAgentBench encompasses 300 patient-specific clinically-derived tasks from 10 categories written by human physicians, realistic profiles of 100 patients with over 700,000 data elements, a FHIR-compliant interactive environment, and an accompanying codebase. The environment uses the standard APIs and communication infrastructure used in modern EMR systems, so it can be easily migrated into live EMR systems. MedAgentBench presents an unsaturated agent-oriented benchmark that current state-of-the-art LLMs exhibit some ability to succeed at. The best model (Claude 3.5 Sonnet v2) achieves a success rate of 69.67%. However, there is still substantial space for improvement which gives the community a next direction to optimize. Furthermore, there is significant variation in performance across task categories. MedAgentBench establishes this and is publicly available at https://github.com/stanfordmlgroup/MedAgentBench , offering a valuable framework for model developers to track progress and drive continuous improvements in the agent capabilities of large language models within the medical domain.

cs.LG↗

arXiv2025

ClashEval: Quantifying the tug-of-war between an LLM's internal prior and external evidence

Retrieval augmented generation (RAG) is frequently used to mitigate hallucinations and provide up-to-date knowledge for large language models (LLMs). However, given that document retrieval is an imprecise task and sometimes results in erroneous or even harmful content being presented in context, this raises the question of how LLMs handle retrieved information: If the provided content is incorrect, does the model know to ignore it, or does it recapitulate the error? Conversely, when the model's initial response is incorrect, does it always know to use the retrieved information to correct itself, or does it insist on its wrong prior response? To answer this, we curate a dataset of over 1200 questions across six domains (e.g., drug dosages, Olympic records, locations) along with content relevant to answering each question. We further apply precise perturbations to the answers in the content that range from subtle to blatant errors. We benchmark six top-performing LLMs, including GPT-4o, on this dataset and find that LLMs are susceptible to adopting incorrect retrieved content, overriding their own correct prior knowledge over 60% of the time. However, the more unrealistic the retrieved content is (i.e. more deviated from truth), the less likely the model is to adopt it. Also, the less confident a model is in its initial response (via measuring token probabilities), the more likely it is to adopt the information in the retrieved content. We exploit this finding and demonstrate simple methods for improving model accuracy where there is conflicting retrieved content. Our results highlight a difficult task and benchmark for LLMs -- namely, their ability to correctly discern when it is wrong in light of correct retrieved content and to reject cases when the provided content is incorrect.

cs.CL↗

arXiv2025

SiriuS: Self-improving Multi-agent Systems via Bootstrapped Reasoning

Multi-agent AI systems powered by large language models (LLMs) are increasingly applied to solve complex tasks. However, these systems often rely on fragile, manually designed prompts and heuristics, making optimization difficult. A key challenge in optimizing multi-agent systems is acquiring suitable training data for specialized agents. We introduce SiriuS, a self-improving, reasoning-driven optimization framework for multi-agent systems. Central to our approach is the construction of an experience library: a repository of high-quality reasoning trajectories. The library is built by retaining reasoning steps that lead to successful outcomes, providing a robust training set for optimizing multi-agent system. Additionally, we introduce a library augmentation procedure that refines unsuccessful trajectories, further enriching the library. SiriuS boosts performance by 2.86\% to 21.88\% on reasoning and biomedical QA and enhances agent negotiation in competitive settings. Our results show that SiriuS enhances multi-agent performance while generating reusable data for self-correction and self-play enhancement in the future.

