Ermo Hua

Biqing Qi, Kaiyan Zhang, Kai Tian et al.

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

Yuxin Zuo, Kaiyan Zhang, Li Sheng et al. · pku, tsinghua

This paper investigates Reinforcement Learning (RL) on data without explicit labels for reasoning tasks in Large Language Models (LLMs). The core challenge of the problem is reward estimation during inference while not having access to ground-truth information. While this setting appears elusive, we find that common practices in Test-Time Scaling (TTS), such as majority voting, yield surprisingly effective rewards suitable for driving RL training. In this work, we introduce Test-Time Reinforcement Learning (TTRL), a novel method for training LLMs using RL on unlabeled data. TTRL enables self-evolution of LLMs by utilizing the priors in the pre-trained models. Our experiments demonstrate that TTRL consistently improves performance across a variety of tasks and models. Notably, TTRL boosts the pass@1 performance of Qwen-2.5-Math-7B by approximately 211% on the AIME 2024 with only unlabeled test data. Furthermore, although TTRL is only supervised by the maj@n metric, TTRL has demonstrated performance to consistently surpass the upper limit of the initial model maj@n, and approach the performance of models trained directly on test data with ground-truth labels. Our experimental findings validate the general effectiveness of TTRL across various tasks and highlight TTRL's potential for broader tasks and domains. GitHub: https://github.com/PRIME-RL/TTRL

Yuxin Zuo, Shang Qu, Yifei Li et al. · tsinghua

We introduce MedXpertQA, a highly challenging and comprehensive benchmark to evaluate expert-level medical knowledge and advanced reasoning. MedXpertQA includes 4,460 questions spanning 17 specialties and 11 body systems. It includes two subsets, Text for text evaluation and MM for multimodal evaluation. Notably, MM introduces expert-level exam questions with diverse images and rich clinical information, including patient records and examination results, setting it apart from traditional medical multimodal benchmarks with simple QA pairs generated from image captions. MedXpertQA applies rigorous filtering and augmentation to address the insufficient difficulty of existing benchmarks like MedQA, and incorporates specialty board questions to improve clinical relevance and comprehensiveness. We perform data synthesis to mitigate data leakage risk and conduct multiple rounds of expert reviews to ensure accuracy and reliability. We evaluate 18 leading models on \benchmark. Moreover, medicine is deeply connected to real-world decision-making, providing a rich and representative setting for assessing reasoning abilities beyond mathematics and code. To this end, we develop a reasoning-oriented subset to facilitate the assessment of o1-like models. Code and data are available at: https://github.com/TsinghuaC3I/MedXpertQA

Kaiyan Zhang, Yuxin Zuo, Bingxiang He et al. · pku, tsinghua

In this paper, we survey recent advances in Reinforcement Learning (RL) for reasoning with Large Language Models (LLMs). RL has achieved remarkable success in advancing the frontier of LLM capabilities, particularly in addressing complex logical tasks such as mathematics and coding. As a result, RL has emerged as a foundational methodology for transforming LLMs into LRMs. With the rapid progress of the field, further scaling of RL for LRMs now faces foundational challenges not only in computational resources but also in algorithm design, training data, and infrastructure. To this end, it is timely to revisit the development of this domain, reassess its trajectory, and explore strategies to enhance the scalability of RL toward Artificial SuperIntelligence (ASI). In particular, we examine research applying RL to LLMs and LRMs for reasoning abilities, especially since the release of DeepSeek-R1, including foundational components, core problems, training resources, and downstream applications, to identify future opportunities and directions for this rapidly evolving area. We hope this review will promote future research on RL for broader reasoning models. Github: https://github.com/TsinghuaC3I/Awesome-RL-for-LRMs

Kaiyan Zhang, Jianyu Wang, Ermo Hua et al.

