Large Language Models as Biomedical Hypothesis Generators: A Comprehensive Evaluation

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.

Towards Building Specialized Generalist AI with System 1 and System 2 Fusion

In this perspective paper, we introduce the concept of Specialized Generalist Artificial Intelligence (SGAI or simply SGI) as a crucial milestone toward Artificial General Intelligence (AGI). Compared to directly scaling general abilities, SGI is defined as AI that specializes in at least one task, surpassing human experts, while also retaining general abilities. This fusion path enables SGI to rapidly achieve high-value areas. We categorize SGI into three stages based on the level of mastery over professional skills and generality performance. Additionally, we discuss the necessity of SGI in addressing issues associated with large language models, such as their insufficient generality, specialized capabilities, uncertainty in innovation, and practical applications. Furthermore, we propose a conceptual framework for developing SGI that integrates the strengths of Systems 1 and 2 cognitive processing. This framework comprises three layers and four key components, which focus on enhancing individual abilities and facilitating collaborative evolution. We conclude by summarizing the potential challenges and suggesting future directions. We hope that the proposed SGI will provide insights into further research and applications towards achieving AGI.

EVA-Score: Evaluation of Long-form Summarization on Informativeness through Extraction and Validation

Summarization is a fundamental task in natural language processing (NLP) and since large language models (LLMs), such as GPT-4 and Claude, come out, increasing attention has been paid to long-form summarization whose input sequences are much longer, indicating more information contained. The current evaluation metrics either use similarity-based metrics like ROUGE and BERTScore which rely on similarity and fail to consider informativeness or LLM-based metrics, lacking quantitative analysis of information richness and are rather subjective. In this paper, we propose a new evaluation metric called EVA-Score using Atomic Fact Chain Generation and Document-level Relation Extraction together to automatically calculate the informativeness and give a definite number as an information score. Experiment results show that our metric shows a state-of-the-art correlation with humans. We also re-evaluate the performance of LLMs on long-form summarization comprehensively from the information aspect, forecasting future ways to use LLMs for long-form summarization.

Neural Residual Diffusion Models for Deep Scalable Vision Generation

The most advanced diffusion models have recently adopted increasingly deep stacked networks (e.g., U-Net or Transformer) to promote the generative emergence capabilities of vision generation models similar to large language models (LLMs). However, progressively deeper stacked networks will intuitively cause numerical propagation errors and reduce noisy prediction capabilities on generative data, which hinders massively deep scalable training of vision generation models. In this paper, we first uncover the nature that neural networks being able to effectively perform generative denoising lies in the fact that the intrinsic residual unit has consistent dynamic property with the input signal's reverse diffusion process, thus supporting excellent generative abilities. Afterwards, we stand on the shoulders of two common types of deep stacked networks to propose a unified and massively scalable Neural Residual Diffusion Models framework (Neural-RDM for short), which is a simple yet meaningful change to the common architecture of deep generative networks by introducing a series of learnable gated residual parameters that conform to the generative dynamics. Experimental results on various generative tasks show that the proposed neural residual models obtain state-of-the-art scores on image's and video's generative benchmarks. Rigorous theoretical proofs and extensive experiments also demonstrate the advantages of this simple gated residual mechanism consistent with dynamic modeling in improving the fidelity and consistency of generated content and supporting large-scale scalable training. Code is available at https://github.com/Anonymous/Neural-RDM.

Fast and Slow Generating: An Empirical Study on Large and Small Language Models Collaborative Decoding

Large Language Models (LLMs) demonstrate impressive performance in diverse applications, yet they face significant drawbacks, including high inference latency, expensive training cost, and generation of hallucination. Collaborative decoding between large and small language models (SLMs) offers a novel approach to address these challenges. Inspired by dual-process cognitive theory, we integrate these methods into a unified framework termed Fast and Slow Generating (FS-GEN). This paper explores several techniques within the FS-GEN framework, including speculative decoding, contrastive decoding, and emulator or proxy fine-tuning. We provide a comprehensive analysis of these methodologies, offering insights into their similarities and differences under this framework. Our study delves into the differential knowledge capabilities of LLMs versus SLMs through the FS-GEN lens, revealing that fewer than 20% of collaborative interactions are required across various methods. These interactions adhere to a scaling law relative to the parameter ratios, thereby facilitating predictable collaboration. Furthermore, we investigate the specific positions where collaboration is most effective from an uncertainty perspective, yielding novel insights that could refine FS-GEN methods. Our findings reveal that the essential difference between models of different sizes lies in the uncertainty of the next token prediction, where interventions by larger models are most needed to assist the smaller ones. Code for Reproduction: https://github.com/TsinghuaC3I/FS-GEN

