A Query Model to Capture Event Pattern Matching in RDF Stream Processing Query Languages

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Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

Cloud function (CF) services, such as AWS Lambda, have been applied as the new computing infrastructure in implementing analytical query engines. For bursty and sparse workloads, CF-based query engine is more elastic than the traditional query engines runn ...

The heterogeneity of today's Web sources requires information retrieval (IR) systems to handle multi-modal queries. Such queries define a user's information needs by different data modalities, such as keywords, hashtags, user profiles, and other media. Rec ...

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

Computational protein design has emerged as a powerful tool capable of identifying sequences compatible with pre-defined protein structures. The sequence design protocols, implemented in the Rosetta suite, have become widely used in the protein engineering ...

Digitization and preservation of large heritage induce high maintenance costs to keep up with the technical standards and ensure sustainable access. Creating impactful usage is instrumental to justify the resources for long-term preservation. The Museum fü ...

Transformers have been proven a successful model for a variety of tasks in sequence modeling. However, computing the attention matrix, which is their key component, has quadratic complexity with respect to the sequence length, thus making them prohibitivel ...

The phenomenal growth of graph data from a wide variety of real-world applications has rendered graph querying to be a problem of paramount importance. Traditional techniques use structural as well as node similarities to find matches of a given query grap ...

The intrinsic high entropy metadata, known as quality scores, are largely the cause of the substantial size of sequence data files. Yet, there is no consensus on a viable reduction of the resolution of the quality score scale, arguably because of collatera ...

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

High-throughput sequencing of DNA molecules has revolutionized biomedical research by enabling the quantitative analysis of the genome to study its function, structure and dynamics. It is driving sequencing-based experiments in life sciences as evidenced b ...

Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This pape ...

The recent explosion in the number and size of spatio-temporal data sets from urban environments and social sensors creates new opportunities for data-driven approaches to understand and improve cities. Visual analytics systems like Urbane aim to empower d ...

We build a conversational agent which knowledge base is an online forum for parents of autistic children. We collect about 35,000 threads totalling some 600,000 replies, and label 1% of them for usefulness using Amazon Mechanical Turk. We train a Random Fo ...

Many map-reduce frameworks as well as NoSQL systems rely on collection programming as their interface of choice due to its rich semantics along with an easily parallelizable set of primitives. Unfortunately, the potential of collection programming is not ...

The paper presents the results of design explorations for the implementation of the Smith-Waterman (S-W) algorithm executing DNA and protein sequences alignment. Both design explorations studies and the corresponding FPGA implementations are obtained by wr ...

Diabetes Type 1 is a metabolic disease which results in a lack of insulin production, causing high glucose levels in the blood. It is crucial for diabetic patients to balance this glucose level, and they depend on external substances to do so. In order to ...

Next-generation genome sequencing technology has reached a point at which it is becoming cost-effective to sequence all patients. Biobanks and researchers are faced with an oncoming deluge of genomic data, whose processing requires new and scalable bioinfo ...

The state-of-the-art techniques for processing multi-term queries in P2P environments are query flooding and inverted list intersection. However, it has been shown that due to scalability reasons both methods fail to support full-text search in large scale ...

A Query Model to Capture Event Pattern Matching in RDF Stream Processing Query Languages

Chattez avec Graph Search

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Generative power of a protein language model trained on multiple sequence alignments

Using Cloud Functions as Accelerator for Elastic Data Analytics

Efficient and Effective Multi-Modal Queries Through Heterogeneous Network Embedding

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

A Rosetta-based protein design protocol converging to natural sequences

Automatic Content Curation of Visual Heritage

Fast Transformers with Clustered Attention

RAQ: Relationship-Aware Graph Querying in Large Networks

Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

On the relevance of quality score metadata in genomic sequence data for omics applications

IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback

Interactive Visual Exploration of Spatio-Temporal Urban Data Sets using Urbane

Building a Question-Answering Chatbot using Forum Data in the Semantic Space

Compilation Techniques for Incremental Collection Processing

High level synthesis of Smith-Waterman dataflow implementations

Semantic representation and processing of hypoglycemic events derived from wearable sensor data

Persona: A High-Performance Bioinformatics Framework

Distributed Cache Table: Efficient Query-Driven Processing of Multi-Term Queries in P2P Networks