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Protein language models often take into consideration the alignment between a protein sequence and its textual description. However, they do not take structural information into consideration. Traditional methods treat sequence and…
Recently, there has been a resurgence of interest in rigorous algorithms for the inference of cancer progression from genomic data. The motivations are manifold: (i) growing NGS and single cell data from cancer patients, (ii) need for novel…
Bibliographic coupling (BC) and co-citation (CC) are the two most common citation-based coupling measures of similarity between scientific items. One can interpret these measures as second-neighbor relations distinguished by the direction…
Cross-lingual document alignment aims to identify pairs of documents in two distinct languages that are of comparable content or translations of each other. In this paper, we exploit the signals embedded in URLs to label web documents at…
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…
The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
It has been conceived that children learn new objects through their affordances, that is, the actions that can be taken on them. We suggest that web pages also have affordances defined in terms of the users' information need they meet. An…
Cancers evolve from mutation of a single cell with sequential clonal and subclonal expansion of somatic mutation acquisition. Inferring clonal and subclonal structures from bulk or single cell tumor genomic sequencing data has a huge impact…
We introduce the ParClusterers Benchmark Suite (PCBS) -- a collection of highly scalable parallel graph clustering algorithms and benchmarking tools that streamline comparing different graph clustering algorithms and implementations. The…
The task of clustering a set of objects based on multiple sources of data arises in several modern applications. We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These…
The quality and accessibility of multilingual datasets are crucial for advancing machine translation. However, previous corpora built from United Nations documents have suffered from issues such as opaque process, difficulty of…
Parallel sentences are a relatively scarce but extremely useful resource for many applications including cross-lingual retrieval and statistical machine translation. This research explores our new methodologies for mining such data from…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
We propose different methods for alternative representation and visual augmentation of sheet music that help users gain an overview of general structure, repeating patterns, and the similarity of segments. To this end, we explored mapping…
Embeddings mapping high-dimensional discrete input to lower-dimensional continuous vector spaces have been widely adopted in machine learning applications as a way to capture domain semantics. Interviewing 13 embedding users across…
Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
To reproduce eScience, several challenges need to be solved: scientific workflows need to be automated; the involved software versions need to be provided in an unambiguous way; input data needs to be easily accessible; High-Performance…