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.

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}

On the token distance modeling ability of higher RoPE attention dimension

Length extrapolation algorithms based on Rotary position embedding (RoPE) have shown promising results in extending the context length of language models. However, understanding how position embedding can capture longer-range contextual information remains elusive. Based on the intuition that different dimensions correspond to different frequency of changes in RoPE encoding, we conducted a dimension-level analysis to investigate the correlation between a hidden dimension of an attention head and its contribution to capturing long-distance dependencies. Using our correlation metric, we identified a particular type of attention heads, which we named Positional Heads, from various length-extrapolated models. These heads exhibit a strong focus on long-range information interaction and play a pivotal role in long input processing, as evidence by our ablation. We further demonstrate the correlation between the efficiency of length extrapolation and the extension of the high-dimensional attention allocation of these heads. The identification of Positional Heads provides insights for future research in long-text comprehension.

CALF: Benchmarking Evaluation of LFQA Using Chinese Examinations

Long-Form Question Answering (LFQA) refers to generating in-depth, paragraph-level responses to open-ended questions. Although lots of LFQA methods are developed, evaluating LFQA effectively and efficiently remains challenging due to its high complexity and cost. Therefore, there is no standard benchmark for LFQA evaluation till now. To address this gap, we make the first attempt by proposing a well-constructed, reference-based benchmark named Chinese exAmination for LFQA Evaluation (CALF), aiming to rigorously assess the performance of automatic evaluation metrics for LFQA. The CALF benchmark is derived from Chinese examination questions that have been translated into English. It includes up to 1476 examples consisting of knowledge-intensive and nuanced responses. Our evaluation comprises three different settings to ana lyze the behavior of automatic metrics comprehensively. We conducted extensive experiments on 7 traditional evaluation metrics, 3 prompt-based metrics, and 3 trained evaluation metrics, and tested on agent systems for the LFQA evaluation. The results reveal that none of the current automatic evaluation metrics shows comparable performances with humans, indicating that they cannot capture dense information contained in long-form responses well. In addition, we provide a detailed analysis of the reasons why automatic evaluation metrics fail when evaluating LFQA, offering valuable insights to advance LFQA evaluation systems. Dataset and associated codes can be accessed at our GitHub repository.

MSI-Agent: Incorporating Multi-Scale Insight into Embodied Agents for Superior Planning and Decision-Making

Long-term memory is significant for agents, in which insights play a crucial role. However, the emergence of irrelevant insight and the lack of general insight can greatly undermine the effectiveness of insight. To solve this problem, in this paper, we introduce Multi-Scale Insight Agent (MSI-Agent), an embodied agent designed to improve LLMs' planning and decision-making ability by summarizing and utilizing insight effectively across different scales. MSI achieves this through the experience selector, insight generator, and insight selector. Leveraging a three-part pipeline, MSI can generate task-specific and high-level insight, store it in a database, and then use relevant insight from it to aid in decision-making. Our experiments show that MSI outperforms another insight strategy when planning by GPT3.5. Moreover, We delve into the strategies for selecting seed experience and insight, aiming to provide LLM with more useful and relevant insight for better decision-making. Our observations also indicate that MSI exhibits better robustness when facing domain-shifting scenarios.

MAG-SQL: Multi-Agent Generative Approach with Soft Schema Linking and Iterative Sub-SQL Refinement for Text-to-SQL

Recent In-Context Learning based methods have achieved remarkable success in Text-to-SQL task. However, there is still a large gap between the performance of these models and human performance on datasets with complex database schema and difficult questions, such as BIRD. Besides, existing work has neglected to supervise intermediate steps when solving questions iteratively with question decomposition methods, and the schema linking methods used in these works are very rudimentary. To address these issues, we propose MAG-SQL, a multi-agent generative approach with soft schema linking and iterative Sub-SQL refinement. In our framework, an entity-based method with tables' summary is used to select the columns in database, and a novel targets-conditions decomposition method is introduced to decompose those complex questions. Additionally, we build a iterative generating module which includes a Sub-SQL Generator and Sub-SQL Refiner, introducing external oversight for each step of generation. Through a series of ablation studies, the effectiveness of each agent in our framework has been demonstrated. When evaluated on the BIRD benchmark with GPT-4, MAG-SQL achieves an execution accuracy of 61.08\%, compared to the baseline accuracy of 46.35\% for vanilla GPT-4 and the baseline accuracy of 57.56\% for MAC-SQL. Besides, our approach makes similar progress on Spider.

SR-CIS: Self-Reflective Incremental System with Decoupled Memory and Reasoning

The ability of humans to rapidly learn new knowledge while retaining old memories poses a significant challenge for current deep learning models. To handle this challenge, we draw inspiration from human memory and learning mechanisms and propose the Self-Reflective Complementary Incremental System (SR-CIS). Comprising the deconstructed Complementary Inference Module (CIM) and Complementary Memory Module (CMM), SR-CIS features a small model for fast inference and a large model for slow deliberation in CIM, enabled by the Confidence-Aware Online Anomaly Detection (CA-OAD) mechanism for efficient collaboration. CMM consists of task-specific Short-Term Memory (STM) region and a universal Long-Term Memory (LTM) region. By setting task-specific Low-Rank Adaptive (LoRA) and corresponding prototype weights and biases, it instantiates external storage for parameter and representation memory, thus deconstructing the memory module from the inference module. By storing textual descriptions of images during training and combining them with the Scenario Replay Module (SRM) post-training for memory combination, along with periodic short-to-long-term memory restructuring, SR-CIS achieves stable incremental memory with limited storage requirements. Balancing model plasticity and memory stability under constraints of limited storage and low data resources, SR-CIS surpasses existing competitive baselines on multiple standard and few-shot incremental learning benchmarks.

Safe-SD: Safe and Traceable Stable Diffusion with Text Prompt Trigger for Invisible Generative Watermarking

Recently, stable diffusion (SD) models have typically flourished in the field of image synthesis and personalized editing, with a range of photorealistic and unprecedented images being successfully generated. As a result, widespread interest has been ignited to develop and use various SD-based tools for visual content creation. However, the exposure of AI-created content on public platforms could raise both legal and ethical risks. In this regard, the traditional methods of adding watermarks to the already generated images (i.e. post-processing) may face a dilemma (e.g., being erased or modified) in terms of copyright protection and content monitoring, since the powerful image inversion and text-to-image editing techniques have been widely explored in SD-based methods. In this work, we propose a Safe and high-traceable Stable Diffusion framework (namely Safe-SD) to adaptively implant the graphical watermarks (e.g., QR code) into the imperceptible structure-related pixels during the generative diffusion process for supporting text-driven invisible watermarking and detection. Different from the previous high-cost injection-then-detection training framework, we design a simple and unified architecture, which makes it possible to simultaneously train watermark injection and detection in a single network, greatly improving the efficiency and convenience of use. Moreover, to further support text-driven generative watermarking and deeply explore its robustness and high-traceability, we elaborately design lambda sampling and encryption algorithm to fine-tune a latent diffuser wrapped by a VAE for balancing high-fidelity image synthesis and high-traceable watermark detection. We present our quantitative and qualitative results on two representative datasets LSUN, COCO and FFHQ, demonstrating state-of-the-art performance of Safe-SD and showing it significantly outperforms the previous approaches.

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.