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DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Motivation: The analysis of antibodies and T-cell receptors (TCRs) concentrations in serum is a fundamental problem in immunoinformatics. Repertoire construction is a preliminary step of analysis of clonal lineages, understanding of immune…
Recent successes in deep learning have started to impact neuroscience. Of particular significance are claims that current segmentation algorithms achieve "super-human" accuracy in an area known as connectomics. However, as we will show,…
The origin of species has been the mystery of mysteries in natural science. By analogy, the origin of synthetic information, we suggest, is the mystery of mysteries in information science. The question carries a moral weight that a…
Recent advances in Large Language Models have led to Large Reasoning Models, which produce step-by-step reasoning traces. These traces offer insight into how models think and their goals, improving explainability and helping users follow…
The inversion of linear systems is a fundamental step in many inverse problems. Computational challenges exist when trying to invert large linear systems, where limited computing resources mean that only part of the system can be kept in…
Computed tomography has propelled scientific advances in fields from biology to materials science. This technology allows for the elucidation of 3-dimensional internal structure by the attenuation of x-rays through an object at different…
Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
When debugging unintended program behavior, developers can often identify the point in the execution where the actual behavior diverges from the desired behavior. For example, a variable may get assigned a wrong value, which then negatively…
This paper deals with gene networks whose dynamics is assumed to be generated by a continuous-time, linear, time invariant, finite dimensional system (LTI) at steady state. In particular, we deal with the problem of network reconstruction…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
Computed tomography (CT) has become an essential part of modern science and medicine. A CT scanner consists of an X-ray source that is spun around an object of interest. On the opposite end of the X-ray source, a detector captures X-rays…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Systematic techniques to improve quality of deep neural networks (DNNs) are critical given the increasing demand for practical applications including safety-critical ones. The key challenge comes from the little controllability in updating…
Erasure coding techniques are getting integrated in networked distributed storage systems as a way to provide fault-tolerance at the cost of less storage overhead than traditional replication. Redundancy is maintained over time through…
The advancement of sensing technology has driven the widespread application of high-dimensional data. However, issues such as missing entries during acquisition and transmission negatively impact the accuracy of subsequent tasks. Tensor…
Accelerating the data acquisition of dynamic magnetic resonance imaging (MRI) leads to a challenging ill-posed inverse problem, which has received great interest from both the signal processing and machine learning community over the last…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…