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Concept

Multiple sequence alignment

Publications associées (30)

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

TTool: A Supervised Artificial Intelligence-Assisted Visual Pose Detector for Tool Heads in Augmented Reality Woodworking

Yves Weinand, Julien Gamerro, Andrea Settimi, Florian Aymanns, Naravich Chutisilp

We present TimberTool (TTool v2.1.1), a software designed for woodworking tasks assisted by augmented reality (AR), emphasizing its essential function of the real-time localization of a tool head’s poses within camera frames. The localization process, a fu ...

2024

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

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

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

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Smart filter aided domain adversarial neural network for fault diagnosis in noisy industrial scenarios

Olga Fink, Gaëtan Michel Frusque

The application of unsupervised domain adaptation (UDA)-based fault diagnosis methods has shown significant efficacy in industrial settings, facilitating the transfer of operational experience and fault signatures between different operating conditions, di ...

2023

Species-specific regulation of XIST by the JPX/FTX orthologs

Olga Marie Louise Rosspopoff

X chromosome inactivation (XCI) is an essential process, yet it initiates with remarkable diversity in various mammalian species. XIST, the main trigger of XCI, is controlled in the mouse by an interplay of lncRNA genes (LRGs), some of which evolved concom ...

OXFORD UNIV PRESS2023

Learnable Wavelet Transform and Domain Adversarial Learning for Enhanced Bearing Fault Diagnosis

Olga Fink, Gaëtan Michel Frusque, Qi Li

Research Publishing2023

Robust Outlier Rejection for 3D Registration with Variational Bayes

Mathieu Salzmann, Jiancheng Yang, Zheng Dang, Zhen Wei

Learning-based outlier (mismatched correspondence) rejection for robust 3D registration generally formulates the outlier removal as an inlier/outlier classification problem. The core for this to be successful is to learn the discriminative inlier/outlier f ...

Ieee Computer Soc2023

fGOT: Graph Distances Based on Filters and Optimal Transport

Pascal Frossard, Mireille El Gheche, Hermina Petric Maretic

Graph comparison deals with identifying similarities and dissimilarities between graphs. A major obstacle is the unknown alignment of graphs, as well as the lack of accurate and inexpensive comparison metrics. In this work we introduce the filter graph dis ...

ASSOC ADVANCEMENT ARTIFICIAL INTELLIGENCE2022

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

Nature Portfolio2022

Network Alignment with Holistic Embeddings (Extended Abstract)

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

Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. However, existing alignment models either cannot handle large-scale graphs or fail to leverage different types of network information ...

IEEE COMPUTER SOC2022

Automatic pathological speech assessment

Parvaneh Janbakhshi

Many pathologies cause impairments in the speech production mechanism resulting in reduced speech intelligibility and communicative ability. To assist the clinical diagnosis, treatment and management of speech disorders, automatic pathological speech asses ...

EPFL2022

Studying Alignment in a Collaborative Learning Activity via Automatic Methods: The Link Between What We Say and Do

Barbara Bruno, Utku Norman

A dialogue is successful when there is alignment between the speakers at different linguistic levels. In this work, we consider the dialogue occurring between interlocutors engaged in a collaborative learning task, where they are not only evaluated on how ...

2022

Femtosecond laser-based optomechanical processes for permanent and high-precision fine alignment of optical systems

Saood Ibni Nazir

Miniaturization has been at the forefront of scientific research in the past decade covering diverse areas such as electronics, mechanics, and optics. While 'small is beautiful' may be a vast generalization, the true benefits of miniaturization are especia ...

EPFL2021

Phase separation of self-propelled disks with ferromagnetic and nematic alignment

Ignacio Pagonabarraga Mora, Elena Sesé Sansa

We present a comprehensive study of a model system of repulsive self-propelled disks in two dimensions with ferromagnetic and nematic velocity alignment interactions. We characterize the phase behavior of the system as a function of the alignment and self- ...

AMER PHYSICAL SOC2021

Survival of rotational alignment in H-2 scattering from Si(100)

Christopher Scott Reilly

We report a state-prepared, state-resolved study of rotational scattering of a diatomic molecule from a solid surface. Specifically, H-2 molecules with 80 meV kinetic energy are rotationally aligned in the j = 3 rotational state via stimulated Raman pumpin ...

AIP Publishing2021

Automatic Content Curation of Visual Heritage

Mathieu Salzmann, Frédéric Kaplan, Nicolas Henchoz, Delphine Ribes Lemay, Lara Jacqueline Défayes, André Viegas Andrade

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

Representing graphs through data with learning and optimal transport

Hermina Petric Maretic

Graphs offer a simple yet meaningful representation of relationships between data. This representation is often used in machine learning algorithms in order to incorporate structural or geometric information about data. However, it can also be used in an i ...

EPFL2021

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

Jaume Bonet Martinez

Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. We present RADI/raDIMod, a variation of the original DCA algorithm that grou ...

OXFORD UNIV PRESS2021