arXiv subjects

Zifeng Wang

Publications and source records attributed to Zifeng Wang.

At least 37 records · Page 2Linked to original sources

arXiv2025

Developing Large Language Models for Clinical Research Using One Million Clinical Trials

Developing artificial intelligence (AI) for clinical research requires a comprehensive data foundation that supports model training and rigorous evaluation. Here, we introduce TrialPanorama, a large-scale structured resource that aggregates 1.6M clinical trial records from fifteen global registries and links them with biomedical ontologies and associated literature. To demonstrate its utility, we build a pipeline that constructs 152K training and testing samples for eight key clinical research tasks. Three tasks support systematic review workflows, including study search, study screening, and evidence summarization. Five tasks focus on trial design and optimization, including arm design, eligibility criteria design, endpoint selection, sample size estimation, and trial completion assessment and rationalization. Benchmarking cutting-edge large language models (LLMs) reveals that generic LLMs have limited capability in clinical reasoning. In contrast, an 8B LLM we developed on TrialPanorama using supervised finetuning and reinforcement learning wins over the 70B generic counterparts in all eight tasks, with a relative improvement of 73.7%, 67.6%, 38.4%, 37.8%, 26.5%, 20.7%, 20.0%, 18.1%, and 5.2%, respectively. We envision that TrialPanorama provides a solid foundation for future scaling of AI for clinical research.

cs.AI↗

arXiv2025

s3: You Don't Need That Much Data to Train a Search Agent via RL

Retrieval-augmented generation (RAG) systems empower large language models (LLMs) to access external knowledge during inference. Recent advances have enabled LLMs to act as search agents via reinforcement learning (RL), improving information acquisition through multi-turn interactions with retrieval engines. However, existing approaches either optimize retrieval using search-only metrics (e.g., NDCG) that ignore downstream utility or fine-tune the entire LLM to jointly reason and retrieve-entangling retrieval with generation and limiting the real search utility and compatibility with frozen or proprietary models. In this work, we propose s3, a lightweight, model-agnostic framework that decouples the searcher from the generator and trains the searcher using a Gain Beyond RAG reward: the improvement in generation accuracy over naive RAG. s3 requires only 2.4k training samples to outperform baselines trained on over 70x more data, consistently delivering stronger downstream performance across six general QA and five medical QA benchmarks.

cs.AI↗

arXiv2025

Heterogeneous Swarms: Jointly Optimizing Model Roles and Weights for Multi-LLM Systems

We propose Heterogeneous Swarms, an algorithm to design multi-LLM systems by jointly optimizing model roles and weights. We represent multi-LLM systems as directed acyclic graphs (DAGs) of LLMs with topological message passing for collaborative generation. Given a pool of LLM experts and a utility function, Heterogeneous Swarms employs two iterative steps: role-step and weight-step. For role-step, we interpret model roles as learning a DAG that specifies the flow of inputs and outputs between LLMs. Starting from a swarm of random continuous adjacency matrices, we decode them into discrete DAGs, call the LLMs in topological order, evaluate on the utility function (e.g. accuracy on a task), and optimize the adjacency matrices with particle swarm optimization based on the utility score. For weight-step, we assess the contribution of individual LLMs in the multi-LLM systems and optimize model weights with swarm intelligence. We propose JFK-score to quantify the individual contribution of each LLM in the best-found DAG of the role-step, then optimize model weights with particle swarm optimization based on the JFK-score. Experiments demonstrate that Heterogeneous Swarms outperforms 15 role- and/or weight-based baselines by 18.5% on average across 12 tasks. Further analysis reveals that Heterogeneous Swarms discovers multi-LLM systems with heterogeneous model roles and substantial collaborative gains, and benefits from the diversity of language models.

cs.CL↗

arXiv2025

MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129 categories derived from 12 authentic real-world biomedical scenarios. Tasks are encapsulated within executable sandbox environments, each featuring detailed task specifications, interactive feedback mechanisms, verifiable ground truth annotations, and scalable training trajectory generation. Extensive benchmarking of 29 LLMs reveals substantial performance disparities in biomedical data science between commercial and open-source LLMs. Leveraging efficient multi-threaded and multi-turn trajectory sampling in MedAgentGym, Med-Copilot achieves performance gains of +43.02% and +45.28% from offline and online reinforcement learning, respectively, demonstrating MedAgentGym as an effective training ground while establishing itself as a cost-effective, privacy-preserving alternative competitive with proprietary LLMs (gpt-4o). By offering a unified execution environment with a comprehensive benchmark and accessible, extensible training resources, MedAgentGym delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical data science.

