MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation

Motivation: In recent years, protein function prediction has broken through the bottleneck of sequence features, significantly improving prediction accuracy using high-precision protein structures predicted by AlphaFold2. While single-species protein function prediction methods have achieved remarkable success, multi-species protein function prediction methods are still in the stage of using PPI networks and sequence features. Providing effective cross-species label propagation for species with sparse protein annotations remains a challenging issue. To address this problem, we propose the MSNGO model, which integrates structural features and network propagation methods. Our validation shows that using structural features can significantly improve the accuracy of multi-species protein function prediction. Results: We employ graph representation learning techniques to extract amino acid representations from protein structure contact maps and train a structural model using a graph convolution pooling module to derive protein-level structural features. After incorporating the sequence features from ESM-2, we apply a network propagation algorithm to aggregate information and update node representations within a heterogeneous network. The results demonstrate that MSNGO outperforms previous multi-species protein function prediction methods that rely on sequence features and PPI networks. Availability: https://github.com/blingbell/MSNGO.

Can Large Language Models Help Experimental Design for Causal Discovery?

Designing proper experiments and selecting optimal intervention targets is a longstanding problem in scientific or causal discovery. Identifying the underlying causal structure from observational data alone is inherently difficult. Obtaining interventional data, on the other hand, is crucial to causal discovery, yet it is usually expensive and time-consuming to gather sufficient interventional data to facilitate causal discovery. Previous approaches commonly utilize uncertainty or gradient signals to determine the intervention targets. However, numerical-based approaches may yield suboptimal results due to the inaccurate estimation of the guiding signals at the beginning when with limited interventional data. In this work, we investigate a different approach, whether we can leverage Large Language Models (LLMs) to assist with the intervention targeting in causal discovery by making use of the rich world knowledge about the experimental design in LLMs. Specifically, we present Large Language Model Guided Intervention Targeting (LeGIT) -- a robust framework that effectively incorporates LLMs to augment existing numerical approaches for the intervention targeting in causal discovery. Across 4 realistic benchmark scales, LeGIT demonstrates significant improvements and robustness over existing methods and even surpasses humans, which demonstrates the usefulness of LLMs in assisting with experimental design for scientific discovery.

SEE: See Everything Every Time -- Adaptive Brightness Adjustment for Broad Light Range Images via Events

Event cameras, with a high dynamic range exceeding $120dB$, significantly outperform traditional embedded cameras, robustly recording detailed changing information under various lighting conditions, including both low- and high-light situations. However, recent research on utilizing event data has primarily focused on low-light image enhancement, neglecting image enhancement and brightness adjustment across a broader range of lighting conditions, such as normal or high illumination. Based on this, we propose a novel research question: how to employ events to enhance and adaptively adjust the brightness of images captured under broad lighting conditions? To investigate this question, we first collected a new dataset, SEE-600K, consisting of 610,126 images and corresponding events across 202 scenarios, each featuring an average of four lighting conditions with over a 1000-fold variation in illumination. Subsequently, we propose a framework that effectively utilizes events to smoothly adjust image brightness through the use of prompts. Our framework captures color through sensor patterns, uses cross-attention to model events as a brightness dictionary, and adjusts the image's dynamic range to form a broad light-range representation (BLR), which is then decoded at the pixel level based on the brightness prompt. Experimental results demonstrate that our method not only performs well on the low-light enhancement dataset but also shows robust performance on broader light-range image enhancement using the SEE-600K dataset. Additionally, our approach enables pixel-level brightness adjustment, providing flexibility for post-processing and inspiring more imaging applications. The dataset and source code are publicly available at:https://github.com/yunfanLu/SEE.

LongReD: Mitigating Short-Text Degradation of Long-Context Large Language Models via Restoration Distillation

Large language models (LLMs) have gained extended context windows through scaling positional encodings and lightweight continual pre-training. However, this often leads to degraded performance on short-text tasks, while the reasons for this degradation remain insufficiently explored. In this work, we identify two primary factors contributing to this issue: distribution drift in hidden states and attention scores, and catastrophic forgetting during continual pre-training. To address these challenges, we propose Long Context Pre-training with Restoration Distillation (LongReD), a novel approach designed to mitigate short-text performance degradation through minimizing the distribution discrepancy between the extended and original models. Besides training on long texts, LongReD distills the hidden state of selected layers from the original model on short texts. Additionally, LongReD also introduces a short-to-long distillation, aligning the output distribution on short texts with that on long texts by leveraging skipped positional indices. Experiments on common text benchmarks demonstrate that LongReD effectively preserves the model's short-text performance while maintaining comparable or even better capacity to handle long texts than baselines.

Holistically Guided Monte Carlo Tree Search for Intricate Information Seeking

In the era of vast digital information, the sheer volume and heterogeneity of available information present significant challenges for intricate information seeking. Users frequently face multistep web search tasks that involve navigating vast and varied data sources. This complexity demands every step remains comprehensive, accurate, and relevant. However, traditional search methods often struggle to balance the need for localized precision with the broader context required for holistic understanding, leaving critical facets of intricate queries underexplored. In this paper, we introduce an LLM-based search assistant that adopts a new information seeking paradigm with holistically guided Monte Carlo tree search (HG-MCTS). We reformulate the task as a progressive information collection process with a knowledge memory and unite an adaptive checklist with multi-perspective reward modeling in MCTS. The adaptive checklist provides explicit sub-goals to guide the MCTS process toward comprehensive coverage of complex user queries. Simultaneously, our multi-perspective reward modeling offers both exploration and retrieval rewards, along with progress feedback that tracks completed and remaining sub-goals, refining the checklist as the tree search progresses. By striking a balance between localized tree expansion and global guidance, HG-MCTS reduces redundancy in search paths and ensures that all crucial aspects of an intricate query are properly addressed. Extensive experiments on real-world intricate information seeking tasks demonstrate that HG-MCTS acquires thorough knowledge collections and delivers more accurate final responses compared with existing baselines.

