the Department of Information Science and Engineering, Southeast University, Nanjing, China, the Key Laboratory of Child Development and Learning Science of Ministry of Education, Research Center for Learning Science, Southeast University, Nanjing, China
Abstract: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.
Abstract:Visual object tracking aims to locate a targeted object in a video sequence based on an initial bounding box. Recently, Vision-Language~(VL) trackers have proposed to utilize additional natural language descriptions to enhance versatility in various applications. However, VL trackers are still inferior to State-of-The-Art (SoTA) visual trackers in terms of tracking performance. We found that this inferiority primarily results from their heavy reliance on manual textual annotations, which include the frequent provision of ambiguous language descriptions. In this paper, we propose ChatTracker to leverage the wealth of world knowledge in the Multimodal Large Language Model (MLLM) to generate high-quality language descriptions and enhance tracking performance. To this end, we propose a novel reflection-based prompt optimization module to iteratively refine the ambiguous and inaccurate descriptions of the target with tracking feedback. To further utilize semantic information produced by MLLM, a simple yet effective VL tracking framework is proposed and can be easily integrated as a plug-and-play module to boost the performance of both VL and visual trackers. Experimental results show that our proposed ChatTracker achieves a performance comparable to existing methods.
Abstract:Although previous research on large language models (LLMs) and large multi-modal models (LMMs) has systematically explored mathematical problem-solving (MPS) within visual contexts, the analysis of how these models process visual information during problem-solving remains insufficient. To address this gap, we present VisAidMath, a benchmark for evaluating the MPS process related to visual information. We follow a rigorous data curation pipeline involving both automated processes and manual annotations to ensure data quality and reliability. Consequently, this benchmark includes 1,200 challenging problems from various mathematical branches, vision-aid formulations, and difficulty levels, collected from diverse sources such as textbooks, examination papers, and Olympiad problems. Based on the proposed benchmark, we conduct comprehensive evaluations on ten mainstream LLMs and LMMs, highlighting deficiencies in the visual-aided reasoning process. For example, GPT-4V only achieves 45.33% accuracy in the visual-aided reasoning task, even with a drop of 2 points when provided with golden visual aids. In-depth analysis reveals that the main cause of deficiencies lies in hallucination regarding the implicit visual reasoning process, shedding light on future research directions in the visual-aided MPS process.
Abstract:Self-supervised learning (SSL) has achieved impressive results across several computer vision tasks, even rivaling supervised methods. However, its performance degrades on real-world datasets with long-tailed distributions due to difficulties in capturing inherent class imbalances. Although supervised long-tailed learning offers significant insights, the absence of labels in SSL prevents direct transfer of these strategies.To bridge this gap, we introduce Adaptive Paradigm Synergy (APS), a cross-paradigm objective that seeks to unify the strengths of both paradigms. Our approach reexamines contrastive learning from a spatial structure perspective, dynamically adjusting the uniformity of latent space structure through adaptive temperature tuning. Furthermore, we draw on a re-weighting strategy from supervised learning to compensate for the shortcomings of temperature adjustment in explicit quantity perception.Extensive experiments on commonly used long-tailed datasets demonstrate that APS improves performance effectively and efficiently. Our findings reveal the potential for deeper integration between supervised and self-supervised learning, paving the way for robust models that handle real-world class imbalance.
Abstract:Retrieval-augmented generation (RAG) enhances the question-answering (QA) abilities of large language models (LLMs) by integrating external knowledge. However, adapting general-purpose RAG systems to specialized fields such as science and medicine poses unique challenges due to distribution shifts and limited access to domain-specific data. To tackle this, we propose SimRAG, a self-training approach that equips the LLM with joint capabilities of question answering and question generation for domain adaptation. Our method first fine-tunes the LLM on instruction-following, question-answering, and search-related data. Then, it prompts the same LLM to generate diverse domain-relevant questions from unlabeled corpora, with an additional filtering strategy to retain high-quality synthetic examples. By leveraging these synthetic examples, the LLM can improve their performance on domain-specific RAG tasks. Experiments on 11 datasets, spanning two backbone sizes and three domains, demonstrate that SimRAG outperforms baselines by 1.2\%--8.6\%.