cs.CL↗

arXiv2025

A Model-Free Terminal Iterative Learning Control Scheme for Multi-Layer Printing Alignment Control Problems

Roll-to-roll (R2R) printing technologies are promising for high-volume continuous production of substrate-based electronic products. One of the major challenges in R2R flexible electronics printing is achieving tight alignment tolerances, as specified by the device resolution (usually at the micro-meter level), for multi-layer printed electronics. The alignment of the printed patterns in different layers is known as registration. Conventional registration control methods rely on real-time feedback controllers, such as PID control, to regulate the web tension and the web speed. However, those methods may lose effectiveness in compensating for recurring disturbances and supporting effective mitigation of registration errors. In this paper, we propose a Spatial-Terminal Iterative Learning Control (STILC) method integrated with PID control to iteratively learn and reduce registration error cycle-by-cycle, converging it to zero. This approach enables unprecedented precision in the creation, integration, and manipulation of multi-layer microstructures in R2R processes. We theoretically prove the convergence of the proposed STILC-PID hybrid approach and validate its effectiveness through a simulated registration error scenario caused by axis mismatch between roller and motor, a common issue in R2R systems. The results demonstrate that the STILC-PID hybrid control method can fully eliminate the registration error after a feasible number of iterations. Additionally, we analyze the impact of different learning gains on the convergence performance of STILC.

eess.SY↗

arXiv2025

SAIF: Sparse Adversarial and Imperceptible Attack Framework

Adversarial attacks hamper the decision-making ability of neural networks by perturbing the input signal. The addition of calculated small distortion to images, for instance, can deceive a well-trained image classification network. In this work, we propose a novel attack technique called Sparse Adversarial and Interpretable Attack Framework (SAIF). Specifically, we design imperceptible attacks that contain low-magnitude perturbations at a small number of pixels and leverage these sparse attacks to reveal the vulnerability of classifiers. We use the Frank-Wolfe (conditional gradient) algorithm to simultaneously optimize the attack perturbations for bounded magnitude and sparsity with $O(1/\sqrt{T})$ convergence. Empirical results show that SAIF computes highly imperceptible and interpretable adversarial examples, and outperforms state-of-the-art sparse attack methods on the ImageNet dataset.

cs.CV↗

arXiv2025

In Prospect and Retrospect: Reflective Memory Management for Long-term Personalized Dialogue Agents

Large Language Models (LLMs) have made significant progress in open-ended dialogue, yet their inability to retain and retrieve relevant information from long-term interactions limits their effectiveness in applications requiring sustained personalization. External memory mechanisms have been proposed to address this limitation, enabling LLMs to maintain conversational continuity. However, existing approaches struggle with two key challenges. First, rigid memory granularity fails to capture the natural semantic structure of conversations, leading to fragmented and incomplete representations. Second, fixed retrieval mechanisms cannot adapt to diverse dialogue contexts and user interaction patterns. In this work, we propose Reflective Memory Management (RMM), a novel mechanism for long-term dialogue agents, integrating forward- and backward-looking reflections: (1) Prospective Reflection, which dynamically summarizes interactions across granularities-utterances, turns, and sessions-into a personalized memory bank for effective future retrieval, and (2) Retrospective Reflection, which iteratively refines the retrieval in an online reinforcement learning (RL) manner based on LLMs' cited evidence. Experiments show that RMM demonstrates consistent improvement across various metrics and benchmarks. For example, RMM shows more than 10% accuracy improvement over the baseline without memory management on the LongMemEval dataset.

cs.CL↗

arXiv2025

Universal Model Routing for Efficient LLM Inference

Model routing is a simple technique for reducing the inference cost of large language models (LLMs), wherein one maintains a pool of candidate LLMs, and learns to route each prompt to the smallest feasible LLM. Existing works focus on learning a router for a fixed pool of LLMs. In this paper, we consider the problem of dynamic routing, where new, previously unobserved LLMs are available at test time. We propose UniRoute, a new approach to this problem that relies on representing each LLM as a feature vector, derived based on predictions on a set of representative prompts. Based on this, we detail two effective instantiations of UniRoute, relying on cluster-based routing and a learned cluster map respectively. We show that these are estimates of a theoretically optimal routing rule, and quantify their errors via an excess risk bound. Experiments on a range of public benchmarks show the effectiveness of UniRoute in routing amongst more than 30 unseen LLMs.

