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Mar 11

A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

MindSearch: Mimicking Human Minds Elicits Deep AI Searcher

Information seeking and integration is a complex cognitive task that consumes enormous time and effort. Inspired by the remarkable progress of Large Language Models, recent works attempt to solve this task by combining LLMs and search engines. However, these methods still obtain unsatisfying performance due to three challenges: (1) complex requests often cannot be accurately and completely retrieved by the search engine once (2) corresponding information to be integrated is spread over multiple web pages along with massive noise, and (3) a large number of web pages with long contents may quickly exceed the maximum context length of LLMs. Inspired by the cognitive process when humans solve these problems, we introduce MindSearch to mimic the human minds in web information seeking and integration, which can be instantiated by a simple yet effective LLM-based multi-agent framework. The WebPlanner models the human mind of multi-step information seeking as a dynamic graph construction process: it decomposes the user query into atomic sub-questions as nodes in the graph and progressively extends the graph based on the search result from WebSearcher. Tasked with each sub-question, WebSearcher performs hierarchical information retrieval with search engines and collects valuable information for WebPlanner. The multi-agent design of MindSearch enables the whole framework to seek and integrate information parallelly from larger-scale (e.g., more than 300) web pages in 3 minutes, which is worth 3 hours of human effort. MindSearch demonstrates significant improvement in the response quality in terms of depth and breadth, on both close-set and open-set QA problems. Besides, responses from MindSearch based on InternLM2.5-7B are preferable by humans to ChatGPT-Web and Perplexity.ai applications, which implies that MindSearch can already deliver a competitive solution to the proprietary AI search engine.

FuseChat: Knowledge Fusion of Chat Models

While training large language models (LLMs) from scratch can indeed lead to models with distinct capabilities and strengths, it incurs substantial costs and may lead to redundancy in competencies. Knowledge fusion aims to integrate existing LLMs of diverse architectures and capabilities into a more potent LLM through lightweight continual training, thereby reducing the need for costly LLM development. In this work, we propose a new framework for the knowledge fusion of chat LLMs through two main stages, resulting in FuseChat. Firstly, we conduct pairwise knowledge fusion on source chat LLMs of varying structures and scales to create multiple target LLMs with identical structure and size via lightweight fine-tuning. During this process, a statistics-based token alignment approach is introduced as the cornerstone for fusing LLMs with different structures. Secondly, we merge these target LLMs within the parameter space, where we propose a novel method for determining the merging coefficients based on the magnitude of parameter updates before and after fine-tuning. We implement and validate FuseChat using six prominent chat LLMs with diverse architectures and scales, including OpenChat-3.5-7B, Starling-LM-7B-alpha, NH2-SOLAR-10.7B, InternLM2-Chat-20B, Mixtral-8x7B-Instruct, and Qwen-1.5-Chat-72B. Experimental results on two instruction-following benchmarks, AlpacaEval 2.0 and MT-Bench, demonstrate the superiority of FuseChat-7B over baselines of various sizes. Our model is even comparable to the larger Mixtral-8x7B-Instruct and approaches GPT-3.5-Turbo-1106 on MT-Bench. Our code, model weights, and data are public at https://github.com/fanqiwan/FuseAI.

Herald: A Natural Language Annotated Lean 4 Dataset

Verifiable formal languages like Lean have profoundly impacted mathematical reasoning, particularly through the use of large language models (LLMs) for automated reasoning. A significant challenge in training LLMs for these formal languages is the lack of parallel datasets that align natural language with formal language proofs. To address this challenge, this paper introduces a novel framework for translating the Mathlib4 corpus (a unified library of mathematics in formal language Lean 4) into natural language. Building upon this, we employ a dual augmentation strategy that combines tactic-based and informal-based approaches, leveraging the Lean-jixia system, a Lean 4 analyzer. We present the results of this pipeline on Mathlib4 as Herald (Hierarchy and Retrieval-based Translated Lean Dataset). We also propose the Herald Translator, which is fine-tuned on Herald. Herald translator achieves a 93.2% accuracy (Pass@128) on formalizing statements in the miniF2F-test and a 22.5% accuracy on our internal graduate-level textbook dataset, outperforming InternLM2-Math-Plus-7B (74.0% and 7.5%) and TheoremLlama (50.1% and 4.0%). Furthermore, we propose a section-level translation framework for real-world applications. As a direct application of Herald translator, we have successfully translated a template section in the Stack project, marking a notable progress in the automatic formalization of graduate-level mathematical literature. Our model, along with the datasets, will be open-sourced to the public soon.

