Related papers: Improving spliced alignment for identification of …
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…
Best subset of groups selection (BSGS) is the process of selecting a small part of non-overlapping groups to achieve the best interpretability on the response variable. It has attracted increasing attention and has far-reaching applications…
Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon…
Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to…
We propose Differentiable Satisfiability and Differentiable Answer Set Programming (Differentiable SAT/ASP) for multi-model optimization. Models (answer sets or satisfying truth assignments) are sampled using a novel SAT/ASP solving…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
Semidefinite programming (SDP) is a powerful tool for tackling a wide range of computationally hard problems such as clustering. Despite the high accuracy, semidefinite programs are often too slow in practice with poor scalability on large…
Multimodal fusion breaks through the boundaries between diverse modalities and has already achieved notable performances. However, in many specialized fields, it is struggling to obtain sufficient alignment data for training, which…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
Cross-modal alignment is a crucial task in multimodal learning aimed at achieving semantic consistency between vision and language. This requires that image-text pairs exhibit similar semantics. Traditional algorithms pursue embedding…
Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
Chordal decomposition techniques are used to reduce large structured positive semidefinite matrix constraints in semidefinite programs (SDPs). The resulting equivalent problem contains multiple smaller constraints on the nonzero blocks (or…
In many classification problems it is desirable to output well-calibrated probabilities on the different classes. We propose a robust, non-parametric method of calibrating probabilities called SplineCalib that utilizes smoothing splines to…
In this paper, we consider the problem of planar graph-based simultaneous localization and mapping (SLAM) that involves both poses of the autonomous agent and positions of observed landmarks. We present CPL-SLAM, an efficient and…
Organoids, sophisticated in vitro models of human tissues, are crucial for medical research due to their ability to simulate organ functions and assess drug responses accurately. Accurate organoid instance segmentation is critical for…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
Semi-supervised learning (SSL) is a promising machine learning paradigm to address the issue of label scarcity in medical imaging. SSL methods were originally developed in image classification. The state-of-the-art SSL methods in image…