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Advances in third-generation sequencing have enabled portable and real-time genomic sequencing, but real-time data processing remains a bottleneck, hampering on-site genomic analysis due to prohibitive time and energy costs. These…

Nanobodies -- single-domain antibody fragments derived from camelid heavy-chain-only antibodies -- exhibit unique advantages such as compact size, high stability, and strong binding affinity, making them valuable tools in therapeutics and…

Nanopore sequencing, a next-generation sequencing technology, holds the potential to revolutionize multiple facets of life sciences, forensics, and healthcare. While previous research has focused on its technical intricacies and biomedical…

RNA plays a pivotal role in diverse biological processes, ranging from gene regulation to catalysis. Recent advances in RNA design, such as RfamGen, Ribodiffusion and RDesign, have demonstrated promising results, with successful designs of…

Recent advancements in sensing, measurement, and computing technologies have significantly expanded the potential for signal-based applications, leveraging the synergy between signal processing and Machine Learning (ML) to improve both…

Many benchmarks for automated causal inference evaluate a system's performance based on a single numerical output, such as an Average Treatment Effect (ATE). This approach conflates two distinct steps in causal analysis: identification -…

In recent years, speaker recognition systems based on raw waveform inputs have received increasing attention. However, the performance of such systems are typically inferior to the state-of-the-art handcrafted feature-based counterparts,…

Sound sources localization using multichannel signal processing has been a subject of active research for decades. In recent years, the use of deep learning in audio signal processing has allowed to drastically improve performances for…

Continuous dynamical systems, characterized by differential equations, are ubiquitously used to model several important problems: plasma dynamics, flow through porous media, weather forecasting, and epidemic dynamics. Recently, a wide range…

Retrieval-Augmented Generation (RAG) enhances the response capabilities of language models by integrating external knowledge sources. However, document chunking as an important part of RAG system often lacks effective evaluation tools. This…

Benchmarking quantum devices is a foundational task for the sustained development of quantum technologies. However, accurate in situ characterization of large-scale quantum devices remains a formidable challenge: such systems experience…

Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost, and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and…

We describe a new convolutional framework for waveform evaluation, WEnets, and build a Narrowband Audio Waveform Evaluation Network, or NAWEnet, using this framework. NAWEnet is single-ended (or no-reference) and was trained three separate…

This thesis addresses challenges related to data and parameter efficiency in neural language models, with a focus on representation analysis and the introduction of new optimization techniques. The first part examines the properties and…

Deep Neural Networks (DNN) are core components for classification and regression tasks of many software systems. Companies incur in high costs for testing DNN with datasets representative of the inputs expected in operation, as these need…

Kernel methods are ubiquitous tools in machine learning. However, there is often little reason for the common practice of selecting a kernel a priori. Even if a universal approximating kernel is selected, the quality of the finite sample…

Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…

Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…

In drug discovery, mapping interactions between genes within cellular systems is a crucial early step. Such maps are not only foundational for understanding the molecular mechanisms underlying disease biology but also pivotal for…

Large Language Models (LLMs) have greatly advanced code auto-completion systems, with a potential for substantial productivity enhancements for developers. However, current benchmarks mainly focus on single-file tasks, leaving an assessment…