With the advancement of language models (LMs), their exposure to private data is increasingly inevitable, and their deployment (especially for smaller ones) on personal devices, such as PCs and smartphones, has become a prevailing trend. In contexts laden with user information, enabling models to both safeguard user privacy and execute commands efficiently emerges as an essential research imperative. In this paper, we propose CoGenesis, a collaborative generation framework integrating large (hosted on cloud infrastructure) and small models (deployed on local devices) to address privacy concerns logically. Initially, we design a pipeline to create personalized writing instruction datasets enriched with extensive context details as the testbed of this research issue. Subsequently, we introduce two variants of CoGenesis based on sketch and logits respectively. Our experimental findings, based on our synthesized dataset and two additional open-source datasets, indicate that: 1) Large-scale models perform well when provided with user context but struggle in the absence of such context. 2) While specialized smaller models fine-tuned on the synthetic dataset show promise, they still lag behind their larger counterparts. 3) Our CoGenesis framework, utilizing mixed-scale models, showcases competitive performance, providing a feasible solution to privacy issues.

Yuhua Jiang, Shuang Cheng, Yihao Liu et al.

Specialized Generalist Models (SGMs) aim to preserve broad capabilities while achieving expert-level performance in target domains. However, traditional LLM structures including Transformer, Linear Attention, and hybrid models do not employ specialized memory mechanism guided by task information. In this paper, we present Nirvana, an SGM with specialized memory mechanism, linear time complexity, and test-time task information extraction. Besides, we propose the Task-Aware Memory Trigger ($\textit{Trigger}$) that flexibly adjusts memory mechanism based on the current task's requirements. In Trigger, each incoming sample is treated as a self-supervised fine-tuning task, enabling Nirvana to adapt its task-related parameters on the fly to domain shifts. We also design the Specialized Memory Updater ($\textit{Updater}$) that dynamically memorizes the context guided by Trigger. We conduct experiments on both general language tasks and specialized medical tasks. On a variety of natural language modeling benchmarks, Nirvana achieves competitive or superior results compared to the existing LLM structures. To prove the effectiveness of Trigger on specialized tasks, we test Nirvana's performance on a challenging medical task, i.e., Magnetic Resonance Imaging (MRI). We post-train frozen Nirvana backbone with lightweight codecs on paired electromagnetic signals and MRI images. Despite the frozen Nirvana backbone, Trigger guides the model to adapt to the MRI domain with the change of task-related parameters. Nirvana achieves higher-quality MRI reconstruction compared to conventional MRI models as well as the models with traditional LLMs' backbone, and can also generate accurate preliminary clinical reports accordingly.

Kaiyan Zhang, Jianyu Wang, Ning Ding et al.

Large Language Models (LLMs) exhibit impressive capabilities across various applications but encounter substantial challenges such as high inference latency, considerable training costs, and the generation of hallucinations. Collaborative decoding between large and small language models (SLMs) presents a promising strategy to mitigate these issues through methods including speculative decoding, contrastive decoding, and emulator or proxy fine-tuning. However, the specifics of such collaborations, particularly from a unified perspective, remain largely unexplored. Inspired by dual-process cognitive theory, we propose a unified framework in this paper, termed Fast and Slow Generating (FS-GEN). Within this framework, LLMs (sometimes along with SLMs) are categorized as System 2 (slow and deliberate), while independent SLMs are designated as System 1 (fast and intuitive). We provide a comprehensive analysis of these collaborative methodologies, elucidating their common properties and shedding light on the differential knowledge capabilities of System 2 versus System 1 through the FS-GEN framework. Our findings indicate that only a small proportion of collaborative interactions (approximately less than 20\% in most instances) are necessary across various methods. These interactions between System 1 and System 2 conform to a scaling law related to the parameter ratios, enabling predictable collaboration. Furthermore, we explore the specific conditions under which collaboration proves most effective, particularly from an uncertainty perspective, offering novel insights that may guide future optimization efforts. Our research underscores that the fundamental distinction between System 1 and System 2 lies in the uncertainty of next token predictions, where interventions by System 2 are crucial to support System 1. Code for Reproduction: https://github.com/TsinghuaC3I/FS-GEN

Kaiyan Zhang, Sihang Zeng, Ermo Hua et al.

