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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…
Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…
Herding is a technique to sequentially generate deterministic samples from a probability distribution. In this work, we propose a continuous herded Gibbs sampler that combines kernel herding on continuous densities with the Gibbs sampling…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
Making large language models (LLMs) more efficient in memory, latency, and serving cost is crucial for edge deployment, interactive applications, and sustainable inference at scale. Pruning is a promising technique, but existing pruning…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
Discovering valuable insights from rich data is a crucial task for exploratory data analysis. Sequential pattern mining (SPM) has found widespread applications across various domains. In recent years, low-utility sequential pattern mining…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
Large Language Models (LLMs) have demonstrated remarkable proficiency in language comprehension and generation; however, their widespread adoption is constrained by substantial bandwidth and computational demands. While pruning and low-rank…
The problem of finding aperiodic low auto-correlation binary sequences (LABS) presents a significant computational challenge, particularly as the sequence length increases. Such sequences have important applications in communication…
This paper shows how Long Short-term Memory recurrent neural networks can be used to generate complex sequences with long-range structure, simply by predicting one data point at a time. The approach is demonstrated for text (where the data…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
Spiking Neural Networks (SNNs) event-driven nature enables efficient encoding of spatial and temporal features, making them suitable for dynamic time-dependent data processing. Despite their biological relevance, SNNs have seen limited…
High throughput technologies have become the practice of choice for comparative studies in biomedical applications. Limited number of sample points due to sequencing cost or access to organisms of interest necessitates the development of…
How can we efficiently compress Convolutional Neural Network (CNN) while retaining their accuracy on classification tasks? Depthwise Separable Convolution (DSConv), which replaces a standard convolution with a depthwise convolution and a…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…