2,384 research outputs found
Automatic differentiation in machine learning: a survey
Derivatives, mostly in the form of gradients and Hessians, are ubiquitous in
machine learning. Automatic differentiation (AD), also called algorithmic
differentiation or simply "autodiff", is a family of techniques similar to but
more general than backpropagation for efficiently and accurately evaluating
derivatives of numeric functions expressed as computer programs. AD is a small
but established field with applications in areas including computational fluid
dynamics, atmospheric sciences, and engineering design optimization. Until very
recently, the fields of machine learning and AD have largely been unaware of
each other and, in some cases, have independently discovered each other's
results. Despite its relevance, general-purpose AD has been missing from the
machine learning toolbox, a situation slowly changing with its ongoing adoption
under the names "dynamic computational graphs" and "differentiable
programming". We survey the intersection of AD and machine learning, cover
applications where AD has direct relevance, and address the main implementation
techniques. By precisely defining the main differentiation techniques and their
interrelationships, we aim to bring clarity to the usage of the terms
"autodiff", "automatic differentiation", and "symbolic differentiation" as
these are encountered more and more in machine learning settings.Comment: 43 pages, 5 figure
The Parallelism Motifs of Genomic Data Analysis
Genomic data sets are growing dramatically as the cost of sequencing
continues to decline and small sequencing devices become available. Enormous
community databases store and share this data with the research community, but
some of these genomic data analysis problems require large scale computational
platforms to meet both the memory and computational requirements. These
applications differ from scientific simulations that dominate the workload on
high end parallel systems today and place different requirements on programming
support, software libraries, and parallel architectural design. For example,
they involve irregular communication patterns such as asynchronous updates to
shared data structures. We consider several problems in high performance
genomics analysis, including alignment, profiling, clustering, and assembly for
both single genomes and metagenomes. We identify some of the common
computational patterns or motifs that help inform parallelization strategies
and compare our motifs to some of the established lists, arguing that at least
two key patterns, sorting and hashing, are missing
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