Large Language Models (LLMs) have demonstrated remarkable capabilities across various domains and are moving towards more specialized areas. Recent advanced proprietary models such as GPT-4 and Gemini have achieved significant advancements in biomedicine, which have also raised privacy and security challenges. The construction of specialized generalists hinges largely on high-quality datasets, enhanced by techniques like supervised fine-tuning and reinforcement learning from human or AI feedback, and direct preference optimization. However, these leading technologies (e.g., preference learning) are still significantly limited in the open source community due to the scarcity of specialized data. In this paper, we present the UltraMedical collections, which consist of high-quality manual and synthetic datasets in the biomedicine domain, featuring preference annotations across multiple advanced LLMs. By utilizing these datasets, we fine-tune a suite of specialized medical models based on Llama-3 series, demonstrating breathtaking capabilities across various medical benchmarks. Moreover, we develop powerful reward models skilled in biomedical and general reward benchmark, enhancing further online preference learning within the biomedical LLM community. Datasets and models are available at https://github.com/TsinghuaC3I/UltraMedical

Ermo Hua, Che Jiang, Xingtai Lv et al. · tsinghua

Extending the context length of Language Models (LMs) by improving Rotary Position Embedding (RoPE) has become a trend. While prior works mainly address RoPE's limitations within attention, this paper uncovers the adverse effects on length generalization from nearly all parts of LMs. Using Discrete Signal Processing theory, we show that RoPE enables periodic attention by implicitly achieving Non-Uniform Discrete Fourier Transform. However, this periodicity is undermined by the spectrum damage caused by: 1) linear layers and activation functions; 2) insufficiently trained frequency components brought by time-domain truncation. Building on our observations, we propose Fourier Position Embedding (FoPE), which enhances attention's frequency-domain properties to improve both its periodic extension and length generalization. FoPE constructs \textit{Fourier Series} and zero-outs the destructive frequency components, increasing model robustness against the spectrum damage. Experiments across various model scales and benchmarks show that, within varying context windows, FoPE maintains a more stable performance compared to other baselines. Several analyses and ablations bring further support to our method and theoretical modeling.

Xuekai Zhu, Daixuan Cheng, Hengli Li et al. · tsinghua

Model collapse in synthetic data indicates that iterative training on self-generated data leads to a gradual decline in performance. With the proliferation of AI models, synthetic data will fundamentally reshape the web data ecosystem. Future GPT-$\{n\}$ models will inevitably be trained on a blend of synthetic and human-produced data. In this paper, we focus on two questions: what is the impact of synthetic data on language model training, and how to synthesize data without model collapse? We first pre-train language models across different proportions of synthetic data, revealing a negative correlation between the proportion of synthetic data and model performance. We further conduct statistical analysis on synthetic data to uncover distributional shift phenomenon and over-concentration of n-gram features. Inspired by the above findings, we propose token editing on human-produced data to obtain semi-synthetic data. As a proof of concept, we theoretically demonstrate that token-level editing can prevent model collapse, as the test error is constrained by a finite upper bound. We conduct extensive experiments on pre-training from scratch, continual pre-training, and supervised fine-tuning. The results validate our theoretical proof that token-level editing improves model performance.

Xinwei Long, Zhiyuan Ma, Ermo Hua et al.

Retrieval-augmented generation (RAG) has emerged to address the knowledge-intensive visual question answering (VQA) task. Current methods mainly employ separate retrieval and generation modules to acquire external knowledge and generate answers, respectively. We propose ReAuSE, an alternative to the previous RAG model for the knowledge-based VQA task, which seamlessly integrates knowledge retriever into the generative multi-modal large language model, serving as a built-in search engine. Specifically, our model functions both as a generative retriever and an accurate answer generator. It not only helps retrieve documents from the knowledge base by producing identifiers for each document, but it also answers visual questions based on the retrieved documents. Furthermore, we propose a reinforced retrieval calibration module from relevance feedback to improve retrieval performance and align with the preferences for accurate answer generation. Extensive experiments on two representative OKVQA and A-OKVQA datasets demonstrate significant improvements ranging from 2.9\% to 9.6\% across all evaluation metrics when compared to strong baselines.

