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

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

Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero, Mohan Vamsi Nallapareddy

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, ...

PMLR2024

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

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

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 ...

eLIFE SCIENCES PUBL LTD2023

Using Cloud Functions as Accelerator for Elastic Data Analytics

Anastasia Ailamaki, Haoqiong Bian, Tiannan Sha

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 ...

ACM2023

Efficient and Effective Multi-Modal Queries Through Heterogeneous Network Embedding

Karl Aberer, Quoc Viet Hung Nguyen, Thanh Trung Huynh, Thành Tâm Nguyên, Chi Thang Duong

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 ...

IEEE COMPUTER SOC2022

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

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 ...

Nature Portfolio2022

A Rosetta-based protein design protocol converging to natural sequences

Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Zander Harteveld, Giulia Sormani

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 ...

AMER INST PHYSICS2021

Automatic Content Curation of Visual Heritage

Mathieu Salzmann, Frédéric Kaplan, Delphine Ribes Lemay, Nicolas Henchoz, Valentine Bernasconi

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 ...

2021

Fast Transformers with Clustered Attention

François Fleuret, Angelos Katharopoulos, Apoorv Vyas

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 ...

2020

RAQ: Relationship-Aware Graph Querying in Large Networks

Akhil Arora, Arnab Bhattacharya

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 ...

ASSOC COMPUTING MACHINERY2019

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

Marco Mattavelli, Claudio Paolo Alberti, Ana Angelica Hernandez Lopez

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 ...

2019

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