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.

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.

Enhancing Neural Radiance Fields with Depth and Normal Completion Priors from Sparse Views

Neural Radiance Fields (NeRF) are an advanced technology that creates highly realistic images by learning about scenes through a neural network model. However, NeRF often encounters issues when there are not enough images to work with, leading to problems in accurately rendering views. The main issue is that NeRF lacks sufficient structural details to guide the rendering process accurately. To address this, we proposed a Depth and Normal Dense Completion Priors for NeRF (CP\_NeRF) framework. This framework enhances view rendering by adding depth and normal dense completion priors to the NeRF optimization process. Before optimizing NeRF, we obtain sparse depth maps using the Structure from Motion (SfM) technique used to get camera poses. Based on the sparse depth maps and a normal estimator, we generate sparse normal maps for training a normal completion prior with precise standard deviations. During optimization, we apply depth and normal completion priors to transform sparse data into dense depth and normal maps with their standard deviations. We use these dense maps to guide ray sampling, assist distance sampling and construct a normal loss function for better training accuracy. To improve the rendering of NeRF's normal outputs, we incorporate an optical centre position embedder that helps synthesize more accurate normals through volume rendering. Additionally, we employ a normal patch matching technique to choose accurate rendered normal maps, ensuring more precise supervision for the model. Our method is superior to leading techniques in rendering detailed indoor scenes, even with limited input views.

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

Zero-Shot Generalization during Instruction Tuning: Insights from Similarity and Granularity

Understanding alignment techniques begins with comprehending zero-shot generalization brought by instruction tuning, but little of the mechanism has been understood. Existing work has largely been confined to the task level, without considering that tasks are artificially defined and, to LLMs, merely consist of tokens and representations. This line of research has been limited to examining transfer between tasks from a task-pair perspective, with few studies focusing on understanding zero-shot generalization from the perspective of the data itself. To bridge this gap, we first demonstrate through multiple metrics that zero-shot generalization during instruction tuning happens very early. Next, we investigate the facilitation of zero-shot generalization from both data similarity and granularity perspectives, confirming that encountering highly similar and fine-grained training data earlier during instruction tuning, without the constraints of defined "tasks", enables better generalization. Finally, we propose a more grounded training data arrangement method, Test-centric Multi-turn Arrangement, and show its effectiveness in promoting continual learning and further loss reduction. For the first time, we show that zero-shot generalization during instruction tuning is a form of similarity-based generalization between training and test data at the instance level. We hope our analysis will advance the understanding of zero-shot generalization during instruction tuning and contribute to the development of more aligned LLMs. Our code is released at https://github.com/HBX-hbx/dynamics_of_zero-shot_generalization.

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.

Intuitive Fine-Tuning: Towards Unifying SFT and RLHF into a Single Process

Supervised Fine-Tuning (SFT) and Reinforcement Learning from Human Feedback (RLHF) are two fundamental processes for enhancing the capabilities of Language Models (LMs) post pre-training, aligning them better with human preferences. Although SFT advances in training efficiency, RLHF delivers better alignment, thus they are often combined. However, common practices simply apply them sequentially without unifying their optimization targets, resulting in a trade-off between fitting different objectives, and ignoring the opportunities to bridge the paradigm gap and take the strength from both. To obtain a unified understanding, we interpret SFT and RLHF using two sub-processes -- Preference Estimation and Transition Optimization -- defined at token level within the Markov Decision Process (MDP) framework. This modeling shows that SFT is only a specialized case of RLHF with inferior estimation and optimization. RLHF evaluates the quality of model's entire generated answer, whereas SFT only scores predicted tokens based on preceding tokens from target answers. Therefore, SFT overestimates the ability of model, leading to inferior optimization. Building on this view, we introduce Intuitive Fine-tuning (IFT) to integrate SFT and RLHF into a single process. IFT captures LMs' intuitive sense of the entire answers through a temporal residual connection, while using 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 sequential recipes of SFT and some typical alignment methods across several tasks, particularly those requires generation, reasoning, and fact-following abilities. An explainable Frozen Lake game further validates the effectiveness of IFT.

Memory-Space Visual Prompting for Efficient Vision-Language Fine-Tuning

Current solutions for efficiently constructing large vision-language (VL) models follow a two-step paradigm: projecting the output of pre-trained vision encoders to the input space of pre-trained language models as visual prompts; and then transferring the models to downstream VL tasks via end-to-end parameter-efficient fine-tuning (PEFT). However, this paradigm still exhibits inefficiency since it significantly increases the input length of the language models. In this paper, in contrast to integrating visual prompts into inputs, we regard visual prompts as additional knowledge that facilitates language models in addressing tasks associated with visual information. Motivated by the finding that Feed-Forward Network (FFN) of language models acts as "key-value memory", we introduce a novel approach termed memory-space visual prompting (MemVP), wherein visual prompts are concatenated with the weights of FFN for visual knowledge injection. Experimental results across various VL tasks and language models reveal that MemVP significantly reduces the training time and inference latency of the finetuned VL models and surpasses the performance of previous PEFT methods. Code: https://github.com/JieShibo/MemVP

TeamTrack: A Dataset for Multi-Sport Multi-Object Tracking in Full-pitch Videos

Multi-object tracking (MOT) is a critical and challenging task in computer vision, particularly in situations involving objects with similar appearances but diverse movements, as seen in team sports. Current methods, largely reliant on object detection and appearance, often fail to track targets in such complex scenarios accurately. This limitation is further exacerbated by the lack of comprehensive and diverse datasets covering the full view of sports pitches. Addressing these issues, we introduce TeamTrack, a pioneering benchmark dataset specifically designed for MOT in sports. TeamTrack is an extensive collection of full-pitch video data from various sports, including soccer, basketball, and handball. Furthermore, we perform a comprehensive analysis and benchmarking effort to underscore TeamTrack's utility and potential impact. Our work signifies a crucial step forward, promising to elevate the precision and effectiveness of MOT in complex, dynamic settings such as team sports. The dataset, project code and competition is released at: https://atomscott.github.io/TeamTrack/.