Ning Ding, Shang Qu, Linhai Xie et al. · tsinghua

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both specialized general models grounded in real-world scientific data and iterative, exploratory frameworks that mirror human scientific methodologies. In this paper, we present PROTEUS, a fully automated system for scientific discovery from raw proteomics data. PROTEUS uses large language models (LLMs) to perform hierarchical planning, execute specialized bioinformatics tools, and iteratively refine analysis workflows to generate high-quality scientific hypotheses. The system takes proteomics datasets as input and produces a comprehensive set of research objectives, analysis results, and novel biological hypotheses without human intervention. We evaluated PROTEUS on 12 proteomics datasets collected from various biological samples (e.g. immune cells, tumors) and different sample types (single-cell and bulk), generating 191 scientific hypotheses. These were assessed using both automatic LLM-based scoring on 5 metrics and detailed reviews from human experts. Results demonstrate that PROTEUS consistently produces reliable, logically coherent results that align well with existing literature while also proposing novel, evaluable hypotheses. The system's flexible architecture facilitates seamless integration of diverse analysis tools and adaptation to different proteomics data types. By automating complex proteomics analysis workflows and hypothesis generation, PROTEUS has the potential to considerably accelerate the pace of scientific discovery in proteomics research, enabling researchers to efficiently explore large-scale datasets and uncover biological insights.

Ermo Hua, Biqing Qi, Kaiyan Zhang et al.

Supervised Fine-Tuning (SFT) and Preference Optimization (PO) are key processes for aligning Language Models (LMs) with human preferences post pre-training. While SFT excels in efficiency and PO in effectiveness, they are often combined sequentially without integrating their optimization objectives. This approach ignores the opportunities to bridge their paradigm gap and take the strengths from both. In this paper, we interpret SFT and PO with two sub-processes -- Preference Estimation and Transition Optimization -- defined at token level within the Markov Decision Process (MDP). This modeling shows that SFT is only a special case of PO with inferior estimation and optimization. PO estimates the model's preference by its entire generation, while SFT only scores model's subsequent predicted tokens based on prior tokens from ground truth answer. These priors deviates from model's distribution, hindering the preference estimation and transition optimization. Building on this view, we introduce Intuitive Fine-Tuning (IFT) to integrate SFT and PO into a single process. Through a temporal residual connection, IFT brings better estimation and optimization by capturing LMs' intuitive sense of its entire answers. But it solely relies on a single policy and the same volume of non-preference-labeled data as SFT. Our experiments show that IFT performs comparably or even superiorly to SFT and some typical PO methods across several tasks, particularly those require generation, reasoning, and fact-following abilities. An explainable Frozen Lake game further validates the effectiveness of IFT for getting competitive policy.

Xingtai Lv, Ning Ding, Kaiyan Zhang et al. · tsinghua

Improving the effectiveness and efficiency of large language models (LLMs) simultaneously is a critical yet challenging research goal. In this paper, we find that low-rank pre-training, normally considered as efficient methods that will compromise performance, can be scalably effective when reduced parameters are precisely targeted. Specifically, applying the low-dimensional module only to the attention layer -- resolves this issue and enhances both effectiveness and efficiency. We refer to this structure as Low-dimensional Projected Attention (LPA) and provide an explanatory analysis. Through extensive experimentation at parameter scales of 130M, 370M, and scaling up to 3B, we have validated the effectiveness and scalability of LPA. Our results show that LPA model can save up to 12.4% in time while achieving an approximate 5% improvement in test perplexity (ppl) and on downstream tasks compared with the vanilla Transformer.

