Publication Library
Path-RAG Knowledge-Guided Key Region Retrieval for Open-ended Pathology Visual Question Answering
Description: See: https://github.com/embedded-robotics/path-rag. Accurate diagnosis and prognosis assisted by pathology images are essential for cancer treatment selection and planning. Despite the recent trend of adopting deep-learning approaches for analyzing complex pathology images, they fall short as they often overlook the domain-expert understanding of tissue structure and cell composition. In this work, we focus on a challenging Open-ended Pathology VQA (PathVQA-Open) task and propose a novel framework named Path-RAG, which leverages HistoCartography to retrieve relevant domain knowledge from pathology images and significantly improves performance on PathVQA-Open. Admitting the complexity of pathology image analysis, Path-RAG adopts a human-centered AI approach by retrieving domain knowledge using HistoCartography to select the relevant patches from pathology images. Our experiments suggest that domain guidance can significantly boost the accuracy of LLaVA-Med from 38% to 47%, with a notable gain of 28% for H&E-stained pathology images in the PathVQA-Open dataset. For longer-form question and answer pairs, our model consistently achieves significant improvements of 32.5% in ARCH-Open PubMed and 30.6% in ARCH-Open Books on H\&E images.
Created At: 13 December 2024
Updated At: 13 December 2024
Intelligent System for Automated Molecular Patent Infringement Assessment
Description: Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, a critical bottleneck persists in the inability of current automated frameworks to assess whether newly designed molecules infringe upon existing patents, posing significant legal and financial risks. We introduce PatentFinder, a novel tool-enhanced and multi-agent framework that accurately and comprehensively evaluates small molecules for patent infringement. It incorporates both heuristic and model-based tools tailored for decomposed subtasks, featuring: MarkushParser, which is capable of optical chemical structure recognition of molecular and Markush structures, and MarkushMatcher, which enhances large language models' ability to extract substituent groups from molecules accurately. On our benchmark dataset MolPatent-240, PatentFinder outperforms baseline approaches that rely solely on large language models, demonstrating a 13.8\% increase in F1-score and a 12\% rise in accuracy. Experimental results demonstrate that PatentFinder mitigates label bias to produce balanced predictions and autonomously generates detailed, interpretable patent infringement reports. This work not only addresses a pivotal challenge in automated drug discovery but also demonstrates the potential of decomposing complex scientific tasks into manageable subtasks for specialized, tool-augmented agents.
Created At: 13 December 2024
Updated At: 13 December 2024
Creating a Cooperative AI Policymaking Platform through Open Source Collaboration
Description: Advances in artificial intelligence (AI) present significant risks and opportunities, requiring improved governance to mitigate societal harms and promote equitable benefits. Current incentive structures and regulatory delays may hinder responsible AI development and deployment, particularly in light of the transformative potential of large language models (LLMs). To address these challenges, we propose developing the following three contributions: (1) a large multimodal text and economic-timeseries foundation model that integrates economic and natural language policy data for enhanced forecasting and decision-making, (2) algorithmic mechanisms for eliciting diverse and representative perspectives, enabling the creation of data-driven public policy recommendations, and (3) an AI-driven web platform for supporting transparent, inclusive, and data-driven policymaking.
Created At: 13 December 2024
Updated At: 13 December 2024
AI-Compass A Comprehensive and Effective Multi-module Testing Tool for AI Systems
Description: AI systems, in particular with deep learning techniques, have demonstrated superior performance for various real-world applications. Given the need for tailored optimization in specific scenarios, as well as the concerns related to the exploits of subsurface vulnerabilities, a more comprehensive and in-depth testing AI system becomes a pivotal topic. We have seen the emergence of testing tools in real-world applications that aim to expand testing capabilities. However, they often concentrate on ad-hoc tasks, rendering them unsuitable for simultaneously testing multiple aspects or components. Furthermore, trustworthiness issues arising from adversarial attacks and the challenge of interpreting deep learning models pose new challenges for developing more comprehensive and in-depth AI system testing tools. In this study, we design and implement a testing tool, \tool, to comprehensively and effectively evaluate AI systems. The tool extensively assesses multiple measurements towards adversarial robustness, model interpretability, and performs neuron analysis. The feasibility of the proposed testing tool is thoroughly validated across various modalities, including image classification, object detection, and text classification. Extensive experiments demonstrate that \tool is the state-of-the-art tool for a comprehensive assessment of the robustness and trustworthiness of AI systems. Our research sheds light on a general solution for AI systems testing landscape.
Created At: 13 December 2024
Updated At: 13 December 2024
Biomedical SAM 2 Segment Anything in Biomedical Images and Videos
Description: Medical image segmentation and video object segmentation are essential for diagnosing and analyzing diseases by identifying and measuring biological structures. Recent advances in natural domain have been driven by foundation models like the Segment Anything Model 2 (SAM-2). To explore the performance of SAM-2 in biomedical applications, we designed three evaluation pipelines for single-frame 2D image segmentation, multi-frame 3D image segmentation and multi-frame video segmentation with varied prompt designs, revealing SAM-2's limitations in medical contexts. Consequently, we developed BioSAM-2, an enhanced foundation model optimized for biomedical data based on SAM-2. Our experiments show that BioSAM-2 not only surpasses the performance of existing state-of-the-art foundation models but also matches or even exceeds specialist models, demonstrating its efficacy and potential in the medical domain.
Created At: 13 December 2024
Updated At: 13 December 2024