Automating Exploratory Proteomics Research via Language Models

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.

Scalable Efficient Training of Large Language Models with Low-dimensional Projected Attention

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.

A Static and Dynamic Attention Framework for Multi Turn Dialogue Generation

Recently, research on open domain dialogue systems have attracted extensive interests of academic and industrial researchers. The goal of an open domain dialogue system is to imitate humans in conversations. Previous works on single turn conversation generation have greatly promoted the research of open domain dialogue systems. However, understanding multiple single turn conversations is not equal to the understanding of multi turn dialogue due to the coherent and context dependent properties of human dialogue. Therefore, in open domain multi turn dialogue generation, it is essential to modeling the contextual semantics of the dialogue history, rather than only according to the last utterance. Previous research had verified the effectiveness of the hierarchical recurrent encoder-decoder framework on open domain multi turn dialogue generation. However, using RNN-based model to hierarchically encoding the utterances to obtain the representation of dialogue history still face the problem of a vanishing gradient. To address this issue, in this paper, we proposed a static and dynamic attention-based approach to model the dialogue history and then generate open domain multi turn dialogue responses. Experimental results on Ubuntu and Opensubtitles datasets verify the effectiveness of the proposed static and dynamic attention-based approach on automatic and human evaluation metrics in various experimental settings. Meanwhile, we also empirically verify the performance of combining the static and dynamic attentions on open domain multi turn dialogue generation.

A Stack-Propagation Framework for Low-Resource Personalized Dialogue Generation

With the resurgent interest in building open-domain dialogue systems, the dialogue generation task has attracted increasing attention over the past few years. This task is usually formulated as a conditional generation problem, which aims to generate a natural and meaningful response given dialogue contexts and specific constraints, such as persona. And maintaining a consistent persona is essential for the dialogue systems to gain trust from the users. Although tremendous advancements have been brought, traditional persona-based dialogue models are typically trained by leveraging a large number of persona-dense dialogue examples. Yet, such persona-dense training data are expensive to obtain, leading to a limited scale. This work presents a novel approach to learning from limited training examples by regarding consistency understanding as a regularization of response generation. To this end, we propose a novel stack-propagation framework for learning a generation and understanding pipeline.Specifically, the framework stacks a Transformer encoder and two Transformer decoders, where the first decoder models response generation and the second serves as a regularizer and jointly models response generation and consistency understanding. The proposed framework can benefit from the stacked encoder and decoders to learn from much smaller personalized dialogue data while maintaining competitive performance. Under different low-resource settings, subjective and objective evaluations prove that the stack-propagation framework outperforms strong baselines in response quality and persona consistency and largely overcomes the shortcomings of traditional models that rely heavily on the persona-dense dialogue data.

Efficient Diffusion Models: A Comprehensive Survey from Principles to Practices

As one of the most popular and sought-after generative models in the recent years, diffusion models have sparked the interests of many researchers and steadily shown excellent advantage in various generative tasks such as image synthesis, video generation, molecule design, 3D scene rendering and multimodal generation, relying on their dense theoretical principles and reliable application practices. The remarkable success of these recent efforts on diffusion models comes largely from progressive design principles and efficient architecture, training, inference, and deployment methodologies. However, there has not been a comprehensive and in-depth review to summarize these principles and practices to help the rapid understanding and application of diffusion models. In this survey, we provide a new efficiency-oriented perspective on these existing efforts, which mainly focuses on the profound principles and efficient practices in architecture designs, model training, fast inference and reliable deployment, to guide further theoretical research, algorithm migration and model application for new scenarios in a reader-friendly way. \url{https://github.com/ponyzym/Efficient-DMs-Survey}

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.

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.

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.