InternLM-XComposer2.5-OmniLive: A Comprehensive Multimodal System for Long-term Streaming Video and Audio Interactions

Creating AI systems that can interact with environments over long periods, similar to human cognition, has been a longstanding research goal. Recent advancements in multimodal large language models (MLLMs) have made significant strides in open-world understanding. However, the challenge of continuous and simultaneous streaming perception, memory, and reasoning remains largely unexplored. Current MLLMs are constrained by their sequence-to-sequence architecture, which limits their ability to process inputs and generate responses simultaneously, akin to being unable to think while perceiving. Furthermore, relying on long contexts to store historical data is impractical for long-term interactions, as retaining all information becomes costly and inefficient. Therefore, rather than relying on a single foundation model to perform all functions, this project draws inspiration from the concept of the Specialized Generalist AI and introduces disentangled streaming perception, reasoning, and memory mechanisms, enabling real-time interaction with streaming video and audio input. The proposed framework InternLM-XComposer2.5-OmniLive (IXC2.5-OL) consists of three key modules: (1) Streaming Perception Module: Processes multimodal information in real-time, storing key details in memory and triggering reasoning in response to user queries. (2) Multi-modal Long Memory Module: Integrates short-term and long-term memory, compressing short-term memories into long-term ones for efficient retrieval and improved accuracy. (3) Reasoning Module: Responds to queries and executes reasoning tasks, coordinating with the perception and memory modules. This project simulates human-like cognition, enabling multimodal large language models to provide continuous and adaptive service over time.

InternLM-XComposer2.5-Reward: A Simple Yet Effective Multi-Modal Reward Model

Despite the promising performance of Large Vision Language Models (LVLMs) in visual understanding, they occasionally generate incorrect outputs. While reward models (RMs) with reinforcement learning or test-time scaling offer the potential for improving generation quality, a critical gap remains: publicly available multi-modal RMs for LVLMs are scarce, and the implementation details of proprietary models are often unclear. We bridge this gap with InternLM-XComposer2.5-Reward (IXC-2.5-Reward), a simple yet effective multi-modal reward model that aligns LVLMs with human preferences. To ensure the robustness and versatility of IXC-2.5-Reward, we set up a high-quality multi-modal preference corpus spanning text, image, and video inputs across diverse domains, such as instruction following, general understanding, text-rich documents, mathematical reasoning, and video understanding. IXC-2.5-Reward achieves excellent results on the latest multi-modal reward model benchmark and shows competitive performance on text-only reward model benchmarks. We further demonstrate three key applications of IXC-2.5-Reward: (1) Providing a supervisory signal for RL training. We integrate IXC-2.5-Reward with Proximal Policy Optimization (PPO) yields IXC-2.5-Chat, which shows consistent improvements in instruction following and multi-modal open-ended dialogue; (2) Selecting the best response from candidate responses for test-time scaling; and (3) Filtering outlier or noisy samples from existing image and video instruction tuning training data. To ensure reproducibility and facilitate further research, we have open-sourced all model weights and training recipes at https://github.com/InternLM/InternLM-XComposer

InternLM-XComposer2-4KHD: A Pioneering Large Vision-Language Model Handling Resolutions from 336 Pixels to 4K HD

The Large Vision-Language Model (LVLM) field has seen significant advancements, yet its progression has been hindered by challenges in comprehending fine-grained visual content due to limited resolution. Recent efforts have aimed to enhance the high-resolution understanding capabilities of LVLMs, yet they remain capped at approximately 1500 x 1500 pixels and constrained to a relatively narrow resolution range. This paper represents InternLM-XComposer2-4KHD, a groundbreaking exploration into elevating LVLM resolution capabilities up to 4K HD (3840 x 1600) and beyond. Concurrently, considering the ultra-high resolution may not be necessary in all scenarios, it supports a wide range of diverse resolutions from 336 pixels to 4K standard, significantly broadening its scope of applicability. Specifically, this research advances the patch division paradigm by introducing a novel extension: dynamic resolution with automatic patch configuration. It maintains the training image aspect ratios while automatically varying patch counts and configuring layouts based on a pre-trained Vision Transformer (ViT) (336 x 336), leading to dynamic training resolution from 336 pixels to 4K standard. Our research demonstrates that scaling training resolution up to 4K HD leads to consistent performance enhancements without hitting the ceiling of potential improvements. InternLM-XComposer2-4KHD shows superb capability that matches or even surpasses GPT-4V and Gemini Pro in 10 of the 16 benchmarks. The InternLM-XComposer2-4KHD model series with 7B parameters are publicly available at https://github.com/InternLM/InternLM-XComposer.

InternLM-XComposer: A Vision-Language Large Model for Advanced Text-image Comprehension and Composition

We propose InternLM-XComposer, a vision-language large model that enables advanced image-text comprehension and composition. The innovative nature of our model is highlighted by three appealing properties: 1) Interleaved Text-Image Composition: InternLM-XComposer can effortlessly generate coherent and contextual articles that seamlessly integrate images, providing a more engaging and immersive reading experience. Simply provide a title, and our system will generate the corresponding manuscript. It can intelligently identify the areas in the text where images would enhance the content and automatically insert the most appropriate visual candidates. 2) Comprehension with Rich Multilingual Knowledge: The text-image comprehension is empowered by training on extensive multi-modal multilingual concepts with carefully crafted strategies, resulting in a deep understanding of visual content. 3) State-of-the-art Performance: Our model consistently achieves state-of-the-art results across various mainstream benchmarks for vision-language foundational models, including MME Benchmark, MMBench, MMBench-CN, Seed-Bench, and CCBench (Chinese Cultural Benchmark). Collectively, InternLM-XComposer seamlessly blends advanced text-image comprehension and composition, revolutionizing vision-language interaction and offering new insights and opportunities. The InternLM-XComposer model series with 7B parameters are publicly available at https://github.com/InternLM/InternLM-XComposer.