Related papers: AliBI: An Alignment-Based Index for Genomic Datase…
We propose a clustering-based generalized low rank approximation method, which takes advantage of appealing features from both the generalized low rank approximation of matrices (GLRAM) and cluster analysis. It exploits a more general form…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
Neural models have transformed the fundamental information retrieval problem of mapping a query to a giant set of items. However, the need for efficient and low latency inference forces the community to reconsider efficient approximate…
This paper provides a framework in order to statistically model sequences from human genome, which is allowing a formulation to synthesize gene sequences. We start by converting the alphabetic sequence of genome to decimal sequence by…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…
Storing and archiving data produced by next-generation sequencing (NGS) is a huge burden for research institutions. Reference-based compression algorithms are effective in dealing with these data. Our work focuses on compressing FASTQ…
The Adjusted Rand Index (ARI) is a widely used method for comparing hard clusterings, but requires a choice of random model that is often left implicit. Several recent works have extended the Rand Index to fuzzy clusterings, but the…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
Comparative diagnostic in brain tumor evaluation makes possible to use the available information of a medical center to compare similar cases when a new patient is evaluated. By leveraging Artificial Intelligence models, the proposed system…
Indexing intervals is a fundamental problem, finding a wide range of applications. Recent work on managing large collections of intervals in main memory focused on overlap joins and temporal aggregation problems. In this paper, we propose…
Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational resources. In this study, we present an efficient de…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
We present COBS, a COmpact Bit-sliced Signature index, which is a cross-over between an inverted index and Bloom filters. Our target application is to index $k$-mers of DNA samples or $q$-grams from text documents and process approximate…
Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
Artificial intelligence (AI) has introduced numerous opportunities for human assistance and task automation in medicine. However, it suffers from poor generalization in the presence of shifts in the data distribution. In the context of…
This paper introduces new tools for genomic signal processing, which can assist for genomic attribute extracting or describing biologically meaningful features embedded in a DNA. The codongrams and a2grams are offered as an alternative to…
The use of brain images as markers for diseases or behavioral differences is challenged by the small effects size and the ensuing lack of power, an issue that has incited researchers to rely more systematically on large cohorts. Coupled…