EDBT 2026 Demo / reviewers in the wild / expert
Minsi Lu
dblp:358/9629
· DBLP profile ↗
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
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › epigenomics
chromatin conformation analysis |
0.8 | 1 | 2024 | 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 |
0.7 | 1 | 2023 | DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening · NeurIPS 2023 |
Bioinformatics and computational biology
drug discovery |
0.7 | 1 | 2023 | DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening · NeurIPS 2023 |
Bioinformatics and computational biology › drug discovery
virtual screening |
0.7 | 1 | 2023 | DrugCLIP: Contrasive Protein-Molecule Representation Learning for Virtual Screening · NeurIPS 2023 |
Bioinformatics and computational biology › epigenomics › chromatin interaction analysis
chromatin loop calling |
0.2 | 1 | 2024 | 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 |
0.2 | 1 | 2023 | 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
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion modelabstractMOTIVATION: 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 |
NeurIPS | 6 |