VLDB 2026 Research / reviewers in the wild / expert
Patrick Hsu
dblp:241/8037
· DBLP profile ↗
1ranked-venue papers
0as first author
1since 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 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% |
Topics — the 2 heaviest of 2, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › synthetic biology
biological sequence design |
0.8 | 1 | 2024 | Designing Cell-Type-Specific Promoter Sequences Using Conservative Model-Based Optimization · NeurIPS 2024 |
Bioinformatics and computational biology
gene regulation |
0.8 | 1 | 2024 | Designing Cell-Type-Specific Promoter Sequences Using Conservative Model-Based Optimization · NeurIPS 2024 |
Methods — techniques the papers use, named apart from their topics
model-based optimization · 0.8conservative objective models · 0.8
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | Designing Cell-Type-Specific Promoter Sequences Using Conservative Model-Based OptimizationabstractGene therapies have the potential to treat disease by delivering therapeutic genetic cargo to disease-associated cells. One limitation to their widespread use is the lack of short regulatory sequences, or promoters, that differentially induce the expression of delivered genetic cargo in target cells, minimizing side effects in other cell types. Such cell-type-specific promoters are difficult to discover using existing methods, requiring either manual curation or access to large datasets of promoter-driven expression from both targeted and untargeted cells. Model-based optimization (MBO) has emerged as an effective method to design biological sequences in an automated manner, and has recently been used in promoter design methods. However, these methods have only been tested using large training datasets that are expensive to collect, and focus on designing promoters for markedly different cell types, overlooking the complexities associated with designing promoters for closely related cell types that share similar regulatory features. Therefore, we introduce a comprehensive framework for utilizing MBO to design promoters in a data-efficient manner, with an emphasis on discovering promoters for similar cell types. We use conservative objective models (COMs) for MBO and highlight practical considerations such as best practices for improving sequence diversity, getting estimates of model uncertainty, and choosing the optimal set of sequences for experimental validation. Using three leukemia cell lines (Jurkat, K562, and THP1), we show that our approach discovers many novel cell-type-specific promoters after experimentally validating the designed sequences. For K562 cells, in particular, we discover a promoter that has 75.85\% higher cell-type-specificity than the best promoter from the initial dataset used to train our models. Our code and data will be available at https://github.com/young-geng/promoter_design. Aniketh Janardhan Reddy, Xinyang Geng, Michael Herschl, Sathvik Kolli, Aviral Kumar, Patrick Hsu, Sergey Levine, Nilah Ioannidis |
NeurIPS | 6 |