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Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
Neuromorphic computing, characterized by its event-driven computation and massive parallelism, is particularly effective for handling data-intensive tasks in low-power environments, such as computing the minimum spanning tree (MST) for…
Stochastic nested optimization, including stochastic compositional, min-max and bilevel optimization, is gaining popularity in many machine learning applications. While the three problems share the nested structure, existing works often…
Motivation: The mapping of RNA-seq reads to their transcripts of origin is a fundamental task in transcript expression estimation and differential expression scoring. Where ambiguities in mapping exist due to transcripts sharing sequence,…
This paper addresses the problem of detecting and characterizing local variability in time series and other forms of sequential data. The goal is to identify and characterize statistically significant variations, at the same time…
Variant Stochastic cracking is a significantly more resilient approach to adaptive indexing. It showed [1]that Stochastic cracking uses each query as a hint on how to reorganize data, but not blindly so; it gains resilience and avoids…
Kernel segmentation aims at partitioning a data sequence into several non-overlapping segments that may have nonlinear and complex structures. In general, it is formulated as a discrete optimization problem with combinatorial constraints. A…
This paper deals with the problem of simulating dense dispersed systems composed by large numbers of particles undergoing ballistic aggregation. The most classical approaches for dealing with such problems are represented by the so-called…
The subset sum problem (SSP) can be briefly stated as: given a target integer $E$ and a set $A$ containing $n$ positive integer $a_j$, find a subset of $A$ summing to $E$. The \textit{density} $d$ of an SSP instance is defined by the ratio…
Dense subgraph extraction is a fundamental problem in graph analysis and data mining, aimed at identifying cohesive and densely connected substructures within a given graph. It plays a crucial role in various domains, including social…
The reconstruction of interaction networks between random events is a critical problem arising from statistical physics and politics, sociology, biology, psychology, and beyond. The Ising model lays the foundation for this reconstruction…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
In this thesis, we propose several modelling strategies to tackle evolving data in different contexts. In the framework of static clustering, we start by introducing a soft kernel spectral clustering (SKSC) algorithm, which can better deal…
We develop a framework for graph sparsification and sketching, based on a new tool, short cycle decomposition -- a decomposition of an unweighted graph into an edge-disjoint collection of short cycles, plus few extra edges. A simple…
Graphs arising in statistical problems, signal processing, large networks, combinatorial optimization, and data analysis are often dense, which causes both computational and storage bottlenecks. One way of \textit{sparsifying} a…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
In this paper, we present a novel approach based on the random walk process for finding meaningful representations of a graph model. Our approach leverages the transient behavior of many short random walks with novel initialization…
We address the problem of reverse engineering of stripped executables, which contain no debug information. This is a challenging problem because of the low amount of syntactic information available in stripped executables, and the diverse…
Spiking Neural Networks (SNNs) have emerged as a compelling, energy-efficient alternative to traditional Artificial Neural Networks (ANNs) for static image tasks such as image classification and segmentation. However, in the more complex…