Kuan-Hao Chao, a PhD student in the Department of Computer Science affiliated with the Center for Computational Biology, has been awarded a 2024 Mark O. Robbins Prize in High-Performance Computing.
The Robbins Prize was instigated in 2020 to recognize outstandingly talented PhD students who reflect Robbins’ contributions to computational science and engineering.
Chao utilizes high-performance computing to process large-scale genomic sequences and train deep learning models to decode patterns in DNA sequences. He is advised by Steven Salzberg, the Bloomberg Distinguished Professor of Computational Biology and Genomics, and Mihaela Pertea, an associate professor of biomedical engineering also affiliated with the Department of Computer Science.
Chao’s current work includes developing deep residual convolutional neural networks—a type of deep learning model—to predict RNA splice sites from DNA sequences, enabling a better understanding of splicing machinery and the prediction of the effects of mutations. He is also collaborating with Calico, a biotechnology company owned by Alphabet Inc., to build a large DNA language model from thousands of fungus genomes to better understand yeast gene regulation in the hopes of providing insights that can be applied to more complex organisms, like humans.
His other achievements in computational genomics include the assembly and annotation of the first complete Southern Chinese Han genome, Han1, and the development of a new graph recognition algorithm and toolkit to help address the limitations of the current human reference genome—both parts of an ongoing effort to combat the Eurocentric bias in human genomics research. Chao also developed LiftOn, a tool that improves the transference of annotations from the current standard human reference genome to a more recent assembly that represents the first truly complete human genome sequence.
Winners of the Robbins prize will receive a commemorative plaque and will be invited to present their work at an upcoming conference sponsored by Advanced Research Computing at Hopkins.
Mark O. Robbins was a professor in the Department of Physics and Astronomy at Johns Hopkins from 1986 until his untimely death in 2020. He was a renowned condensed matter and statistical physicist who played a key role in supporting the development of computational facilities at Johns Hopkins through his leadership for the Maryland Advanced Research Computing Center in the Institute for Data Intensive Engineering and Science (IDIES).
The Robbins Prize is made possible thanks to generous donations from IDIES, the Department of Chemical and Biomolecular Engineering, the Hopkins Extreme Materials Institute, the Department of Mechanical Engineering, and the the Department of Physics and Astronomy.