From Intention To Implementation: Automating Biomedical Research via LLMs

Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to revolutionize this process by automating various steps. Still, significant challenges remain, including the need for multidisciplinary expertise, logicality of experimental design, and performance measurements. This paper introduces BioResearcher, the first end-to-end automated system designed to streamline the entire biomedical research process involving dry lab experiments. BioResearcher employs a modular multi-agent architecture, integrating specialized agents for search, literature processing, experimental design, and programming. By decomposing complex tasks into logically related sub-tasks and utilizing a hierarchical learning approach, BioResearcher effectively addresses the challenges of multidisciplinary requirements and logical complexity. Furthermore, BioResearcher incorporates an LLM-based reviewer for in-process quality control and introduces novel evaluation metrics to assess the quality and automation of experimental protocols. BioResearcher successfully achieves an average execution success rate of 63.07% across eight previously unmet research objectives. The generated protocols averagely outperform typical agent systems by 22.0% on five quality metrics. The system demonstrates significant potential to reduce researchers' workloads and accelerate biomedical discoveries, paving the way for future innovations in automated research systems.

Generative Context Distillation

Prompts used in recent large language model based applications are often fixed and lengthy, leading to significant computational overhead. To address this challenge, we propose Generative Context Distillation (GCD), a lightweight prompt internalization method that employs a joint training approach. This method not only replicates the behavior of models with prompt inputs but also generates the content of the prompt along with reasons for why the model's behavior should change accordingly. We demonstrate that our approach effectively internalizes complex prompts across various agent-based application scenarios. For effective training without interactions with the dedicated environments, we introduce a data synthesis technique that autonomously collects conversational datasets by swapping the roles of the agent and environment. This method is especially useful in scenarios where only a predefined prompt is available without a corresponding training dataset. By internalizing complex prompts, Generative Context Distillation enables high-performance and efficient inference without the need for explicit prompts.

Velocitune: A Velocity-based Dynamic Domain Reweighting Method for Continual Pre-training

It is well-known that a diverse corpus is critical for training large language models, which are typically constructed from a mixture of various domains. In general, previous efforts resort to sampling training data from different domains with static proportions, as well as adjusting data proportions during training. However, few methods have addressed the complexities of domain-adaptive continual pre-training. To fill this gap, we propose Velocitune, a novel framework dynamically assesses learning velocity and adjusts data proportions accordingly, favoring slower-learning domains while shunning faster-learning ones, which is guided by a scaling law to indicate the desired learning goal for each domain with less associated cost. To evaluate the effectiveness of Velocitune, we conduct experiments in a reasoning-focused dataset with CodeLlama, as well as in a corpus specialised for system command generation with Llama3 and Mistral. Velocitune achieves performance gains in both math and code reasoning tasks and command-line generation benchmarks. Further analysis reveals that key factors driving Velocitune's effectiveness include target loss prediction and data ordering.

Automated Proof Generation for Rust Code via Self-Evolution

Ensuring correctness is crucial for code generation. Formal verification offers a definitive assurance of correctness, but demands substantial human effort in proof construction and hence raises a pressing need for automation. The primary obstacle lies in the severe lack of data - there is much less proof than code for LLMs to train upon. In this paper, we introduce SAFE, a novel framework that overcomes the lack of human-written proof to enable automated proof generation of Rust code. SAFE establishes a self-evolving cycle where data synthesis and fine-tuning collaborate to enhance the model capability, leveraging the definitive power of a symbolic verifier in telling correct proof from incorrect ones. SAFE also re-purposes the large number of synthesized incorrect proofs to train the self-debugging capability of the fine-tuned models, empowering them to fix incorrect proofs based on the verifier's feedback. SAFE demonstrates superior efficiency and precision compared to GPT-4o. Through tens of thousands of synthesized proofs and the self-debugging mechanism, we improve the capability of open-source models, initially unacquainted with formal verification, to automatically write proof for Rust code. This advancement leads to a significant improvement in performance, achieving a 70.50% accuracy rate in a benchmark crafted by human experts, a significant leap over GPT-4o's performance of 24.46%.

Alchemy: Amplifying Theorem-Proving Capability through Symbolic Mutation

Formal proofs are challenging to write even for experienced experts. Recent progress in Neural Theorem Proving (NTP) shows promise in expediting this process. However, the formal corpora available on the Internet are limited compared to the general text, posing a significant data scarcity challenge for NTP. To address this issue, this work proposes Alchemy, a general framework for data synthesis that constructs formal theorems through symbolic mutation. Specifically, for each candidate theorem in Mathlib, we identify all invocable theorems that can be used to rewrite or apply to it. Subsequently, we mutate the candidate theorem by replacing the corresponding term in the statement with its equivalent form or antecedent. As a result, our method increases the number of theorems in Mathlib by an order of magnitude, from 110k to 6M. Furthermore, we perform continual pretraining and supervised finetuning on this augmented corpus for large language models. Experimental results demonstrate the effectiveness of our approach, achieving a 5% absolute performance improvement on Leandojo benchmark. Additionally, our synthetic data achieve a 2.5% absolute performance gain on the out-of-distribution miniF2F benchmark. To provide further insights, we conduct a comprehensive analysis of synthetic data composition and the training paradigm, offering valuable guidance for developing a strong theorem prover.

