William Andrew Simon

William Andrew Simon, Una Pale, Tomas Teijeiro et al.

HyperDimensional Computing (HDC) as a machine learning paradigm is highly interesting for applications involving continuous, semi-supervised learning for long-term monitoring. However, its accuracy is not yet on par with other Machine Learning (ML) approaches. Frameworks enabling fast design space exploration to find practical algorithms are necessary to make HD computing competitive with other ML techniques. To this end, we introduce HDTorch, an open-source, PyTorch-based HDC library with CUDA extensions for hypervector operations. We demonstrate HDTorch's utility by analyzing four HDC benchmark datasets in terms of accuracy, runtime, and memory consumption, utilizing both classical and online HD training methodologies. We demonstrate average (training)/inference speedups of (111x/68x)/87x for classical/online HD, respectively. Moreover, we analyze the effects of varying hyperparameters on runtime and accuracy. Finally, we demonstrate how HDTorch enables exploration of HDC strategies applied to large, real-world datasets. We perform the first-ever HD training and inference analysis of the entirety of the CHB-MIT EEG epilepsy database. Results show that the typical approach of training on a subset of the data does not necessarily generalize to the entire dataset, an important factor when developing future HD models for medical wearable devices.

William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi et al.

Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently processed in energy-hungry computer clusters and centers, necessitating data transfer, consuming substantial energy, and wasting valuable time. Therefore, there is a need for fast, energy-efficient, and cost-efficient technologies that enable genomics research without requiring data centers and cloud platforms. We recently launched the BioPIM Project to leverage emerging processing-in-memory (PIM) technologies to enable energy- and cost-efficient analysis of bioinformatics workloads. The BioPIM Project focuses on co-designing algorithms and data structures commonly used in genomics with several PIM architectures to achieve the highest cost, energy, and time savings.

Riselda Kodra, Hadjer Benmeziane, Irem Boybat et al.

The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile signals coming from sequencing devices in parallel with determining their nucleotide sequences, a process known as basecalling, via a multi-objective deep neural network for simultaneous basecalling and multi-class genome classification. We introduce a new loss strategy where losses for basecalling and classification are back-propagated separately, with model weights combined for the shared layers, and a pre-configured ranking strategy allowing top-K species accuracy, giving users flexibility to choose between higher accuracy or higher speed at identifying the species. We achieve state-of-the-art basecalling accuracies, while classification accuracies meet and exceed the results of state-of-the-art binary classifiers, attaining an average of 92.5%/98.9% accuracy at identifying the top-1/3 species among a total of 17 genomes in the Wick bacterial dataset. The work presented here has implications for future studies in metagenomic profiling by accelerating the bottleneck step of matching the DNA sequence to the correct genome.