Related papers: SOPanG 2: online searching over a pan-genome witho…
We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in $O(1)$ time per step while using $O(\log \sigma * n) + o(\log \sigma * \sigma * n)$ bits of space. This is done by replacing the…
Expectation Propagation (EP)-based Multiple-Input Multiple-Output (MIMO) detector is regarded as a state-of-the-art MIMO detector because of its exceptional performance. However, we find that the EP MIMO detector cannot guarantee to achieve…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolutionary Sparse Learning with Paired Species Contrast (ESL-PSC) is an approach to identify genes…
Edit distance with moves (EDM) is a string-to-string distance measure that includes substring moves in addition to ordinal editing operations to turn one string to the other. Although optimizing EDM is intractable, it has many applications…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Recent studies have used GAN to transfer expressions between human faces. However, existing models have many flaws: relying on emotion labels, lacking continuous expressions, and failing to capture the expression details. To address these…
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
This paper introduces PAG-a novel optimization and decoding approach that guides autoregressive generation of document identifiers in generative retrieval models through simultaneous decoding. To this aim, PAG constructs a set-based and…
In recent years, aligning a sequence to a pangenome has become a central problem in genomics and pangenomics. A fast and accurate solution to this problem can serve as a toolkit to many crucial tasks such as read-correction, Multiple…
Entity Set Expansion (ESE) is a critical task aiming at expanding entities of the target semantic class described by seed entities. Most existing ESE methods are retrieval-based frameworks that need to extract contextual features of…
The requirements for many applications of state-of-the-art speech recognition systems include not only low word error rate (WER) but also low latency. Specifically, for many use-cases, the system must be able to decode utterances in a…
Nonparametric two-sample testing is a classical problem in inferential statistics. While modern two-sample tests, such as the edge count test and its variants, can handle multivariate and non-Euclidean data, contemporary gargantuan datasets…
This paper aims to address the challenge of data generation beyond the training data and proposes a framework for Structural Extrapolated Data GEneration (SEDGE) based on suitable assumptions on the underlying data-generating process. We…
Traditional error detection approaches require user-defined parameters and rules. Thus, the user has to know both the error detection system and the data. However, we can also formulate error detection as a semi-supervised classification…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
Retrieval-augmented question answering over heterogeneous corpora requires connected evidence across text, tables, and graph nodes. While entity-level knowledge graphs support structured access, they are costly to construct and maintain,…
In many retrieval systems the original high dimensional data (e.g., images) is mapped to a lower dimensional feature through a learned embedding model. The task of retrieving the most similar data from a gallery set to a given query data is…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…