Integrative Decoding: Improve Factuality via Implicit Self-consistency

Self-consistency-based approaches, which involve repeatedly sampling multiple outputs and selecting the most consistent one as the final response, prove to be remarkably effective in improving the factual accuracy of large language models. Nonetheless, existing methods usually have strict constraints on the task format, largely limiting their applicability. In this paper, we present Integrative Decoding (ID), to unlock the potential of self-consistency in open-ended generation tasks. ID operates by constructing a set of inputs, each prepended with a previously sampled response, and then processes them concurrently, with the next token being selected by aggregating of all their corresponding predictions at each decoding step. In essence, this simple approach implicitly incorporates self-consistency in the decoding objective. Extensive evaluation shows that ID consistently enhances factuality over a wide range of language models, with substantial improvements on the TruthfulQA (+11.2%), Biographies (+15.4%) and LongFact (+8.5%) benchmarks. The performance gains amplify progressively as the number of sampled responses increases, indicating the potential of ID to scale up with repeated sampling.

Task Oriented In-Domain Data Augmentation

Large Language Models (LLMs) have shown superior performance in various applications and fields. To achieve better performance on specialized domains such as law and advertisement, LLMs are often continue pre-trained on in-domain data. However, existing approaches suffer from two major issues. First, in-domain data are scarce compared with general domain-agnostic data. Second, data used for continual pre-training are not task-aware, such that they may not be helpful to downstream applications. We propose TRAIT, a task-oriented in-domain data augmentation framework. Our framework is divided into two parts: in-domain data selection and task-oriented synthetic passage generation. The data selection strategy identifies and selects a large amount of in-domain data from general corpora, and thus significantly enriches domain knowledge in the continual pre-training data. The synthetic passages contain guidance on how to use domain knowledge to answer questions about downstream tasks. By training on such passages, the model aligns with the need of downstream applications. We adapt LLMs to two domains: advertisement and math. On average, TRAIT improves LLM performance by 8% in the advertisement domain and 7.5% in the math domain.

Gradient-Mask Tuning Elevates the Upper Limits of LLM Performance

Large language models (LLMs) have revolutionized lots of fields of research. Although it is well-known that fine-tuning is essential for enhancing the capabilities of LLMs, existing research suggests that there is potential redundancy in the fine-tuning process and therefore proposes to update only a subset of parameters. However, these methods fail to leverage the task-specific information to identify important parameters during training. Based on the insight that gradients inherently contain information on task-specific data, we propose Gradient-Mask Tuning (GMT), a method that selectively updates parameters during training based on their gradient information. Specifically, we compute the absolute values of the gradients and apply masking to those with relatively smaller magnitudes. Our empirical results across various tasks demonstrate that GMT not only outperforms traditional fine-tuning methods but also elevates the upper limits of LLM performance. Further analysis indicates that GMT exhibits insensitivity to mask ratio and possesses computational efficiency comparable to vanilla SFT.

MS MARCO Web Search: a Large-scale Information-rich Web Dataset with Millions of Real Click Labels

Recent breakthroughs in large models have highlighted the critical significance of data scale, labels and modals. In this paper, we introduce MS MARCO Web Search, the first large-scale information-rich web dataset, featuring millions of real clicked query-document labels. This dataset closely mimics real-world web document and query distribution, provides rich information for various kinds of downstream tasks and encourages research in various areas, such as generic end-to-end neural indexer models, generic embedding models, and next generation information access system with large language models. MS MARCO Web Search offers a retrieval benchmark with three web retrieval challenge tasks that demand innovations in both machine learning and information retrieval system research domains. As the first dataset that meets large, real and rich data requirements, MS MARCO Web Search paves the way for future advancements in AI and system research. MS MARCO Web Search dataset is available at: https://github.com/microsoft/MS-MARCO-Web-Search.

Mitigating Heterogeneity among Factor Tensors via Lie Group Manifolds for Tensor Decomposition Based Temporal Knowledge Graph Embedding

Recent studies have highlighted the effectiveness of tensor decomposition methods in the Temporal Knowledge Graphs Embedding (TKGE) task. However, we found that inherent heterogeneity among factor tensors in tensor decomposition significantly hinders the tensor fusion process and further limits the performance of link prediction. To overcome this limitation, we introduce a novel method that maps factor tensors onto a unified smooth Lie group manifold to make the distribution of factor tensors approximating homogeneous in tensor decomposition. We provide the theoretical proof of our motivation that homogeneous tensors are more effective than heterogeneous tensors in tensor fusion and approximating the target for tensor decomposition based TKGE methods. The proposed method can be directly integrated into existing tensor decomposition based TKGE methods without introducing extra parameters. Extensive experiments demonstrate the effectiveness of our method in mitigating the heterogeneity and in enhancing the tensor decomposition based TKGE models.