arXiv subjects

Jielong Lu

Publications and source records attributed to Jielong Lu.

4 recordsLinked to original sources

arXiv2026

Pretraining Reusable Inference Across Views with Synthetic Task Priors

Modern pretrained encoders make representations from heterogeneous views increasingly reusable, but the procedure that determines view utility and combines evidence is still relearned for each downstream task. Consequently, knowledge about view relevance, complementarity, reliability, and missingness is repeatedly discarded rather than transferred across tasks. We therefore reformulate multi-view learning as learning a reusable, task-conditioned inference procedure rather than a fixed fusion function. Based on this perspective, we propose SIMPLE, a prior-fitted multi-view in-context learner that predicts query labels by conditioning on a small labeled support set. Since existing real-world datasets cover only a limited range of view configurations and task structures, we construct a controllable synthetic task prior in embedding space. It generates diverse support-query episodes with varying class structures, shared and view-specific factors, representation geometries, cross-view dependencies, reliability levels, missingness patterns, and distribution shifts. A hierarchical inference architecture then performs reasoning within views, across views, and across support and query samples. Experiments on multi-view and multi-omics benchmarks demonstrate that the frozen variant of SIMPLE achieves competitive performance without updating the inference backbone, while lightweight adapter calibration attains leading performance on most evaluated datasets. Together, the results under frozen, one-shot, and missing-view settings support the central hypothesis that multi-view reasoning itself can be pretrained and reused, while lightweight adapter calibration provides task-specific alignment when needed.

cs.LG↗

arXiv2026

DeepBD: A Grounded Agentic Workflow for Variant Prioritization and Diagnosis of Genetic Birth Defects

Birth defects are a major cause of fetal loss, neonatal morbidity and long-term disability. In the subset with suspected genetic etiologies, exome and genome sequencing have moved many cases from variant detection to post-sequencing interpretation: clinicians must rank patient-specific candidate variants under incomplete fetal or infant phenotypes and heterogeneous evidence from population genetics, variant-effect prediction, gene-disease validity, phenotype ontologies, cellular and pathway context, protein structure and clinical literature. We present DeepBD, a grounded agentic workflow for variant prioritization and diagnostic interpretation of genetic birth defects. DeepBD organizes the workflow into LLM-assisted case structuring, a pretrained evidence engine, specialist evidence modules and a grounded diagnostic review layer. The evidence engine learns patient-specific variant scores from structured rule evidence, sequence and variant-effect representations and phenotype-conditioned biological context, whereas specialist modules and the agentic layer provide tool-based refinement, candidate-pool review and diagnosis-oriented synthesis from ranked candidates. Developed using an in-house fetal and infant cohort comprising 18,622 cases, DeepBD achieved Recall@1/3/5/10 of 0.658/0.882/0.912/0.929 on an internal held-out solved-case benchmark, outperforming standalone Exomiser, DeepRare and prompted LLM reranking baselines evaluated on Exomiser-derived top-20 candidate variants. Ablation and overlap analyses show that rule evidence, mechanistic context, and specialist refinement provide complementary signals. These findings support a grounded agentic workflow that separates evidence integration, tool-based refinement, and LLM-assisted diagnostic review for retrospective variant prioritization in genetic birth defects.

q-bio.GN↗

arXiv2025

Multi-Omics Analysis for Cancer Subtype Inference via Unrolling Graph Smoothness Priors

Integrating multi-omics datasets through data-driven analysis offers a comprehensive understanding of the complex biological processes underlying various diseases, particularly cancer. Graph Neural Networks (GNNs) have recently demonstrated remarkable ability to exploit relational structures in biological data, enabling advances in multi-omics integration for cancer subtype classification. Existing approaches often neglect the intricate coupling between heterogeneous omics, limiting their capacity to resolve subtle cancer subtype heterogeneity critical for precision oncology. To address these limitations, we propose a framework named Graph Transformer for Multi-omics Cancer Subtype Classification (GTMancer). This framework builds upon the GNN optimization problem and extends its application to complex multi-omics data. Specifically, our method leverages contrastive learning to embed multi-omics data into a unified semantic space. We unroll the multiplex graph optimization problem in that unified space and introduce dual sets of attention coefficients to capture structural graph priors both within and among multi-omics data. This approach enables global omics information to guide the refining of the representations of individual omics. Empirical experiments on seven real-world cancer datasets demonstrate that GTMancer outperforms existing state-of-the-art algorithms.

cs.LG↗

arXiv2025

Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors

In recent years, Graph Convolutional Networks (GCNs) have gained popularity for their exceptional ability to process graph-structured data. Existing GCN-based approaches typically employ a shallow model architecture due to the over-smoothing phenomenon. Current approaches to mitigating over-smoothing primarily involve adding supplementary components to GCN architectures, such as residual connections and random edge-dropping strategies. However, these improvements toward deep GCNs have achieved only limited success. In this work, we analyze the intrinsic message passing mechanism of GCNs and identify a critical issue: messages originating from high-order neighbors must traverse through low-order neighbors to reach the target node. This repeated reliance on low-order neighbors leads to redundant information aggregation, a phenomenon we term over-aggregation. Our analysis demonstrates that over-aggregation not only introduces significant redundancy but also serves as the fundamental cause of over-smoothing in GCNs.

cs.LG↗