arXiv subjects

Jiakang Xu

Publications and source records attributed to Jiakang Xu.

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↗

arXiv2026

Prompt Compression in Diffusion Large Language Models: Evaluating LLMLingua-2 on LLaDA

Prompt compression reduces inference cost and context length in large language models, but prior evaluations focus mainly on autoregressive architectures. This study examines whether LLMLingua-2 transfers effectively to diffusion large language models (DLLMs), specifically LLaDA-8B-Instruct. We evaluate GSM8K, DUC2004, and ShareGPT using 250 prompts per dataset at an approximate 50\% compression ratio, covering mathematical reasoning, prompt reconstruction, and summarization. Outputs from original, compressed, and reconstructed prompts are compared using exact-match accuracy, BLEU, ROUGE, and BERTScore. Results show that high semantic preservation does not necessarily ensure stable downstream behavior in diffusion models. Summarization remains relatively robust, while mathematical reasoning degrades substantially despite high semantic similarity. Reconstruction further shows that semantically similar prompts may omit reasoning-critical information needed for stable denoising. Overall, compression failures are mainly driven by information omission rather than semantic drift, suggesting that autoregressive prompt compression methods may not transfer uniformly to DLLMs. These findings motivate diffusion-aware compression strategies.

cs.CL↗

arXiv2022

Automatic Semantic Modeling for Structural Data Source with the Prior Knowledge from Knowledge Base

A critical step in sharing semantic content online is to map the structural data source to a public domain ontology. This problem is denoted as the Relational-To-Ontology Mapping Problem (Rel2Onto). A huge effort and expertise are required for manually modeling the semantics of data. Therefore, an automatic approach for learning the semantics of a data source is desirable. Most of the existing work studies the semantic annotation of source attributes. However, although critical, the research for automatically inferring the relationships between attributes is very limited. In this paper, we propose a novel method for semantically annotating structured data sources using machine learning, graph matching and modified frequent subgraph mining to amend the candidate model. In our work, Knowledge graph is used as prior knowledge. Our evaluation shows that our approach outperforms two state-of-the-art solutions in tricky cases where only a few semantic models are known.

cs.AI↗