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Adam A. Porter

Publications and source records attributed to Adam A. Porter.

5 recordsLinked to original sources
arXiv2022

Structure of Classifier Boundaries: Case Study for a Naive Bayes Classifier

For a Bayes classifier whose input space is a graph, we study the structure of the boundary, which comprises those points for which at least one neighbor is classified differently. The scientific setting is assignment of DNA reads produced by next generations sequencers to candidate source genomes. We show that the boundary is both large and complicated in structure. A new measure of uncertainty, Neighbor Similarity, which compares the classifier result for an input point to the distribution of results for its neighbors, not only tracks two inherent uncertainty measures for the Bayes classifier, but also can be implemented for classifiers without inherent measures of uncertainty.

stat.ML↗
arXiv2021

Measuring Quality of DNA Sequence Data via Degradation

We propose and apply a novel paradigm for characterization of genome data quality, which quantifies the effects of intentional degradation of quality. The rationale is that the higher the initial quality, the more fragile the genome and the greater the effects of degradation. We demonstrate that this phenomenon is ubiquitous, and that quantified measures of degradation can be used for multiple purposes. We focus on identifying outliers that may be problematic with respect to data quality, but might also be true anomalies or even attempts to subvert the database.

stat.ML↗
arXiv2021

Specified Certainty Classification, with Application to Read Classification for Reference-Guided Metagenomic Assembly

Specified Certainty Classification (SCC) is a new paradigm for employing classifiers whose outputs carry uncertainties, typically in the form of Bayesian posterior probabilities. By allowing the classifier output to be less precise than one of a set of atomic decisions, SCC allows all decisions to achieve a specified level of certainty, as well as provides insights into classifier behavior by examining all decisions that are possible. Our primary illustration is read classification for reference-guided genome assembly, but we demonstrate the breadth of SCC by also analyzing COVID-19 vaccination data.

q-bio.QM↗
arXiv2019

iGen: Dynamic Interaction Inference for Configurable Software

To develop, analyze, and evolve today's highly configurable software systems, developers need deep knowledge of a system's configuration options, e.g., how options need to be set to reach certain locations, what configurations to use for testing, etc. Today, acquiring this detailed information requires manual effort that is difficult, expensive, and error prone. In this paper, we propose iGen, a novel, lightweight dynamic analysis technique that automatically discovers a program's \emph{interactions}---expressive logical formulae that give developers rich and detailed information about how a system's configuration option settings map to particular code coverage. iGen employs an iterative algorithm that runs a system under a small set of configurations, capturing coverage data; processes the coverage data to infer potential interactions; and then generates new configurations to further refine interactions in the next iteration. We evaluated iGen on 29 programs spanning five languages; the breadth of this study would be unachievable using prior interaction inference tools. Our results show that iGen finds precise interactions based on a very small fraction of the number of possible configurations. Moreover, iGen's results confirm several earlier hypotheses about typical interaction distributions and structures.

cs.SE↗