Abstract:Curating a desirable dataset for training has been the core of building highly capable large language models (Touvron et al., 2023; Achiam et al., 2023; Team et al.,2024). Gradient influence scores (Pruthi et al., 2020; Xia et al., 2024) are shown to be correlated with model performance and are commonly used as the criterion for data selection. However, existing methods are built upon either individual sample rankings or inefficient matching process, leading to suboptimal performance or scaling up issues.In this paper, we propose Gradient Trajectory Pursuit (GTP), an algorithm that performs pursuit of gradient trajectories via jointly selecting data points under an L0-norm regularized objective. The proposed algorithm highlights: (1) joint selection instead of independent top-k selection, which automatically de-duplicates samples; (2) higher efficiency with compressive sampling processes, which can be further sped up using a distributed framework. In the experiments, we demonstrate the algorithm in both in-domain and target-domain selection benchmarks and show that it outperforms top-k selection and competitive algorithms consistently, for example, our algorithm chooses as low as 0.5% data to achieve full performance on the targeted instruction tuning tasks
Abstract:Estimating an individual's potential response to continuously varied treatments is crucial for addressing causal questions across diverse domains, from healthcare to social sciences. However, existing methods are limited either to estimating causal effects of binary treatments, or scenarios where all confounding variables are measurable. In this work, we present ContiVAE, a novel framework for estimating causal effects of continuous treatments, measured by individual dose-response curves, considering the presence of unobserved confounders using observational data. Leveraging a variational auto-encoder with a Tilted Gaussian prior distribution, ContiVAE models the hidden confounders as latent variables, and is able to predict the potential outcome of any treatment level for each individual while effectively capture the heterogeneity among individuals. Experiments on semi-synthetic datasets show that ContiVAE outperforms existing methods by up to 62%, demonstrating its robustness and flexibility. Application on a real-world dataset illustrates its practical utility.
Abstract:Public scarce resource allocation plays a crucial role in economics as it directly influences the efficiency and equity in society. Traditional studies including theoretical model-based, empirical study-based and simulation-based methods encounter limitations due to the idealized assumption of complete information and individual rationality, as well as constraints posed by limited available data. In this work, we propose an innovative framework, SRAP-Agent (Simulating and Optimizing Scarce Resource Allocation Policy with LLM-based Agent), which integrates Large Language Models (LLMs) into economic simulations, aiming to bridge the gap between theoretical models and real-world dynamics. Using public housing allocation scenarios as a case study, we conduct extensive policy simulation experiments to verify the feasibility and effectiveness of the SRAP-Agent and employ the Policy Optimization Algorithm with certain optimization objectives. The source code can be found in https://github.com/jijiarui-cather/SRAPAgent_Framework
Abstract:The widespread deployment of large language models (LLMs) has led to impressive advancements, yet information about their training data, a critical factor in their performance, remains undisclosed. Membership inference attacks (MIAs) aim to determine whether a specific instance was part of a target model's training data. MIAs can offer insights into LLM outputs and help detect and address concerns such as data contamination and compliance with privacy and copyright standards. However, applying MIAs to LLMs presents unique challenges due to the massive scale of pre-training data and the ambiguous nature of membership. Additionally, creating appropriate benchmarks to evaluate MIA methods is not straightforward, as training and test data distributions are often unknown. In this paper, we introduce EM-MIA, a novel MIA method for LLMs that iteratively refines membership scores and prefix scores via an expectation-maximization algorithm, leveraging the duality that the estimates of these scores can be improved by each other. Membership scores and prefix scores assess how each instance is likely to be a member and discriminative as a prefix, respectively. Our method achieves state-of-the-art results on the WikiMIA dataset. To further evaluate EM-MIA, we present OLMoMIA, a benchmark built from OLMo resources, which allows us to control the difficulty of MIA tasks with varying degrees of overlap between training and test data distributions. We believe that EM-MIA serves as a robust MIA method for LLMs and that OLMoMIA provides a valuable resource for comprehensively evaluating MIA approaches, thereby driving future research in this critical area.
Abstract:The medical image processing field often encounters the critical issue of scarce annotated data. Transfer learning has emerged as a solution, yet how to select an adequate source task and effectively transfer the knowledge to the target task remains challenging. To address this, we propose a novel sequential transfer scheme with a task affinity metric tailored for medical images. Considering the characteristics of medical image segmentation tasks, we analyze the image and label similarity between tasks and compute the task affinity scores, which assess the relatedness among tasks. Based on this, we select appropriate source tasks and develop an effective sequential transfer strategy by incorporating intermediate source tasks to gradually narrow the domain discrepancy and minimize the transfer cost. Thereby we identify the best sequential transfer path for the given target task. Extensive experiments on three MRI medical datasets, FeTS 2022, iSeg-2019, and WMH, demonstrate the efficacy of our method in finding the best source sequence. Compared with directly transferring from a single source task, the sequential transfer results underline a significant improvement in target task performance, achieving an average of 2.58% gain in terms of segmentation Dice score, notably, 6.00% for FeTS 2022. Code is available at the git repository.