Hongyi Xin

Research Assistant | hxin at cmu.edu

I'm a sixth year PhD student at Carnegie Mellon University. My advisor is professor Carl Kingsford. I am also unofficially advised by professor Can Alkan and I have previously worked with professor Onur Mutlu. My primary field of research is Bioinformatics with casual crossovers to computer architecture and system research.


Doctor Philosophiae in Computer Science
Carnegie Mellon University



LEAP: A Generalization of the Landau-Vishkin Algorithm with Custom Gap Penalties
Hongyi Xin, Jeremie Kim, Sunny Nahar, Can Alkan, Onur Mutlu

An extension to the dynamic-programming algorithm, the Landau-Vishkin algorithm, to support custom gap penalties. We also propose a further optimization to speed up the LCA-searching process using the de Bruijn sequence technique.
PDF Article     Slides PPT    

Optimal Seed Solver: Optimizing Seed Selection in Read Mapping
Hongyi Xin, Richard Zhu, Sunny Nahar, John Emmons, Gennady Pekhimenko,
Carl Kingsford, Can Alkan, Onur Mutlu

A linear dynamic-programming algorithm that divides DNA short reads into non-overlapping seeds such that the over all frequency of all seeds in the reference genome is minimized.
PDF Article     Supplementary Materials     Poster PDF

Oxford Bioinformatics, Volume 32, Issue 11,
May 2016

Shifted Hamming Distance: A Fast and Accurate SIMD-Friendly Filter for Local Alignment in Read Mapping
Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford,
Can Alkan, Onur Mutlu

A SIMD-friendly algorithm that approximates the edit-distance calculation using bit-vectors. Can be used as a filter for general DNA short read mapping.
PDF Article     Supplementary Materials     Poster PDF

Oxford Bioinformatics, Volume 31 Issue 10,
June 2015

Mitigating Prefetcher-Caused Pollution using Informed Caching Policies for Prefetched Blocks
Vivek Seshadri, Samihan Yedkar, Hongyi Xin, Onur Mutlu,
Phillip B. Gibbons,Michael A. Kozuch, Todd Mowry

A mechanism to reduce cache pollution caused by inaccurate prefetching.
PDF Article

TACO, Volume 11 Number 4,
January 2015

Fast and Accurate Mapping of Complete Genomics Reads
Donghyuk Lee, Farhad Hormozdiari, Hongyi Xin, Faraz Hach, Can Alkan,
Onur Mutlu

A mapper for complete genomics DNA sequencing technology.
PDF Article    

Methods (Elsevier), Volume 79-80, June 2015

Linearly Compressed Pages: A Low-Complexity, Low-Latency Main Memory Compression Framework
Gennady Pekhimenko, Vivek Seshadri, Yoongu Kim, Hongyi Xin,
Onur Mutlu, Michael A. Kozuch, Phillip B. Gibbons, and Todd C. Mowry

A memory mechanism that efficiently identifies and compresses data with similar patterns.
PDF Article

MICRO 2013 Davis, CA, December 2013

Accelerating Read Mapping with FastHASH
Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Samihan Yedkar, Onur Mutlu, and Can Alkan

A major upgrade to short read mapper mrFAST, which increase the speed by 6x, with novel filtering and improved seed selection mechanisms.
PDF Article     Supplementary Materials     Slides PPT

BMC Genomics 2013, Volume 14(Suppl 1):S13,
January 2013

A Case for Unlimited Watchpoints
Joseph GreatHouse, Hongyi Xin, Yixin Luo, and Todd Austin

A novel architecture that supports unlimited watchpoints which efficiently tag ranges of virtual memory addresses and raise exceptions when tagged memory is accessed/modified, depending on the flag.
PDF Article     Slides PPT

ASPLOS 2012, London, UK,
March 2012


<Optimal Seeds Solver>
Git-repository:   https://github.com/CMU-SAFARI/optimal-seed-solver

<Shifted Hamming Distance>
Git-repository:   https://github.com/CMU-SAFARI/Shifted-Hamming-Distance


Research Summer Intern
Microsoft Research

During my 3-month internship at MSR Redmond, I worked on mapping linked reads with SNAP. Specifically, I investigated the benefit of using linked reads, from both the mapping perspective and structural variant calling perspective. I also developed a novel mapping strategy to more efficiently map linked reads and integrated the new algorithm into the mapper SNAP.

Summer 2016

Research Summer Intern
IBM Research

During my 3 month internship, I worked on accelerating map-reduce based analytics applications (which typically employs machine learning algorithms) with distributed GPU clusters. I worked with Jayaram K. R., Shu Tao and Anshul Gandhi. I had a great summer there.

Summer 2014


Bread and butter

Absolute C++, Walter Savitch.
From Genes to Genomes, by Jeremy W. Dale, Malcolm Von Schantz and Nick Plant.
A Primer of Genome Science, by Greg Gibson and Spencer V. Muse.
Computer Architecture: a Quantitative Approach, by David Patterson and John Hennessy.
Data Structures and Algorithms, by Alfred V. Aho.
Algorithm Design, by Jon Kleinberg and √Čva Tardos.
Introduction to Algorithm, by Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest, and Clifford Stein.
Calculus: Early Transcendentals, by James Stewart.

Soup of life

Wealth of Nations, by Adam Smith.
Relativity: The Special and General Theory, by Albert Einstein.
War and Peace, by Leo Tolstoy.
Art of War, by Sun Zi.
Zhan Guo Ce, anonymous.
Encouragement of learning, by Fukuzawa Yukichi.
Animal Farm, by George Orwell.
Presentation Zen, by Garr Reynolds.


hxin at cmu.edu


Copywrite © 2016 Hongyi Xin