arXiv subjects

Yidan Gao

Publications and source records attributed to Yidan Gao.

3 recordsLinked to original sources

arXiv2026

Bioinfoysis Technical Report

Large language model agents have shown promise in bioinformatics, but most existing systems focus primarily on producing final answers, treating planning, tool use, and code execution as transient interactions. This design is poorly suited to long-horizon bioinformatics tasks, where conclusions must remain connected to the data, computations, and intermediate evidence that support them. We introduce \textbf{Bioinfoysis}, a multi-agent harness that represents each request as a persistent, artifact-grounded analysis run. Bioinfoysis combines global planning with step-wise, evidence-driven replanning: the planner maintains an executable checklist and revises pending steps using structured handoffs returned after each worker execution. These handoffs bind intermediate results to their responsible agent, checklist step, and plan generation, preventing stale evidence from being silently reused after replanning. A controlled runtime validates generated scripts, tables, and figures before they are used in downstream analysis or reporting, while role-specific context, persistent memory, and governed bioinformatics skills support reliable execution over long analysis trajectories. We evaluate Bioinfoysis on BixBench and two question-answering tracks of LAB-Bench 2. On BixBench, Bioinfoysis achieves state-of-the-art accuracy of 82.4\%. Across four underlying language models, Bioinfoysis increases average accuracy from 27.81\% to 64.13\% on SeqQA2 and from 3.13\% to 31.25\% on DbQA2. These results demonstrate that reliable bioinformatics automation depends not only on model capability, but also on the harness that governs planning, execution, memory, and evidence flow. We hope that the emergence of Bioinfoysis will play a driving and leading role in the development of the bioinformatics community. Our demo website can be seen in https://report.bioinfoysis.com/.

cs.AI↗

arXiv2025

LookUp3D: Data-Driven 3D Scanning

High speed, high-resolution, and accurate 3D scanning would open doors to many new applications in graphics, robotics, science, and medicine by enabling the accurate scanning of deformable objects during interactions. Past attempts to use structured light, time-of-flight, and stereo in high-speed settings have usually required tradeoffs in resolution or inaccuracy. In this paper, we introduce a method that enables, for the first time, 3D scanning at 450 frames per second at 1~Megapixel, or 1,450 frames per second at 0.4~Megapixel in an environment with controlled lighting. The key idea is to use a per-pixel lookup table that maps colors to depths, which is built using a linear stage. Imperfections, such as lens-distortion and sensor defects are baked into the calibration. We describe our method and test it on a novel hardware prototype. We compare the system with both ground-truth geometry as well as commercially available dynamic sensors like the Microsoft Kinect and Intel Realsense. Our results show the system acquiring geometry of objects undergoing high-speed deformations and oscillations and demonstrate the ability to recover physical properties from the reconstructions.

cs.CV↗

arXiv2024

Robust Incremental Structure-from-Motion with Hybrid Features

Structure-from-Motion (SfM) has become a ubiquitous tool for camera calibration and scene reconstruction with many downstream applications in computer vision and beyond. While the state-of-the-art SfM pipelines have reached a high level of maturity in well-textured and well-configured scenes over the last decades, they still fall short of robustly solving the SfM problem in challenging scenarios. In particular, weakly textured scenes and poorly constrained configurations oftentimes cause catastrophic failures or large errors for the primarily keypoint-based pipelines. In these scenarios, line segments are often abundant and can offer complementary geometric constraints. Their large spatial extent and typically structured configurations lead to stronger geometric constraints as compared to traditional keypoint-based methods. In this work, we introduce an incremental SfM system that, in addition to points, leverages lines and their structured geometric relations. Our technical contributions span the entire pipeline (mapping, triangulation, registration) and we integrate these into a comprehensive end-to-end SfM system that we share as an open-source software with the community. We also present the first analytical method to propagate uncertainties for 3D optimized lines via sensitivity analysis. Experiments show that our system is consistently more robust and accurate compared to the widely used point-based state of the art in SfM -- achieving richer maps and more precise camera registrations, especially under challenging conditions. In addition, our uncertainty-aware localization module alone is able to consistently improve over the state of the art under both point-alone and hybrid setups.

cs.CV↗