Genetic Sequence Matching Using D4M Big Data Approaches

Recent technological advances in Next Generation Sequencing tools have led to increasing speeds of DNA sample collection, preparation, and sequencing. One instrument can produce over 600 Gb of genetic sequence data in a single run. This creates new opportunities to efficiently handle the increasing workload. We propose a new method of fast genetic sequence analysis using the Dynamic Distributed Dimensional Data Model (D4M) - an associative array environment for MATLAB developed at MIT Lincoln Laboratory. Based on mathematical and statistical properties, the method leverages big data techniques and the implementation of an Apache Acculumo database to accelerate computations one-hundred fold over other methods. Comparisons of the D4M method with the current gold-standard for sequence analysis, BLAST, show the two are comparable in the alignments they find. This paper will present an overview of the D4M genetic sequence algorithm and statistical comparisons with BLAST.Comment: 6 pages; to appear in IEEE High Performance Extreme Computing (HPEC) 201

Personalized Purchase Prediction of Market Baskets with Wasserstein-Based Sequence Matching

Personalization in marketing aims at improving the shopping experience of customers by tailoring services to individuals. In order to achieve this, businesses must be able to make personalized predictions regarding the next purchase. That is, one must forecast the exact list of items that will comprise the next purchase, i.e., the so-called market basket. Despite its relevance to firm operations, this problem has received surprisingly little attention in prior research, largely due to its inherent complexity. In fact, state-of-the-art approaches are limited to intuitive decision rules for pattern extraction. However, the simplicity of the pre-coded rules impedes performance, since decision rules operate in an autoregressive fashion: the rules can only make inferences from past purchases of a single customer without taking into account the knowledge transfer that takes place between customers. In contrast, our research overcomes the limitations of pre-set rules by contributing a novel predictor of market baskets from sequential purchase histories: our predictions are based on similarity matching in order to identify similar purchase habits among the complete shopping histories of all customers. Our contributions are as follows: (1) We propose similarity matching based on subsequential dynamic time warping (SDTW) as a novel predictor of market baskets. Thereby, we can effectively identify cross-customer patterns. (2) We leverage the Wasserstein distance for measuring the similarity among embedded purchase histories. (3) We develop a fast approximation algorithm for computing a lower bound of the Wasserstein distance in our setting. An extensive series of computational experiments demonstrates the effectiveness of our approach. The accuracy of identifying the exact market baskets based on state-of-the-art decision rules from the literature is outperformed by a factor of 4.0.Comment: Accepted for oral presentation at 25th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2019

Root Mean Square Error of Neural Spike Train Sequence Matching with Optogenetics

Optogenetics is an emerging field of neuroscience where neurons are genetically modified to express light-sensitive receptors that enable external control over when the neurons fire. Given the prominence of neuronal signaling within the brain and throughout the body, optogenetics has significant potential to improve the understanding of the nervous system and to develop treatments for neurological diseases. This paper uses a simple optogenetic model to compare the timing distortion between a randomly-generated target spike sequence and an externally-stimulated neuron spike sequence. The distortion is measured by filtering each sequence and finding the root mean square error between the two filter outputs. The expected distortion is derived in closed form when the target sequence generation rate is sufficiently low. Derivations are verified via simulations.Comment: 6 pages, 5 figures. Will be presented at IEEE Global Communications Conference (IEEE GLOBECOM 2017) in December 201