cs.AI↗

arXiv2025

Safety challenges of AI in medicine in the era of large language models

Recent advancements in artificial intelligence (AI), particularly in large language models (LLMs), have unlocked significant potential to enhance the quality and efficiency of medical care. By introducing a novel way to interact with AI and data through natural language, LLMs offer new opportunities for medical practitioners, patients, and researchers. However, as AI and LLMs become more powerful and especially achieve superhuman performance in some medical tasks, public concerns over their safety have intensified. These concerns about AI safety have emerged as the most significant obstacles to the adoption of AI in medicine. In response, this review examines emerging risks in AI utilization during the LLM era. First, we explore LLM-specific safety challenges from functional and communication perspectives, addressing issues across data collection, model training, and real-world application. We then consider inherent safety problems shared by all AI systems, along with additional complications introduced by LLMs. Last, we discussed how safety issues of using AI in clinical practice and healthcare system operation would undermine trust among patient, clinicians and the public, and how to build confidence in these systems. By emphasizing the development of safe AI, we believe these technologies can be more rapidly and reliably integrated into everyday medical practice to benefit both patients and clinicians.

cs.CY↗

arXiv2025

A Foundational Generative Model for Breast Ultrasound Image Analysis

Foundational models have emerged as powerful tools for addressing various tasks in clinical settings. However, their potential development to breast ultrasound analysis remains untapped. In this paper, we present BUSGen, the first foundational generative model specifically designed for breast ultrasound image analysis. Pretrained on over 3.5 million breast ultrasound images, BUSGen has acquired extensive knowledge of breast structures, pathological features, and clinical variations. With few-shot adaptation, BUSGen can generate repositories of realistic and informative task-specific data, facilitating the development of models for a wide range of downstream tasks. Extensive experiments highlight BUSGen's exceptional adaptability, significantly exceeding real-data-trained foundational models in breast cancer screening, diagnosis, and prognosis. In breast cancer early diagnosis, our approach outperformed all board-certified radiologists (n=9), achieving an average sensitivity improvement of 16.5% (P-value<0.0001). Additionally, we characterized the scaling effect of using generated data which was as effective as the collected real-world data for training diagnostic models. Moreover, extensive experiments demonstrated that our approach improved the generalization ability of downstream models. Importantly, BUSGen protected patient privacy by enabling fully de-identified data sharing, making progress forward in secure medical data utilization. An online demo of BUSGen is available at https://aibus.bio.

cs.AI↗

arXiv2024

Capturing the Temporal Dependence of Training Data Influence

Traditional data influence estimation methods, like influence function, assume that learning algorithms are permutation-invariant with respect to training data. However, modern training paradigms, especially for foundation models using stochastic algorithms and multi-stage curricula, are sensitive to data ordering, thus violating this assumption. This mismatch renders influence functions inadequate for answering a critical question in machine learning: How can we capture the dependence of data influence on the optimization trajectory during training? To address this gap, we formalize the concept of trajectory-specific leave-one-out (LOO) influence, which quantifies the impact of removing a data point from a specific iteration during training, accounting for the exact sequence of data encountered and the model's optimization trajectory. However, exactly evaluating the trajectory-specific LOO presents a significant computational challenge. To address this, we propose data value embedding, a novel technique enabling efficient approximation of trajectory-specific LOO. Specifically, we compute a training data embedding that encapsulates the cumulative interactions between data and the evolving model parameters. The LOO can then be efficiently approximated through a simple dot-product between the data value embedding and the gradient of the given test data. As data value embedding captures training data ordering, it offers valuable insights into model training dynamics. In particular, we uncover distinct phases of data influence, revealing that data points in the early and late stages of training exert a greater impact on the final model. These insights translate into actionable strategies for managing the computational overhead of data selection by strategically timing the selection process, potentially opening new avenues in data curation research.

cs.LG↗

arXiv2024

Improving LLM Group Fairness on Tabular Data via In-Context Learning

Large language models (LLMs) have been shown to be effective on tabular prediction tasks in the low-data regime, leveraging their internal knowledge and ability to learn from instructions and examples. However, LLMs can fail to generate predictions that satisfy group fairness, that is, produce equitable outcomes across groups. Critically, conventional debiasing approaches for natural language tasks do not directly translate to mitigating group unfairness in tabular settings. In this work, we systematically investigate four empirical approaches to improve group fairness of LLM predictions on tabular datasets, including fair prompt optimization, soft prompt tuning, strategic selection of few-shot examples, and self-refining predictions via chain-of-thought reasoning. Through experiments on four tabular datasets using both open-source and proprietary LLMs, we show the effectiveness of these methods in enhancing demographic parity while maintaining high overall performance. Our analysis provides actionable insights for practitioners in selecting the most suitable approach based on their specific requirements and constraints.