Online DPO: Online Direct Preference Optimization with Fast-Slow Chasing

Direct Preference Optimization (DPO) improves the alignment of large language models (LLMs) with human values by training directly on human preference datasets, eliminating the need for reward models. However, due to the presence of cross-domain human preferences, direct continual training can lead to catastrophic forgetting, limiting DPO's performance and efficiency. Inspired by intraspecific competition driving species evolution, we propose a Online Fast-Slow chasing DPO (OFS-DPO) for preference alignment, simulating competition through fast and slow chasing among models to facilitate rapid adaptation. Specifically, we first derive the regret upper bound for online learning, validating our motivation with a min-max optimization pattern. Based on this, we introduce two identical modules using Low-rank Adaptive (LoRA) with different optimization speeds to simulate intraspecific competition, and propose a new regularization term to guide their learning. To further mitigate catastrophic forgetting in cross-domain scenarios, we extend the OFS-DPO with LoRA modules combination strategy, resulting in the Cross domain Online Fast-Slow chasing DPO (COFS-DPO). This method leverages linear combinations of fast modules parameters from different task domains, fully utilizing historical information to achive continual value alignment. Experimental results show that OFS-DPO outperforms DPO in in-domain alignment, while COFS-DPO excels in cross-domain continual learning scenarios.

Enhancing Adversarial Transferability via Information Bottleneck Constraints

From the perspective of information bottleneck (IB) theory, we propose a novel framework for performing black-box transferable adversarial attacks named IBTA, which leverages advancements in invariant features. Intuitively, diminishing the reliance of adversarial perturbations on the original data, under equivalent attack performance constraints, encourages a greater reliance on invariant features that contributes most to classification, thereby enhancing the transferability of adversarial attacks. Building on this motivation, we redefine the optimization of transferable attacks using a novel theoretical framework that centers around IB. Specifically, to overcome the challenge of unoptimizable mutual information, we propose a simple and efficient mutual information lower bound (MILB) for approximating computation. Moreover, to quantitatively evaluate mutual information, we utilize the Mutual Information Neural Estimator (MINE) to perform a thorough analysis. Our experiments on the ImageNet dataset well demonstrate the efficiency and scalability of IBTA and derived MILB. Our code is available at https://github.com/Biqing-Qi/Enhancing-Adversarial-Transferability-via-Information-Bottleneck-Constraints.

UltraMedical: Building Specialized Generalists in Biomedicine

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.

SMR: State Memory Replay for Long Sequence Modeling

Despite the promising performance of state space models (SSMs) in long sequence modeling, limitations still exist. Advanced SSMs like S5 and S6 (Mamba) in addressing non-uniform sampling, their recursive structures impede efficient SSM computation via convolution. To overcome compatibility limitations in parallel convolutional computation, this paper proposes a novel non-recursive non-uniform sample processing strategy. Theoretical analysis of SSMs through the lens of Event-Triggered Control (ETC) theory reveals the Non-Stable State (NSS) problem, where deviations from sampling point requirements lead to error transmission and accumulation, causing the divergence of the SSM's hidden state. Our analysis further reveals that adjustments of input sequences with early memories can mitigate the NSS problem, achieving Sampling Step Adaptation (SSA). Building on this insight, we introduce a simple yet effective plug-and-play mechanism, State Memory Replay (SMR), which utilizes learnable memories to adjust the current state with multi-step information for generalization at sampling points different from those in the training data. This enables SSMs to stably model varying sampling points. Experiments on long-range modeling tasks in autoregressive language modeling and Long Range Arena demonstrate the general effectiveness of the SMR mechanism for a series of SSM models.

Emulating Full Client Participation: A Long-Term Client Selection Strategy for Federated Learning

Client selection significantly affects the system convergence efficiency and is a crucial problem in federated learning. Existing methods often select clients by evaluating each round individually and overlook the necessity for long-term optimization, resulting in suboptimal performance and potential fairness issues. In this study, we propose a novel client selection strategy designed to emulate the performance achieved with full client participation. In a single round, we select clients by minimizing the gradient-space estimation error between the client subset and the full client set. In multi-round selection, we introduce a novel individual fairness constraint, which ensures that clients with similar data distributions have similar frequencies of being selected. This constraint guides the client selection process from a long-term perspective. We employ Lyapunov optimization and submodular functions to efficiently identify the optimal subset of clients, and provide a theoretical analysis of the convergence ability. Experiments demonstrate that the proposed strategy significantly improves both accuracy and fairness compared to previous methods while also exhibiting efficiency by incurring minimal time overhead.