arXiv subjects

Runyu Guan

Publications and source records attributed to Runyu Guan.

4 recordsLinked to original sources

arXiv2026

Agentic AI uncovers conserved cross-tissue protein co-abundance programs inaccessible to single-dataset analysis

Protein co-abundance clusters preserved across tissues can reveal shared disease mechanisms and candidate therapeutic targets, particularly when proteins implicated in organ-confined diseases converge in peripheral or accessible tissues. However, previous cross-tissue studies have focused on biologically pre-selected tissue pairs, leaving most possible combinations and non-obvious relationships unexplored. We present an LLM-agent framework for large-scale, evidence-grounded comparison of tissue-specific protein co-abundance networks. The framework constructs tissue networks, derives pairwise consensus clusters, and integrates evidence from expression atlases, protein interaction and complex databases, pathway annotations, disease catalogues, and literature. Applied to all 820 pairwise combinations of 41 human tissues and fluids, it identified 1,833 conserved co-abundance clusters across 406 tissue pairs. Colon, synovial fluid, blood, cerebrospinal fluid, and bone marrow were the most broadly connected tissues, while the most cluster-rich pairs were dominated by bone marrow. The analysis also highlighted non-obvious relationships: skin-bone marrow exceeded the anatomically adjacent bone-bone marrow pair, while colon-breast contained cancer-relevant clusters involving extracellular-matrix remodeling, lipid metabolism, and immune modulation. Cluster-level analyses generated further mechanistic hypotheses, including a brain-gut extracellular-vesicle/redox/serotonin-cofactor axis and a liver-bone marrow stress-response axis involving genes linked to white matter disease. These results provide a global, comparable landscape of conserved protein co-abundance and a hypothesis-generating resource for mechanistic and therapeutic exploration. Code and data are available at https://github.com/Gry1005/AgenticAI-conserved-cross-tissue-protein-co-abundance.

cs.AI↗

arXiv2022

Towards Transferring Human Preferences from Canonical to Actual Assembly Tasks

To assist human users according to their individual preference in assembly tasks, robots typically require user demonstrations in the given task. However, providing demonstrations in actual assembly tasks can be tedious and time-consuming. Our thesis is that we can learn user preferences in assembly tasks from demonstrations in a representative canonical task. Inspired by previous work in economy of human movement, we propose to represent user preferences as a linear function of abstract task-agnostic features, such as movement and physical and mental effort required by the user. For each user, we learn their preference from demonstrations in a canonical task and use the learned preference to anticipate their actions in the actual assembly task without any user demonstrations in the actual task. We evaluate our proposed method in a model-airplane assembly study and show that preferences can be effectively transferred from canonical to actual assembly tasks, enabling robots to anticipate user actions.

cs.RO↗

arXiv2021

Synthetic Map Generation to Provide Unlimited Training Data for Historical Map Text Detection

Many historical map sheets are publicly available for studies that require long-term historical geographic data. The cartographic design of these maps includes a combination of map symbols and text labels. Automatically reading text labels from map images could greatly speed up the map interpretation and helps generate rich metadata describing the map content. Many text detection algorithms have been proposed to locate text regions in map images automatically, but most of the algorithms are trained on out-ofdomain datasets (e.g., scenic images). Training data determines the quality of machine learning models, and manually annotating text regions in map images is labor-extensive and time-consuming. On the other hand, existing geographic data sources, such as Open- StreetMap (OSM), contain machine-readable map layers, which allow us to separate out the text layer and obtain text label annotations easily. However, the cartographic styles between OSM map tiles and historical maps are significantly different. This paper proposes a method to automatically generate an unlimited amount of annotated historical map images for training text detection models. We use a style transfer model to convert contemporary map images into historical style and place text labels upon them. We show that the state-of-the-art text detection models (e.g., PSENet) can benefit from the synthetic historical maps and achieve significant improvement for historical map text detection.

cs.CV↗

arXiv2019

Accelerating Partial Evaluation in Distributed SPARQL Query Evaluation

Partial evaluation has recently been used for processing SPARQL queries over a large resource description framework (RDF) graph in a distributed environment. However, the previous approach is inefficient when dealing with complex queries. In this study, we further improve the "partial evaluation and assembly" framework for answering SPARQL queries over a distributed RDF graph, while providing performance guarantees. Our key idea is to explore the intrinsic structural characteristics of partial matches to filter out irrelevant partial results, while providing performance guarantees on a network trace (data shipment) or the computational cost (response time). We also propose an efficient assembly algorithm to utilize the characteristics of partial matches to merge them and form final results. To improve the efficiency of finding partial matches further, we propose an optimization that communicates variables' candidates among sites to avoid redundant computations. In addition, although our approach is partitioning-tolerant, different partitioning strategies result in different performances, and we evaluate different partitioning strategies for our approach. Experiments over both real and synthetic RDF datasets confirm the superiority of our approach.

cs.DC↗