Think More, Hallucinate Less: Mitigating Hallucinations via Dual Process of Fast and Slow Thinking

Large language models (LLMs) demonstrate exceptional capabilities, yet still face the hallucination issue. Typical text generation approaches adopt an auto-regressive generation without deliberate reasoning, which often results in untrustworthy and factually inaccurate responses. In this paper, we propose HaluSearch, a novel framework that incorporates tree search-based algorithms (e.g. MCTS) to enable an explicit slow thinking generation process for mitigating hallucinations of LLMs during inference. Specifically, HaluSearch frames text generation as a step-by-step reasoning process, using a self-evaluation reward model to score each generation step and guide the tree search towards the most reliable generation pathway for fully exploiting the internal knowledge of LLMs. To balance efficiency and quality, we introduce a hierarchical thinking system switch mechanism inspired by the dual process theory in cognitive science, which dynamically alternates between fast and slow thinking modes at both the instance and step levels, adapting to the complexity of questions and reasoning states. We conduct extensive experiments on both English and Chinese datasets and the results show that our approach significantly outperforms baseline approaches.

Think&Cite: Improving Attributed Text Generation with Self-Guided Tree Search and Progress Reward Modeling

Despite their outstanding capabilities, large language models (LLMs) are prone to hallucination and producing factually incorrect information. This challenge has spurred efforts in attributed text generation, which prompts LLMs to generate content with supporting evidence. In this paper, we propose a novel framework, called Think&Cite, and formulate attributed text generation as a multi-step reasoning problem integrated with search. Specifically, we propose Self-Guided Monte Carlo Tree Search (SG-MCTS), which capitalizes on the self-reflection capability of LLMs to reflect on the intermediate states of MCTS for guiding the tree expansion process. To provide reliable and comprehensive feedback, we introduce Progress Reward Models to measure the progress of tree search from the root to the current state from two aspects, i.e., generation and attribution progress. We conduct extensive experiments on three datasets and the results show that our approach significantly outperforms baseline approaches.

RAG-Star: Enhancing Deliberative Reasoning with Retrieval Augmented Verification and Refinement

Existing large language models (LLMs) show exceptional problem-solving capabilities but might struggle with complex reasoning tasks. Despite the successes of chain-of-thought and tree-based search methods, they mainly depend on the internal knowledge of LLMs to search over intermediate reasoning steps, limited to dealing with simple tasks involving fewer reasoning steps. In this paper, we propose \textbf{RAG-Star}, a novel RAG approach that integrates the retrieved information to guide the tree-based deliberative reasoning process that relies on the inherent knowledge of LLMs. By leveraging Monte Carlo Tree Search, RAG-Star iteratively plans intermediate sub-queries and answers for reasoning based on the LLM itself. To consolidate internal and external knowledge, we propose an retrieval-augmented verification that utilizes query- and answer-aware reward modeling to provide feedback for the inherent reasoning of LLMs. Our experiments involving Llama-3.1-8B-Instruct and GPT-4o demonstrate that RAG-Star significantly outperforms previous RAG and reasoning methods.

PartGLEE: A Foundation Model for Recognizing and Parsing Any Objects

We present PartGLEE, a part-level foundation model for locating and identifying both objects and parts in images. Through a unified framework, PartGLEE accomplishes detection, segmentation, and grounding of instances at any granularity in the open world scenario. Specifically, we propose a Q-Former to construct the hierarchical relationship between objects and parts, parsing every object into corresponding semantic parts. By incorporating a large amount of object-level data, the hierarchical relationships can be extended, enabling PartGLEE to recognize a rich variety of parts. We conduct comprehensive studies to validate the effectiveness of our method, PartGLEE achieves the state-of-the-art performance across various part-level tasks and obtain competitive results on object-level tasks. The proposed PartGLEE significantly enhances hierarchical modeling capabilities and part-level perception over our previous GLEE model. Further analysis indicates that the hierarchical cognitive ability of PartGLEE is able to facilitate a detailed comprehension in images for mLLMs. The model and code will be released at https://provencestar.github.io/PartGLEE-Vision/ .

Mix-CPT: A Domain Adaptation Framework via Decoupling Knowledge Learning and Format Alignment

Adapting general large language models (LLMs) to specialized domains presents great challenges due to varied data distributions. This adaptation typically requires continual pre-training on massive domain-specific corpora to facilitate knowledge memorization, followed by training to apply this knowledge following human instructions and preferences. However, this method may result in inefficient knowledge memorization due to a lack of awareness of knowledge utilization and imposes substantial demands on LLMs to simultaneously learn knowledge utilization and format alignment with limited training samples. To facilitate the domain adaptation of LLM, we revise this process and propose a new domain adaptation framework including domain knowledge learning and general format alignment, called Mix-CPT. Specifically, we first conduct a knowledge mixture continual pre-training that concurrently focuses on knowledge memorization and utilization, allowing for mutual reinforcement. To avoid catastrophic forgetting during the continual pre-training process, we further incorporate a logit swap self-distillation constraint. Subsequently, leveraging the knowledge and capabilities acquired during continual pre-training, we efficiently perform instruction tuning and alignment with a few general training samples to achieve format alignment. Extensive experiments demonstrate that our proposed Mix-CPT framework can simultaneously improve the task-solving capabilities of LLMs on the target and general domains compared to the traditional adaptation methods.