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Category Archives: Presentations
Challenges in Genomics Data Visualization
Genomics, like many fields, is generating data at an ever increasing rate with the promise to enable personalized medicine, improve agriculture, and advance fundamental research. Data visualization is a key component of the scientific process and often the bottleneck in … Continue reading
Functional Big-Data Genomics
Abstract High-throughput genomic sequencing is characterized by large diverse datasets and numerous analysis methods. It is normal for an individual bioinformatician to work with thousands of data files and employ hundreds of distinct computations during the course of a single … Continue reading
Biocaml: The OCaml Bioinformatics Library
Abstract Biology is an increasingly computational discipline due to rapid advances in experimental techniques, especially DNA sequencing, that are generating data at unprecedented rates. The computational techniques needed range from the complex (.e.g algorithms, distributed computing) to the simple (e.g. … Continue reading
Managing and Analyzing Big-Data in Genomics
Abstract Biology is an increasingly computational discipline. Rapid advances in experimental techniques, especially DNA sequencing, are generating data at exponentially increasing rates. Aside from the algorithmic challenges this poses, researchers must manage large volumes and innumerable varieties of data, run … Continue reading
A Domain Specific Language Stack for Bio HPC
We have given several presentations on our DSL approach to the management and analysis of big-data in the field of Biology. Now, with Karl Ward, we have been extending this approach to the systems layer, enabling more robust management and … Continue reading
Shonan Meeting
I’ll be back in Tokyo, this time for the Shonan Meeting on Bridging the Theory of Staged Programming Languages and the Practice of High-Performance Computing. My talk will be on BINQ, a domain-specific-language for genomic computations.
A Type Theory for Probability Density Functions
Abstract There has been great interest in creating probabilistic programming languages to simplify the coding of statistical tasks; however, there still does not exist a formal language that simultaneously provides (1) continuous probability distributions, (2) the ability to naturally express … Continue reading
Presenting at the CScADS Workshop on Autotuning for Petascale Applications
Thanks to Rich Vuduc for inviting me to give a talk at CScADS. Autotuning is an approach for generating efficient code for high performance computing. I’ll try to summarize how my PL work can contribute to and benefit from this … Continue reading
IBM PL Day 2010
Here are the abstract and slides for my talk at IBM PL Day. Title: Mechanizing Optimization and Statistics Abstract: Scientific and engineering investigations are formalized most often in the language of numerical mathematics. The tools supporting this are numerous but … Continue reading
Toward Interactive Statistical Modeling
Abstract When solving machine learning problems, there is currently little automated support for easily experimenting with alternative statistical models or solution strategies. This is because this activity often requires expertise from several different ï¬elds (e.g., statistics, optimization, linear algebra), and … Continue reading
