Adam Porter

Alan F. Karr, Zac Bowen, Adam A. Porter et al.

Classifiers assign complex input data points to one of a small number of output categories. For a Bayes classifier whose input space is a graph, we study the structure of the \emph{boundary}, which comprises those points for which at least one neighbor is classified differently. The scientific setting is assignment of DNA reads produced by \NGSs\ to candidate source genomes. The boundary is both large and complicated in structure. We introduce a new measure of uncertainty, Neighbor Similarity, that compares the result for an input point to the distribution of results for its neighbors. This measure not only tracks two inherent uncertainty measures for the Bayes classifier, but also can be implemented for classifiers without inherent measures of uncertainty.

Rohan Reddy Mekala, Elias Garratt, Matthias Muehle et al.

Process refinement to consistently produce high-quality material over a large area of the grown crystal, enabling various applications from optics crystals to quantum detectors, has long been a goal for diamond growth. Machine learning offers a promising path toward this goal, but faces challenges such as the complexity of features within datasets, their time-dependency, and the volume of data produced per growth run. Accurate spatial feature extraction from image to image for real-time monitoring of diamond growth is crucial yet complicated due to the low-volume and high feature complexity nature of the datasets. This paper compares various traditional and machine learning-driven approaches for feature extraction in the diamond growth domain, proposing a novel deep learning-driven semantic segmentation approach to isolate and classify accurate pixel masks of geometric features like diamond, pocket holder, and background, along with their derivative features based on shape and size. Using an annotation-focused human-in-the-loop software architecture for training datasets, with modules for selective data labeling using active learning, data augmentations, and model-assisted labeling, our approach achieves effective annotation accuracy and drastically reduces labeling time and cost. Deep learning algorithms prove highly efficient in accurately learning complex representations from datasets with many features. Our top-performing model, based on the DeeplabV3plus architecture, achieves outstanding accuracy in classifying features of interest, with accuracies of 96.31% for pocket holder, 98.60% for diamond top, and 91.64% for diamond side features.

Rohan Reddy Mekala, Elias Garratt, Matthias Muehle et al.

From a process development perspective, diamond growth via chemical vapor deposition has made significant strides. However, challenges persist in achieving high quality and large-area material production. These difficulties include controlling conditions to maintain uniform growth rates for the entire growth surface. As growth progresses, various factors or defect states emerge, altering the uniform conditions. These changes affect the growth rate and result in the formation of crystalline defects at the microscale. However, there is a distinct lack of methods to identify these defect states and their geometry using images taken during the growth process. This paper details seminal work on defect segmentation pipeline using in-situ optical images to identify features that indicate defective states that are visible at the macroscale. Using a semantic segmentation approach as applied in our previous work, these defect states and corresponding derivative features are isolated and classified by their pixel masks. Using an annotation focused human-in-the-loop software architecture to produce training datasets, with modules for selective data labeling using active learning, data augmentations, and model-assisted labeling, our approach achieves effective annotation accuracy and drastically reduces the time and cost of labeling by orders of magnitude. On the model development front, we found that deep learning-based algorithms are the most efficient. They can accurately learn complex representations from feature-rich datasets. Our best-performing model, based on the YOLOV3 and DeeplabV3plus architectures, achieved excellent accuracy for specific features of interest. Specifically, it reached 93.35% accuracy for center defects, 92.83% for polycrystalline defects, and 91.98% for edge defects.

Alan F. Karr, Jason Hauzel, Adam A. Porter et al.

In this paper we apply the structure of genomes as second-order Markov processes specified by the distributions of successive triplets of bases to two bioinformatics problems: identification of outliers in genome databases and read classification in metagenomics, using real coronavirus and adenovirus data.

Alan F. Karr, Jason Hauzel, Adam A. Porter et al.

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.

Alan F. Karr, Jason Hauzel, Prahlad Menon et al.

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.

Rohan Reddy Mekala, Gudjon Einar Magnusson, Adam Porter et al.

Adversarial attacks are small, carefully crafted perturbations, imperceptible to the naked eye; that when added to an image cause deep learning models to misclassify the image with potentially detrimental outcomes. With the rise of artificial intelligence models in consumer safety and security intensive industries such as self-driving cars, camera surveillance and face recognition, there is a growing need for guarding against adversarial attacks. In this paper, we present an approach that uses metamorphic testing principles to automatically detect such adversarial attacks. The approach can detect image manipulations that are so small, that they are impossible to detect by a human through visual inspection. By applying metamorphic relations based on distance ratio preserving affine image transformations which compare the behavior of the original and transformed image; we show that our proposed approach can determine whether or not the input image is adversarial with a high degree of accuracy.

ThanhVu Nguyen, Ugur Koc, Javran Cheng et al.

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.