Minsi Lu

dblp:358/9629 · DBLP profile ↗
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2ranked-venue papers
0as first author
2since 2021 · last 2024
—ORCID · none

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

Artificial intelligence and machine learning · 1 · 1 since 2021Applied, interdisciplinary, general and emerging computing · 1 · 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
2 papers
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Vision and language · 77% Representation and self-supervised learning · 23%

Topics — the 6 heaviest of 6, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › epigenomics
chromatin conformation analysis
0.812024
Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model · Bioinform. 2024
Computer vision › Vision and language › vision-language pretraining
contrastive vision-language pretraining
0.712023
DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening · NeurIPS 2023
Bioinformatics and computational biology
drug discovery
0.712023
DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening · NeurIPS 2023
Bioinformatics and computational biology › drug discovery
virtual screening
0.712023
DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening · NeurIPS 2023
Bioinformatics and computational biology › epigenomics › chromatin interaction analysis
chromatin loop calling
0.212024
Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model · Bioinform. 2024
Machine learning › Representation and self-supervised learning
contrastive learning
0.212023
DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening · NeurIPS 2023

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

protein-molecule representation learning · 1.3contrastive learning · 1.3multi-view learning · 0.8diffusion model · 0.8
YearPublicationVenuePosition
2024 Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model
abstract
MOTIVATION: High-resolution Hi-C contact matrices reveal the detailed three-dimensional architecture of the genome, but high-coverage experimental Hi-C data are expensive to generate. Simultaneously, chromatin structure analyses struggle with extremely sparse contact matrices. To address this problem, computational methods to enhance low-coverage contact matrices have been developed, but existing methods are largely based on resolution enhancement methods for natural images and hence often employ models that do not distinguish between biologically meaningful contacts, such as loops and other stochastic contacts. RESULTS: We present Capricorn, a machine learning model for Hi-C resolution enhancement that incorporates small-scale chromatin features as additional views of the input Hi-C contact matrix and leverages a diffusion probability model backbone to generate a high-coverage matrix. We show that Capricorn outperforms the state of the art in a cross-cell-line setting, improving on existing methods by 17% in mean squared error and 26% in F1 score for chromatin loop identification from the generated high-coverage data. We also demonstrate that Capricorn performs well in the cross-chromosome setting and cross-chromosome, cross-cell-line setting, improving the downstream loop F1 score by 14% relative to existing methods. We further show that our multiview idea can also be used to improve several existing methods, HiCARN and HiCNN, indicating the wide applicability of this approach. Finally, we use DNA sequence to validate discovered loops and find that the fraction of CTCF-supported loops from Capricorn is similar to those identified from the high-coverage data. Capricorn is a powerful Hi-C resolution enhancement method that enables scientists to find chromatin features that cannot be identified in the low-coverage contact matrix. AVAILABILITY AND IMPLEMENTATION: Implementation of Capricorn and source code for reproducing all figures in this paper are available at https://github.com/CHNFTQ/Capricorn.
Tangqi Fang, Yifeng Liu 0004, Addie Woicik, Minsi Lu, Anupama Jha, Xiao Wang 0013, Gang Li 0034, Borislav H. Hristov, Zixuan Liu 0001, William Stafford Noble, Sheng Wang 0012
Bioinform.4
2023 DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening
Bo Qiang, Haichuan Tan, Yinjun Jia, Minsi Ren, Minsi Lu, Wei-Ying Ma, Yanyan Lan
NeurIPS6