相关论文: Barnacle: An Assembly Algorithm for Clone-based Se…
Compositional generalization is a basic mechanism in human language learning, which current neural networks struggle with. A recently proposed Disentangled sequence-to-sequence model (Dangle) shows promising generalization capability by…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
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 introduce the problem of Poisson sampling over joins: compute a sample of the result of a join query by conceptually performing a Bernoulli trial for each join tuple, using a non-uniform and tuple-specific probability. We propose an…
Programmers often reuse code from source code repositories to reduce the development effort. Code clones are candidates for reuse in exploratory or rapid development, as they represent often repeated functionality in software systems. To…
Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities.…
We present a technique for clustering categorical data by generating many dissimilarity matrices and averaging over them. We begin by demonstrating our technique on low dimensional categorical data and comparing it to several other…
Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpora of malicious binaries, obtaining high-quality corpora of…
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly…
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Ensembles of artificial neural networks show improved generalization capabilities that outperform those of single networks. However, for aggregation to be effective, the individual networks must be as accurate and diverse as possible. An…
The automated assembly of complex products requires a system that can automatically plan a physically feasible sequence of actions for assembling many parts together. In this paper, we present ASAP, a physics-based planning approach for…
Assembly sequence planning (ASP) is the essential process for modern manufacturing, proven to be NP-complete thus its effective and efficient solution has been a challenge for researchers in the field. In this paper, we present a…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
Detecting and segmenting human skin regions in digital images is an intensively explored topic of computer vision with a variety of approaches proposed over the years that have been found useful in numerous practical applications. The first…