Xiao Wang

Yingzhou Lu, Minjie Shen, Ling Yue et al.

The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive software solution designed to handle the entire pipeline of omics data processing. GenoCraft offers a unified platform featuring advanced bioinformatics tools, covering all aspects of omics data analysis. It encompasses a range of functionalities, such as normalization, quality control, differential analysis, network analysis, pathway analysis, and diverse visualization techniques. This software makes state-of-the-art omics data analysis more accessible to a wider range of users. With GenoCraft, researchers and data scientists have access to an array of cutting-edge bioinformatics tools under a user-friendly interface, making it a valuable resource for managing and analyzing large-scale omics data. The API with an interactive web interface is publicly available at https://genocraft.stanford. edu/. We also release all the codes in https://github.com/futianfan/GenoCraft.

Xiongbin Gui, Hanlin Lv, Xiao Wang et al.

Background: Recruitment for cohorts involving complex liver diseases, such as hepatocellular carcinoma and liver cirrhosis, often requires interpreting semantically complex criteria. Traditional manual screening methods are time-consuming and prone to errors. While AI-powered pre-screening offers potential solutions, challenges remain regarding accuracy, efficiency, and data privacy. Methods: We developed a novel patient pre-screening pipeline that leverages clinical expertise to guide the precise, safe, and efficient application of large language models. The pipeline breaks down complex criteria into a series of composite questions and then employs two strategies to perform semantic question-answering through electronic health records - (1) Pathway A, Anthropomorphized Experts' Chain of Thought strategy, and (2) Pathway B, Preset Stances within an Agent Collaboration strategy, particularly in managing complex clinical reasoning scenarios. The pipeline is evaluated on three key metrics-precision, time consumption, and counterfactual inference - at both the question and criterion levels. Results: Our pipeline achieved high precision (0.921, in criteria level) and efficiency (0.44s per task). Pathway B excelled in complex reasoning, while Pathway A was effective in precise data extraction with faster processing times. Both pathways achieved comparable precision. The pipeline showed promising results in hepatocellular carcinoma (0.878) and cirrhosis trials (0.843). Conclusions: This data-secure and time-efficient pipeline shows high precision in hepatopathy trials, providing promising solutions for streamlining clinical trial workflows. Its efficiency and adaptability make it suitable for improving patient recruitment. And its capability to function in resource-constrained environments further enhances its utility in clinical settings.

Brian Gordon, Yonatan Bitton, Andreea Marzoca et al.

Large Vision-Language Models (VLMs) now generate highly detailed, paragraphlength image captions, yet evaluating their factual accuracy remains challenging. Current methods often miss fine-grained errors, being designed for shorter texts or lacking datasets with verified inaccuracies. We introduce DOCCI-Critique, a benchmark with 1,400 VLM-generated paragraph captions (100 images, 14 VLMs) featuring over 10,216 sentence-level human annotations of factual correctness and explanatory rationales for errors, all within paragraph context. Building on this, we develop VNLI-Critique, a model for automated sentence-level factuality classification and critique generation. We highlight three key applications: (1) VNLI-Critique demonstrates robust generalization, validated by state-of-the-art performance on the M-HalDetect benchmark and strong results in CHOCOLATE claim verification. (2) The VNLI-Critique driven AutoRater for DOCCI-Critique provides reliable VLM rankings, showing excellent alignment with human factuality judgments (e.g., 0.98 Spearman). (3) An innovative Critic-and-Revise pipeline, where critiques from VNLI-Critique guide LLM-based corrections, achieves substantial improvements in caption factuality (e.g., a 46% gain on DetailCaps-4870). Our work offers a crucial benchmark alongside practical tools, designed to significantly elevate the standards for fine-grained evaluation and foster the improvement of VLM image understanding. Project page: https://google.github.io/unblocking-detail-caption