Related papers: Pangenome-guided sequence assembly via binary opti…

This paper addresses the problem of reassembling images from disjointed fragments. More specifically, given an unordered set of fragments, we aim at reassembling one or several possibly incomplete images. The main contributions of this work…

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present…

Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…

Optimization has been widely used to generate smooth trajectories for motion planning. However, existing trajectory optimization methods show weakness when dealing with large-scale long trajectories. Recent advances in parallel computing…

Deep generative models have emerged as a popular machine learning-based approach for inverse design problems in the life sciences. However, these problems often require sampling new designs that satisfy multiple properties of interest in…

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…

Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as…

Deep learning-based cardiac segmentation has seen significant advancements over the years. Many studies have tackled the challenge of anatomically incorrect segmentation predictions by introducing auxiliary modules. These modules either…

Long-distance quantum communication via entanglement distribution is of great importance for the quantum internet. However, scaling up to such long distances has proved challenging due to the loss of photons, which grows exponentially with…

Trained humans exhibit highly agile spatial skills, enabling them to operate vehicles with complex dynamics in demanding tasks and conditions. Prior work shows that humans achieve this performance by using strategies such as satisficing,…

Sampling-based algorithms are widely used for motion planning in high-dimensional configuration spaces. However, due to low sampling efficiency, their performance often diminishes in complex configuration spaces with narrow corridors.…

This paper introduces a novel approach for cardinality-constrained Poisson regression to address feature selection challenges in high-dimensional count data. We formulate the problem as a mixed-integer conic optimization, enabling the use…

Anomaly detection is a practical and challenging task due to the scarcity of anomaly samples in industrial inspection. Some existing anomaly detection methods address this issue by synthesizing anomalies with noise or external data.…

Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…

Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware acceleration. A promising candidate for all of the above is…

Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…

The sequence in which a complex product is assembled directly impacts the ease and efficiency of the assembly process, whether executed by a human or a robot. A sequence that gives the assembler the greatest freedom of movement is therefore…

In real life, it is always an urge to reach our goal in minimum effort i.e., it should have a minimum constrained path. The path may be shortest route in practical life, either physical or electronic medium. The scenario is to represents…

We study the problem of sampling and reconstruction of bandlimited graph signals where the objective is to select a node subset of prescribed cardinality that ensures interpolation of the original signal with the lowest reconstruction…