arXiv subjects

Yicheng Tao

Publications and source records attributed to Yicheng Tao.

14 recordsLinked to original sources

arXiv2026

VOICE: A Vision-Omics Foundation Model Integrating Direct and Retrieval-Based Prediction of In-situ Single-Cell Gene Expression

Spatial transcriptomics can resolve gene expression at single-cell resolution, but it is costly, limited to targeted panels of a few hundred to a few thousand genes, and applicable to only a small number of samples. H&E imaging, by contrast, is cheap and collected routinely at scale. This makes predicting single-cell expression directly from morphology a practical way to bring molecular analysis to large tissue archives. We therefore present VOICE, a multimodal foundation model that predicts single-cell gene expression from H&E images using paired Xenium data. VOICE first aligns cell centered H&E morphology from a pathology foundation model with single-cell expression embeddings from a transcriptome foundation model, trained using contrastive learning over 23 million cells. Next it predicts expression through two branches. One branch directly regresses expression from morphology. The other branch retrieves measured expression from similar reference cells, recovering genes that do not have morphological signal. Because genes vary in morphological predictability, VOICE fuses the two branches with a per-gene weight. After training, VOICE generalizes to heldout patients, slides, and partially overlapping gene panels from Xenium, and it consistently outperforms prior single-cell expression prediction methods on seven metrics.

cs.CV↗

arXiv2026

Neighborhood-Aware Dual Biomedical Entity Linking

Biomedical entity linking grounds mentions in clinical and scientific text to entities in a curated knowledge base (KB) with ontological structure, which supports downstream applications such as literature-scale information extraction and patient-record normalization. The task has several challenges at once: the KB contains large numbers of entities, mentions are often ambiguous, and gold labels follow annotation conventions specific to each corpus. To address these challenges, we propose PILOT, a three-stage framework made up of neighborhood-aware retrieval, dual reranking, and score fusion. The retriever injects ontological structure from both the query and KB side, by reformulating mentions and pooling entity embeddings. The retrieved pool is then scored from two complementary views, one over surface forms and one over context, and fused together. PILOT achieves the state of the art on average across five widely-used benchmarks and remains efficient at inference.

cs.IR↗

arXiv2026

Diverse Evidence, Better Forecasts: Multi-Agent Deliberation Under Information Asymmetry

Multi-agent systems are increasingly used for forecasting future events, as deliberation among multiple LLMs is believed to improve reasoning and calibration. Yet existing approaches overlook a critical design choice: what information each agent receives. When all agents are given identical evidence, deliberation collapses into herding rather than genuine belief revision, leaving multi-agent systems little better than a single agent. We identify this as a fundamental gap and propose designed information asymmetry to close it: by partitioning evidence into shared public and disjoint private subsets, each agent holds exclusive knowledge that can only reach others through deliberation. We theoretically show that this decomposition reduces inter-agent error correlation, and instantiate it in InfoDelphi, a framework combining relevance-aware evidence routing, rationale-based iterative deliberation, and confidence-weighted aggregation. On PolyGym, a benchmark of 375 binary forecasting questions derived from real-world prediction markets, InfoDelphi outperforms the strongest single-agent and multi-agent baselines by 12--18% in Brier score and 4--8 percentage points in accuracy. More detailed experiments confirm that removing information asymmetry eliminates most deliberation gains, establishing diversity of input as the key enabler of effective multi-agent reasoning.

cs.AI↗

arXiv2026

GRASP: Plan-Guided Graph Retrieval with Adaptive Fusion and Reranking on Semi-Structured Knowledge Bases

Semi-structured knowledge bases (SKBs) embed textual documents in a typed graph of entities and relations, and underpin applications such as product search, academic paper search, and precision-medicine inquiries. Existing hybrid retrieval systems on SKBs either use the graph only for query expansion, mix textual and structural branches under a global weighting, or rely on fine-tuned graph-traversal generators. We present GRASP, a three-stage SKB retrieval framework unifying plan-based graph retrieval, plan-conditioned fusion with a dense retriever, and a fine-tuned reranker over the fused candidates. GRASP substantially advances the state of the art on every metric across the three STaRK benchmarks, lifting average Hit@1 from 62.0 to 73.9. Ablation and sensitivity studies further confirm the effectiveness and robustness of GRASP.

cs.IR↗

arXiv2026

Retrieval-Augmented Code Generation: A Survey with Focus on Repository-Level Approaches

