Tatsunori Hashimoto



Note: I have graduated and moved to stanford university as a post-doc for Percy Liang and John Duchi. I was a fifth-year graduate student in computer science at MIT. Co-advised by Tommi Jaakkola and David Gifford.

Before MIT, I graduated from Harvard University with an A.B. in statistics and mathematics and was advised by Edoardo Airoldi


Writings

Computational biology research

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(w/ R. Sherwood, C. O'Donnell, T. Jaakkola and D. Gifford), Nature biotechnology 32 (2014), 171-178. (journal)
Method for transcription factor binding estimates via analysis of DNAse-I seq data .

Universal Count Correction for High-Throughput Sequencing

(w/ M. Edwards and D. Gifford), PLOS Comp. Bio. 10 (2014), (journal)
Method for controlling marginal overdispersion fo high-throughtput sequending data .

Lineage based identification of cellular states and expression programs.

(w/ T. Jaakkola, D. Gifford), Proceedings of 20th ISMB (2012), (proceedings)
Technique for analyzing lineage-structured gene expression datasets using trace norm penalties

Finding drug discovery rules of thumb with bump hunting

(w/ M. Segall), Proceedings of the ACS (2010) Technique for constructing human-memorizable decision rules based on drug discoery data.

BFL: a node and edge betweenness based fast layout algorithm for large scale networks

(w/ M. Nagasaki, K. Kojima, S. Miyano), BMC Bioinformatics 10 (2009), (journal)

Statistics research

Word, graph, and manifold embedding from Markov processes

(w/ D. Avarez-Melis, T. Jaakkola), Preprint (arXiv)(supplemental data and code)

From random walks to distances on unweighted graphs

(w/ Y.Sun, T. Jaakkola), NIPS 2015, to appear. (preprint)(supplement)

Metric recovery from directed unweighted graphs

(w/ Y. Sun, T. Jaakkola), NIPS workshop on networks (2014, Best student poster), AISTATS (2015), (preprint)
A method to recover both the distance and density on a graph using unweighted edges; shows an equivalence between the random walk and its continuum limit on a geometric graph.

Tree preserving embedding

(w/ A.D Shieh, E.M Airoldi), Proc. Natl. Acad. Sciences (2011), (journal)
Nonlinear dimensionality reduction by preserving cluster constraints defined by clustering

Other research (not primary author)

Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells

(w/ W. Li, D. Gifford, Q. Zhou et al), Nature biotechnology 32 (2014), 1223-1230. (journal)

Quantifying Condition-Dependent Intracellular Protein Levels Enables High-Precision Fitness Estimates

(w/ K.A. Samerotte, E.M. Airoldi), PLOS one. 8 (2013), ( journal )

Code

Universal Count Correction for High-Throughput Sequencing bitbucket

Discovery of directional and nondirectional pioneer transcription factors bitbucket

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