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

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

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

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

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, 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, Tiannan Sha, Haoqiong Bian

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, Thành Tâm Nguyên, Chi Thang Duong, Thanh Trung Huynh

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, Zander Harteveld, Giulia Sormani, Stéphane Rosset

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, Nicolas Henchoz, Delphine Ribes Lemay, Frédéric Kaplan, 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

Arnab Bhattacharya, Akhil Arora

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

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

Kalpani Anuradha Welivita

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 ...

ASSOC COMPUTING MACHINERY2019

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

Ana Angelica Hernandez Lopez

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 ...

EPFL2019

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

Sahand Kashani, James Richard Larus, Stuart Anthony Byma

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 ...

2019

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

Anastasia Ailamaki, Eleni Tzirita Zacharatou, Haoqiong Bian

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 ...

2018

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

Pierre Dillenbourg, Marc Laperrouza, Khalil Mrini

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 ...

2018

Compilation Techniques for Incremental Collection Processing

Daniel Lupei

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 ...

EPFL2017

Distributed Time Series Analytics

Tian Guo

In recent years time series data has become ubiquitous thanks to affordable sensors and advances in embedded technology. Large amount of time-series data are continuously produced in a wide spectrum of applications, such as sensor networks, medical monitor ...

EPFL2017

High level synthesis of Smith-Waterman dataflow implementations

Marco Mattavelli, Endri Bezati, Simone Casale Brunet

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 ...

2017

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

Karl Aberer, Jean Paul Calbimonte Perez, Jean-Eudes Marie Ranvier

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 ...

Ios Press2017

Combine and conquer: Relating BIP and Reo

Simon Bliudze

Coordination languages simplify design and development of concurrent systems. Particularly, exogenous coordination languages, like BIP and Reo, enable system designers to express the interactions among components in a system explicitly. A formal relation b ...

Elsevier Science Inc2017