cs.LG↗

arXiv2024

Enhancing Large Vision Language Models with Self-Training on Image Comprehension

Large vision language models (LVLMs) integrate large language models (LLMs) with pre-trained vision encoders, thereby activating the perception capability of the model to understand image inputs for different queries and conduct subsequent reasoning. Improving this capability requires high-quality vision-language data, which is costly and labor-intensive to acquire. Self-training approaches have been effective in single-modal settings to alleviate the need for labeled data by leveraging model's own generation. However, effective self-training remains a challenge regarding the unique visual perception and reasoning capability of LVLMs. To address this, we introduce Self-Training on Image Comprehension (STIC), which emphasizes a self-training approach specifically for image comprehension. First, the model self-constructs a preference dataset for image descriptions using unlabeled images. Preferred responses are generated through a step-by-step prompt, while dis-preferred responses are generated from either corrupted images or misleading prompts. To further self-improve reasoning on the extracted visual information, we let the model reuse a small portion of existing instruction-tuning data and append its self-generated image descriptions to the prompts. We validate the effectiveness of STIC across seven different benchmarks, demonstrating substantial performance gains of 4.0% on average while using 70% less supervised fine-tuning data than the current method. Further studies investigate various components of STIC and highlight its potential to leverage vast quantities of unlabeled images for self-training. Code and data are made publicly available.

cs.CV↗

arXiv2024

TFG: Unified Training-Free Guidance for Diffusion Models

Given an unconditional diffusion model and a predictor for a target property of interest (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. Existing methods, though effective in various individual applications, often lack theoretical grounding and rigorous testing on extensive benchmarks. As a result, they could even fail on simple tasks, and applying them to a new problem becomes unavoidably difficult. This paper introduces a novel algorithmic framework encompassing existing methods as special cases, unifying the study of training-free guidance into the analysis of an algorithm-agnostic design space. Via theoretical and empirical investigation, we propose an efficient and effective hyper-parameter searching strategy that can be readily applied to any downstream task. We systematically benchmark across 7 diffusion models on 16 tasks with 40 targets, and improve performance by 8.5% on average. Our framework and benchmark offer a solid foundation for conditional generation in a training-free manner.

cs.LG↗

arXiv2024

InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

Protein language models (PLMs) have demonstrated remarkable success in protein modeling and design, yet their internal mechanisms for predicting structure and function remain poorly understood. Here we present a systematic approach to extract and analyze interpretable features from PLMs using sparse autoencoders (SAEs). By training SAEs on embeddings from the PLM ESM-2, we identify up to 2,548 human-interpretable latent features per layer that strongly correlate with up to 143 known biological concepts such as binding sites, structural motifs, and functional domains. In contrast, examining individual neurons in ESM-2 reveals up to 46 neurons per layer with clear conceptual alignment across 15 known concepts, suggesting that PLMs represent most concepts in superposition. Beyond capturing known annotations, we show that ESM-2 learns coherent concepts that do not map onto existing annotations and propose a pipeline using language models to automatically interpret novel latent features learned by the SAEs. As practical applications, we demonstrate how these latent features can fill in missing annotations in protein databases and enable targeted steering of protein sequence generation. Our results demonstrate that PLMs encode rich, interpretable representations of protein biology and we propose a systematic framework to extract and analyze these latent features. In the process, we recover both known biology and potentially new protein motifs. As community resources, we introduce InterPLM (interPLM.ai), an interactive visualization platform for exploring and analyzing learned PLM features, and release code for training and analysis at github.com/ElanaPearl/interPLM.

q-bio.BM↗