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.

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

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.

Mastering Text, Code and Math Simultaneously via Fusing Highly Specialized Language Models

Underlying data distributions of natural language, programming code, and mathematical symbols vary vastly, presenting a complex challenge for large language models (LLMs) that strive to achieve high performance across all three domains simultaneously. Achieving a very high level of proficiency for an LLM within a specific domain often requires extensive training with relevant corpora, which is typically accompanied by a sacrifice in performance in other domains. In this paper, we propose to fuse models that are already highly-specialized directly. The proposed fusing framework, UltraFuser, consists of three distinct specialists that are already sufficiently trained on language, coding, and mathematics. A token-level gating mechanism is introduced to blend the specialists' outputs. A two-stage training strategy accompanied by balanced sampling is designed to ensure stability. To effectively train the fused model, we further construct a high-quality supervised instruction tuning dataset, UltraChat 2, which includes text, code, and mathematical content. This dataset comprises approximately 300,000 instructions and covers a wide range of topics in each domain. Experiments show that our model could simultaneously achieve mastery of the three crucial domains.

Sparse Low-rank Adaptation of Pre-trained Language Models

Fine-tuning pre-trained large language models in a parameter-efficient manner is widely studied for its effectiveness and efficiency. The popular method of low-rank adaptation (LoRA) offers a notable approach, hypothesizing that the adaptation process is intrinsically low-dimensional. Although LoRA has demonstrated commendable performance, it is implemented with a fixed and unalterable intrinsic rank that might not always be the ideal choice. Recognizing the need for more flexible adaptation, we extend the methodology of LoRA to an innovative approach we call sparse low-rank adaptation (SoRA) that enables dynamic adjustments to the intrinsic rank during the adaptation process. We achieve this through the incorporation of a gate unit optimized with proximal gradient method in the training stage, controlling the cardinality of rank under the sparsity of the gate. In the subsequent inference stage, we eliminate the parameter blocks corresponding to the zeroed-out ranks, to reduce each SoRA module back to a concise yet rank-optimal LoRA. Our approach strengthens the representation power of LoRA by initializing it with a higher rank, while efficiently taming a temporarily increased number of parameters via updating in a sparse way. We further introduce a sparsifying scheduler for SoRA, aiming to examine the impact of the number of non-zero parameters on the model's memorization and generalization. Our experimental results demonstrate that SoRA can outperform other baselines even with 70% retained parameters and 70% training time.

OpenDelta: A Plug-and-play Library for Parameter-efficient Adaptation of Pre-trained Models

The scale of large pre-trained models (PTMs) poses significant challenges in adapting to downstream tasks due to the high optimization overhead and storage costs associated with full-parameter fine-tuning. To address this, many studies explore parameter-efficient tuning methods, also framed as "delta tuning", which updates only a small subset of parameters, known as "delta modules", while keeping the backbone model's parameters fixed. However, the practicality and flexibility of delta tuning have been limited due to existing implementations that directly modify the code of the backbone PTMs and hard-code specific delta tuning methods for each PTM. In this paper, we present OpenDelta, an open-source library that overcomes these limitations by providing a plug-and-play implementation of various delta tuning methods. Our novel techniques eliminate the need to modify the backbone PTMs' code, making OpenDelta compatible with different, even novel PTMs. OpenDelta is designed to be simple, modular, and extensible, providing a comprehensive platform for researchers and practitioners to adapt large PTMs efficiently.