cs.CL↗

arXiv2025

Model Swarms: Collaborative Search to Adapt LLM Experts via Swarm Intelligence

We propose Model Swarms, a collaborative search algorithm to adapt LLMs via swarm intelligence, the collective behavior guiding individual systems. Specifically, Model Swarms starts with a pool of LLM experts and a utility function. Guided by the best-found checkpoints across models, diverse LLM experts collaboratively move in the weight space and optimize a utility function representing model adaptation objectives. Compared to existing model composition approaches, Model Swarms offers tuning-free model adaptation, works in low-data regimes with as few as 200 examples, and does not require assumptions about specific experts in the swarm or how they should be composed. Extensive experiments demonstrate that Model Swarms could flexibly adapt LLM experts to a single task, multi-task domains, reward models, as well as diverse human interests, improving over 12 model composition baselines by up to 21.0% across tasks and contexts. Further analysis reveals that LLM experts discover previously unseen capabilities in initial checkpoints and that Model Swarms enable the weak-to-strong transition of experts through the collaborative search process.

cs.CL↗

arXiv2025

Enabling Flexible Multi-LLM Integration for Scalable Knowledge Aggregation

Large language models (LLMs) have shown remarkable promise but remain challenging to continually improve through traditional finetuning, particularly when integrating capabilities from other specialized LLMs. Popular methods like ensemble and weight merging require substantial memory and struggle to adapt to changing data environments. Recent efforts have transferred knowledge from multiple LLMs into a single target model; however, they suffer from interference and degraded performance among tasks, largely due to limited flexibility in candidate selection and training pipelines. To address these issues, we propose a framework that adaptively selects and aggregates knowledge from diverse LLMs to build a single, stronger model, avoiding the high memory overhead of ensemble and inflexible weight merging. Specifically, we design an adaptive selection network that identifies the most relevant source LLMs based on their scores, thereby reducing knowledge interference. We further propose a dynamic weighted fusion strategy that accounts for the inherent strengths of candidate LLMs, along with a feedback-driven loss function that prevents the selector from converging on a single subset of sources. Experimental results demonstrate that our method can enable a more stable and scalable knowledge aggregation process while reducing knowledge interference by up to 50% compared to existing approaches. Code is avaliable at https://github.com/ZLKong/LLM_Integration

cs.CL↗

arXiv2025

BioDSA-1K: Benchmarking Data Science Agents for Biomedical Research

Validating scientific hypotheses is a central challenge in biomedical research, and remains difficult for artificial intelligence (AI) agents due to the complexity of real-world data analysis and evidence interpretation. In this work, we present BioDSA-1K, a benchmark designed to evaluate AI agents on realistic, data-driven biomedical hypothesis validation tasks. BioDSA-1K consists of 1,029 hypothesis-centric tasks paired with 1,177 analysis plans, curated from over 300 published biomedical studies to reflect the structure and reasoning found in authentic research workflows. Each task includes a structured hypothesis derived from the original study's conclusions, expressed in the affirmative to reflect the language of scientific reporting, and one or more pieces of supporting evidence grounded in empirical data tables. While these hypotheses mirror published claims, they remain testable using standard statistical or machine learning methods. The benchmark enables evaluation along four axes: (1) hypothesis decision accuracy, (2) alignment between evidence and conclusion, (3) correctness of the reasoning process, and (4) executability of the AI-generated analysis code. Importantly, BioDSA-1K includes non-verifiable hypotheses: cases where the available data are insufficient to support or refute a claim, reflecting a common yet underexplored scenario in real-world science. We propose BioDSA-1K as a foundation for building and evaluating generalizable, trustworthy AI agents for biomedical discovery.

cs.AI↗

arXiv2025

Speculative Knowledge Distillation: Bridging the Teacher-Student Gap Through Interleaved Sampling

