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Hongru Hu

dblp:342/3565 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper

Topics — the 4 heaviest of 5, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology
gene expression analysis
0.912025
sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models · ICML 2025
Bioinformatics and computational biology › gene expression analysis › gene co-expression analysis
gene module discovery
0.912025
sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models · ICML 2025
Bioinformatics and computational biology
single-cell analysis
0.912025
sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models · ICML 2025
Bioinformatics and computational biology › single-cell analysis
single-cell representation learning
0.912025
sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models · ICML 2025

Methods — techniques the papers use, named apart from their topics

variational autoencoder · 1.7large language model · 1.7gene embedding · 1.7
YearPublicationVenuePosition
2025 sciLaMA: A Single-Cell Representation Learning Framework to Leverage Prior Knowledge from Large Language Models
abstract
Single-cell RNA sequencing (scRNA-seq) enables high-resolution exploration of cellular diversity and gene regulation, yet analyzing such data remains challenging due to technical and methodological limitations. Existing task-specific deep generative models like Variational Auto-Encoder (VAE) and its variants struggle to incorporate external biological knowledge, while transformer-based foundational large Language Models (LLMs or large LaMs) face limitations in computational cost and applicability to tabular gene expression data. Here, we introduce sciLaMA (single-cell interpretable Language Model Adapter), a novel representation learning framework that bridges these gaps by integrating static gene embeddings from multimodal LaMs with scRNA-seq tabular data through a paired-VAE architecture. Our approach generates context-aware representations for both cells and genes and outperforms state-of-the-art methods in key single-cell downstream tasks, including batch effect correction, cell clustering, and cell-state-specific gene marker and module identification, while maintaining computational efficiency. sciLaMA offers a computationally efficient, unified framework for comprehensive single-cell data analysis and biologically interpretable gene module discovery.
Hongru Hu, Yongin Choi, Venkat S. Malladi, Gerald T. Quon
ICML1