Recent advances in large language models (LLMs) have significantly improved automated code generation. While existing approaches have achieved strong performance at the function and file levels, real-world software engineering requires reasoning over entire repositories, including cross-file dependencies, evolving execution environments, and global semantic consistency. This challenge has led to the emergence of Repository-Level Code Generation (RLCG), where models must retrieve, organize, and utilize repository-scale context to generate coherent and executable code changes. To address these challenges, Retrieval-Augmented Generation (RAG) has become an increasingly important paradigm for repository-level code intelligence. In this survey, we present a comprehensive review of Retrieval-Augmented Code Generation (RACG), with a particular focus on repository-level approaches. Rather than viewing RACG as a static ``retrieve-then-generate'' pipeline, we characterize it as a coupled and evolving process involving context construction, retrieval optimization, generation, and environment interaction. We organize existing methods through a unified analytical framework spanning retrieval substrate, control regime, and evaluation setting. Based on this framework, we systematically examine retrieval strategies, graph-based and non-graph-based retrieval paradigms, training-driven optimizations, and autonomous agent architectures. We further summarize widely used datasets, benchmarks, and system configurations, and discuss key challenges including scalability, reliability, efficiency, and the necessity boundary between RACG and long-context LLMs. Through this survey, we aim to provide a structured understanding of the rapidly evolving RACG landscape and highlight promising directions for future AI-powered software engineering research.

cs.SE↗

arXiv2026

AutoPCR: Automated Phenotype Concept Recognition by Prompting

Motivation: Phenotype concept recognition (CR) is a fundamental task in biomedical text mining. However, existing methods either require ontology-specific training, making them struggle to generalize across diverse text styles and evolving biomedical terminology, or depend on general-purpose large language models (LLMs) that lack necessary domain knowledge. Results: To address these limitations, we propose AutoPCR, a prompt-based phenotype CR method designed to automatically generalize to new ontologies and unseen data without ontology-specific training. To further boost performance, we also introduce an optional self-supervised training strategy. Experiments show that AutoPCR achieves the best average and most robust performance across datasets. Further ablation and transfer studies demonstrate its inductive capability and generalizability to new ontologies. Availability and Implementation: Our code is available at https://github.com/yctao7/AutoPCR. Contact: drjieliu@umich.edu

cs.CL↗

arXiv2026

TheoremForge: Scaling up Formal Data Synthesis with Low-Budget Agentic Workflow

The high cost of agentic workflows in formal mathematics hinders large-scale data synthesis, exacerbating the scarcity of open-source corpora. To address this, we introduce \textbf{TheoremForge}, a cost-effective formal data synthesis pipeline that decomposes the formalization process into five sub-tasks, which are \textit{statement formalization}, \textit{proof generation}, \textit{premise selection}, \textit{proof correction} and \textit{proof sketching}. By implementing a \textit{Decoupled Extraction Strategy}, the workflow recovers valid training signals from globally failed trajectories, effectively utilizing wasted computation. Experiments on a 2,000-problem benchmark demonstrate that TheoremForge achieves a Verified Rate of 12.6\%, surpassing the 8.6\% baseline, at an average cost of only \textbf{\$0.481} per successful trajectory using Gemini-3-Flash. Crucially, our strategy increases data yield by \textbf{1.6$\times$} for proof generation compared to standard filtering. These results establish TheoremForge as a scalable framework for constructing a data flywheel to train future expert models. Our code is available \href{https://github.com/timechess/TheoremForge}{here}.

cs.AI↗

arXiv2025

Learning an Effective Premise Retrieval Model for Efficient Mathematical Formalization

Formalized mathematics has recently garnered significant attention for its ability to assist mathematicians across various fields. Premise retrieval, as a common step in mathematical formalization, has been a challenge, particularly for inexperienced users. Existing retrieval methods that facilitate natural language queries require a certain level of mathematical expertise from users, while approaches based on formal languages (e.g., Lean) typically struggle with the scarcity of training data, hindering the training of effective and generalizable retrieval models. In this work, we introduce a novel method that leverages data extracted from Mathlib to train a lightweight and effective premise retrieval model. In particular, the proposed model embeds queries (i.e., proof state provided by Lean) and premises in a latent space, featuring a tokenizer specifically trained on formal corpora. The model is learned in a contrastive learning framework, in which a fine-grained similarity calculation method and a re-ranking module are applied to enhance the retrieval performance. Experimental results demonstrate that our model outperforms existing baselines, achieving higher accuracy while maintaining a lower computational load. We have released an open-source search engine based on our retrieval model at https://premise-search.com/. The source code and the trained model can be found at https://github.com/ruc-ai4math/Premise-Retrieval.

cs.CL↗

arXiv2025

Enhancing Large Language Models for Mobility Analytics with Semantic Location Tokenization