Recent advances in knowledge distillation (KD) have enabled smaller student models to approach the performance of larger teacher models. However, popular methods such as supervised KD and on-policy KD, are adversely impacted by the knowledge gaps between teacher-student in practical scenarios. Supervised KD suffers from a distribution mismatch between training with a static dataset and inference over final student-generated outputs. Conversely, on-policy KD, which uses student-generated samples for training, can suffer from low-quality training examples with which teacher models are not familiar, resulting in inaccurate teacher feedback. To address these limitations, we introduce Speculative Knowledge Distillation (SKD), a novel approach that leverages cooperation between student and teacher models to generate high-quality training data on-the-fly while aligning with the student's inference-time distribution. In SKD, the student proposes tokens, and the teacher replaces poorly ranked ones based on its own distribution, transferring high-quality knowledge adaptively. We evaluate SKD on various text generation tasks, including translation, summarization, math, and instruction following, and show that SKD consistently outperforms existing KD methods across different domains, data sizes, and model initialization strategies.

cs.CL↗

arXiv2025

Geometric Asymmetry-Enhanced Nonreciprocal Supercurrent Transport Revealed by Second-Harmonic Response

Nonreciprocal transport in superconducting systems serves as a powerful probe of symmetry-breaking mechanisms, with the superconducting diode effect emerging as a key manifestation enabling cryogenic rectification. While theoretical models have extensively explored superconducting nonreciprocity, experimental verification remains challenging, as conventional transport measurements struggle to disentangle intrinsic and extrinsic contributions. Nonlinear transport analysis, particularly second-harmonic response, offers an alternative approach by providing a sensitive probe for detecting spatial inversion symmetry breaking in the presence of time-reversal symmetry violation. Here, we systematically investigate the influence of geometric symmetry on nonreciprocal transport by comparing two triangular-extended Hall bar configurations with a symmetric Hall bar control. Second-harmonic nonlinear transport measurements reveal that the triangular extension significantly enhances nonreciprocal response, exhibiting a clear dependence on the base angle of the extension. These findings establish a direct connection between mesoscopic geometry and macroscopic nonreciprocity, demonstrating how spatial symmetry and vortex dynamics govern nonlinear transport. This insight offers a guiding principle for designing superconducting rectification architectures.

cond-mat.supr-con↗

arXiv2025

DeepRetrieval: Hacking Real Search Engines and Retrievers with Large Language Models via Reinforcement Learning

Information retrieval systems are crucial for enabling effective access to large document collections. Recent approaches have leveraged Large Language Models (LLMs) to enhance retrieval performance through query augmentation, but often rely on expensive supervised learning or distillation techniques that require significant computational resources and hand-labeled data. We introduce DeepRetrieval, a reinforcement learning (RL) approach that trains LLMs for query generation through trial and error without supervised data (reference query). Using retrieval metrics as rewards, our system generates queries that maximize retrieval performance. DeepRetrieval outperforms leading methods on literature search with 65.07% (vs. previous SOTA 24.68%) recall for publication search and 63.18% (vs. previous SOTA 32.11%) recall for trial search using real-world search engines. DeepRetrieval also dominates in evidence-seeking retrieval, classic information retrieval and SQL database search. With only 3B parameters, it outperforms industry-leading models like GPT-4o and Claude-3.5-Sonnet on 11/13 datasets. These results demonstrate that our RL approach offers a more efficient and effective paradigm for information retrieval. Our data and code are available at: https://github.com/pat-jj/DeepRetrieval.

cs.IR↗

arXiv2025

Can Large Language Models Replace Data Scientists in Biomedical Research?

