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Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which…
As state of the art neural networks (NNs) continue to grow in size, their resource-efficient implementation becomes ever more important. In this paper, we introduce a compression scheme that reduces the number of computations required for…
Sparse superimposed coding (SSC) has emerged as a promising technique for short-packet transmission in ultra-reliable low-latency communication scenarios. However, conventional SSC schemes often suffer from high encoding and decoding…
Constraint Programming (CP) and Machine Learning (ML) face challenges in text generation due to CP's struggle with implementing "meaning'' and ML's difficulty with structural constraints. This paper proposes a solution by combining both…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…
AMR-to-text generation is used to transduce Abstract Meaning Representation structures (AMR) into text. A key challenge in this task is to efficiently learn effective graph representations. Previously, Graph Convolution Networks (GCNs) were…
Large Language Models (LLMs) can exhibit considerable variation in the quality of their sampled outputs. Reranking and selecting the best generation from the sampled set is a popular way of obtaining strong gains in generation quality. In…
Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…
We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function,…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
The paradigm of Next Token Prediction (NTP) has driven the unprecedented success of Large Language Models (LLMs), but is also the source of their most persistent weaknesses such as poor long-term planning, error accumulation, and…
Biclustering techniques have been widely used to identify homogeneous subgroups within large data matrices, such as subsets of genes similarly expressed across subsets of patients. Mining a max-sum sub-matrix is a related but distinct…
Deep neural networks (DNNs) based saliency detection approaches have succeed in recent years, and improved the performance by a great margin via increasingly sophisticated network architecture. Despite the performance improvement, the…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…