The widespread adoption of location-based services has led to the generation of vast amounts of mobility data, providing significant opportunities to model user movement dynamics within urban environments. Recent advancements have focused on adapting Large Language Models (LLMs) for mobility analytics. However, existing methods face two primary limitations: inadequate semantic representation of locations (i.e., discrete IDs) and insufficient modeling of mobility signals within LLMs (i.e., single templated instruction fine-tuning). To address these issues, we propose QT-Mob, a novel framework that significantly enhances LLMs for mobility analytics. QT-Mob introduces a location tokenization module that learns compact, semantically rich tokens to represent locations, preserving contextual information while ensuring compatibility with LLMs. Furthermore, QT-Mob incorporates a series of complementary fine-tuning objectives that align the learned tokens with the internal representations in LLMs, improving the model's comprehension of sequential movement patterns and location semantics. The proposed QT-Mob framework not only enhances LLMs' ability to interpret mobility data but also provides a more generalizable approach for various mobility analytics tasks. Experiments on three real-world dataset demonstrate the superior performance in both next-location prediction and mobility recovery tasks, outperforming existing deep learning and LLM-based methods.

cs.CL↗

arXiv2024

FANNO: Augmenting High-Quality Instruction Data with Open-Sourced LLMs Only

Instruction fine-tuning stands as a crucial advancement in leveraging large language models (LLMs) for enhanced task performance. However, the annotation of instruction datasets has traditionally been expensive and laborious, often relying on manual annotations or costly API calls of proprietary LLMs. To address these challenges, we introduce FANNO, a fully autonomous, open-sourced framework that revolutionizes the annotation process without the need for pre-existing annotated data. Utilizing a Mistral-7b-instruct model, FANNO efficiently produces diverse and high-quality datasets through a structured process involving document pre-screening, instruction generation, and response generation. Experiments on Open LLM Leaderboard and AlpacaEval benchmark show that the FANNO can generate high-quality data with diversity and complexity for free, comparable to human-annotated or cleaned datasets like Alpaca-GPT4-Cleaned.

cs.CL↗

arXiv2024

Graphical Reasoning: LLM-based Semi-Open Relation Extraction

This paper presents a comprehensive exploration of relation extraction utilizing advanced language models, specifically Chain of Thought (CoT) and Graphical Reasoning (GRE) techniques. We demonstrate how leveraging in-context learning with GPT-3.5 can significantly enhance the extraction process, particularly through detailed example-based reasoning. Additionally, we introduce a novel graphical reasoning approach that dissects relation extraction into sequential sub-tasks, improving precision and adaptability in processing complex relational data. Our experiments, conducted on multiple datasets, including manually annotated data, show considerable improvements in performance metrics, underscoring the effectiveness of our methodologies.

cs.CL↗

arXiv2024

PlanGPT: Enhancing Urban Planning with Tailored Language Model and Efficient Retrieval

In the field of urban planning, general-purpose large language models often struggle to meet the specific needs of planners. Tasks like generating urban planning texts, retrieving related information, and evaluating planning documents pose unique challenges. To enhance the efficiency of urban professionals and overcome these obstacles, we introduce PlanGPT, the first specialized Large Language Model tailored for urban and spatial planning. Developed through collaborative efforts with institutions like the Chinese Academy of Urban Planning, PlanGPT leverages a customized local database retrieval framework, domain-specific fine-tuning of base models, and advanced tooling capabilities. Empirical tests demonstrate that PlanGPT has achieved advanced performance, delivering responses of superior quality precisely tailored to the intricacies of urban planning.

cs.CL↗

arXiv2022

Learning Sparsity and Randomness for Data-driven Low Rank Approximation

Learning-based low rank approximation algorithms can significantly improve the performance of randomized low rank approximation with sketch matrix. With the learned value and fixed non-zero positions for sketch matrices from learning-based algorithms, these matrices can reduce the test error of low rank approximation significantly. However, there is still no good method to learn non-zero positions as well as overcome the out-of-distribution performance loss. In this work, we introduce two new methods Learning Sparsity and Learning Randomness which try to learn a better sparsity patterns and add randomness to the value of sketch matrix. These two methods can be applied with any learning-based algorithms which use sketch matrix directly. Our experiments show that these two methods can improve the performance of previous learning-based algorithm for both test error and out-of-distribution test error without adding too much complexity.

cs.LG↗

arXiv2021

Binary trees using the bookshelf and baseball constructions

This is a largely expository paper in which we discuss various sets having a Catalan number of objects and some well-known bijections between these sets presented in a new and hopefully interesting way. We call these concepts "bookshelf" and "baseball" constructions. No knowledge of these topics is assumed. These are the final student papers for a course at Brandeis University.

math.CO↗