Data science plays a critical role in biomedical research, but it requires professionals with expertise in coding and medical data analysis. Large language models (LLMs) have shown great potential in supporting medical tasks and performing well in general coding tests. However, existing evaluations fail to assess their capability in biomedical data science, particularly in handling diverse data types such as genomics and clinical datasets. To address this gap, we developed a benchmark of data science coding tasks derived from the analyses of 39 published studies. This benchmark comprises 293 coding tasks (128 in Python and 165 in R) performed on real-world TCGA-type genomics and clinical data. Our findings reveal that the vanilla prompting of LLMs yields suboptimal performances due to drawbacks in following input instructions, understanding target data, and adhering to standard analysis practices. Next, we benchmarked six cutting-edge LLMs and advanced adaptation methods, finding two methods to be particularly effective: chain-of-thought prompting, which provides a step-by-step plan for data analysis, which led to a 21% code accuracy improvement (56.6% versus 35.3%); and self-reflection, enabling LLMs to refine the buggy code iteratively, yielding an 11% code accuracy improvement (45.5% versus 34.3%). Building on these insights, we developed a platform that integrates LLMs into the data science workflow for medical professionals. In a user study with five medical professionals, we found that while LLMs cannot fully automate programming tasks, they significantly streamline the programming process. We found that 80% of their submitted code solutions were incorporated from LLM-generated code, with up to 96% reuse in some cases. Our analysis highlights the potential of LLMs to enhance data science efficiency in biomedical research when integrated into expert workflows.

cs.AI↗

arXiv2025

InformGen: An AI Copilot for Accurate and Compliant Clinical Research Consent Document Generation

Leveraging large language models (LLMs) to generate high-stakes documents, such as informed consent forms (ICFs), remains a significant challenge due to the extreme need for regulatory compliance and factual accuracy. Here, we present InformGen, an LLM-driven copilot for accurate and compliant ICF drafting by optimized knowledge document parsing and content generation, with humans in the loop. We further construct a benchmark dataset comprising protocols and ICFs from 900 clinical trials. Experimental results demonstrate that InformGen achieves near 100% compliance with 18 core regulatory rules derived from FDA guidelines, outperforming a vanilla GPT-4o model by up to 30%. Additionally, a user study with five annotators shows that InformGen, when integrated with manual intervention, attains over 90% factual accuracy, significantly surpassing the vanilla GPT-4o model's 57%-82%. Crucially, InformGen ensures traceability by providing inline citations to source protocols, enabling easy verification and maintaining the highest standards of factual integrity.

cs.CL↗

arXiv2025

Magnet: Multi-turn Tool-use Data Synthesis and Distillation via Graph Translation

Large language models (LLMs) have exhibited the ability to effectively utilize external tools to address user queries. However, their performance may be limited in complex, multi-turn interactions involving users and multiple tools. To address this, we propose Magnet, a principled framework for synthesizing high-quality training trajectories to enhance the function calling capability of large language model agents in multi-turn conversations with humans. The framework is based on automatic and iterative translations from a function signature path to a sequence of queries and executable function calls. We model the complicated function interactions in multi-turn cases with graph and design novel node operations to build reliable signature paths. Motivated by context distillation, when guiding the generation of positive and negative trajectories using a teacher model, we provide reference function call sequences as positive hints in context and contrastive, incorrect function calls as negative hints. Experiments show that training with the positive trajectories with supervised fine-tuning and preference optimization against negative trajectories, our 14B model, Magnet-14B-mDPO, obtains 68.01 on BFCL-v3 and 73.30 on ToolQuery, surpassing the performance of the teacher model Gemini-1.5-pro-002 by a large margin in function calling.

cs.CL↗

arXiv2025

Reverse Thinking Makes LLMs Stronger Reasoners

Reverse thinking plays a crucial role in human reasoning. Humans can reason not only from a problem to a solution but also in reverse, i.e., start from the solution and reason towards the problem. This often enhances overall reasoning performance as it enables consistency checks between their forward and backward thinking. To enable Large Language Models (LLMs) to perform reverse thinking, we introduce Reverse-Enhanced Thinking (RevThink), a framework composed of data augmentation and learning objectives. In RevThink, we augment the dataset by collecting structured forward-backward reasoning from a teacher model, consisting of: (1) the original question, (2) forward reasoning, (3) backward question, and (4) backward reasoning. We then employ three objectives to train a smaller student model in a multi-task learning fashion: (a) generate forward reasoning from a question, (b) generate a backward question from a question, and (c) generate backward reasoning from the backward question. Experiments across 12 datasets covering commonsense, math, and logical reasoning show an average 13.53% improvement over the student model's zero-shot performance and a 6.84% improvement over the strongest knowledge distillation baselines. Moreover, our method demonstrates sample efficiency -- using only 10% of the correct forward reasoning from the training data, it outperforms a standard fine-tuning method trained on 10x more forward reasoning. RevThink also exhibits strong generalization to out-of-distribution held-out datasets.

cs.CL↗