Xuekai Zhu, Daixuan Cheng, Dinghuai Zhang et al. · stanford, tsinghua

We propose FlowRL: matching the full reward distribution via flow balancing instead of maximizing rewards in large language model (LLM) reinforcement learning (RL). Recent advanced reasoning models adopt reward-maximizing methods (\eg, PPO and GRPO), which tend to over-optimize dominant reward signals while neglecting less frequent but valid reasoning paths, thus reducing diversity. In contrast, we transform scalar rewards into a normalized target distribution using a learnable partition function, and then minimize the reverse KL divergence between the policy and the target distribution. We implement this idea as a flow-balanced optimization method that promotes diverse exploration and generalizable reasoning trajectories. We conduct experiments on math and code reasoning tasks: FlowRL achieves a significant average improvement of $10.0\%$ over GRPO and $5.1\%$ over PPO on math benchmarks, and performs consistently better on code reasoning tasks. These results highlight reward distribution-matching as a key step toward efficient exploration and diverse reasoning in LLM reinforcement learning.

Xingtai Lv, Youbang Sun, Kaiyan Zhang et al. · tsinghua

State Space Models (SSMs) have emerged as a promising alternative to the popular transformer-based models and have been increasingly gaining attention. Compared to transformers, SSMs excel at tasks with sequential data or longer contexts, demonstrating comparable performances with significant efficiency gains. In this survey, we provide a coherent and systematic overview for SSMs, including their theoretical motivations, mathematical formulations, comparison with existing model classes, and various applications. We divide the SSM series into three main sections, providing a detailed introduction to the original SSM, the structured SSM represented by S4, and the selective SSM typified by Mamba. We put an emphasis on technicality, and highlight the various key techniques introduced to address the effectiveness and efficiency of SSMs. We hope this manuscript serves as an introduction for researchers to explore the theoretical foundations of SSMs.

Shang Qu, Ning Ding, Linhai Xie et al.

This paper introduces PROTEUS, a fully automated system that produces data-driven hypotheses from raw data files. We apply PROTEUS to clinical proteogenomics, a field where effective downstream data analysis and hypothesis proposal is crucial for producing novel discoveries. PROTEUS uses separate modules to simulate different stages of the scientific process, from open-ended data exploration to specific statistical analysis and hypothesis proposal. It formulates research directions, tools, and results in terms of relationships between biological entities, using unified graph structures to manage complex research processes. We applied PROTEUS to 10 clinical multiomics datasets from published research, arriving at 360 total hypotheses. Results were evaluated through external data validation and automatic open-ended scoring. Through exploratory and iterative research, the system can navigate high-throughput and heterogeneous multiomics data to arrive at hypotheses that balance reliability and novelty. In addition to accelerating multiomic analysis, PROTEUS represents a path towards tailoring general autonomous systems to specialized scientific domains to achieve open-ended hypothesis generation from data.

Zeyi Ren, Jingreng Lei, Yichen Jin et al.

The development of edge computing places critical demands on energy-efficient model deployment for multiple-input multiple-output (MIMO) detection tasks. Deploying deep unfolding models such as PGD-Nets and ADMM-Nets into resource-constrained edge devices using quantization methods is challenging. Existing quantization methods based on quantization aware training (QAT) suffer from performance degradation due to their reliance on parametric distribution assumption of activations and static quantization step sizes. To address these challenges, this paper proposes a novel kernel-based adaptive quantization (KAQ) framework for deep unfolding networks. By utilizing a joint kernel density estimation (KDE) and maximum mean discrepancy (MMD) approach to align activation distributions between full-precision and quantized models, the need for prior distribution assumptions is eliminated. Additionally, a dynamic step size updating method is introduced to adjust the quantization step size based on the channel conditions of wireless networks. Extensive simulations demonstrate that the accuracy of proposed KAQ framework outperforms traditional methods and successfully reduces the model's inference latency.