Publications related to Scaffolding protein functional sites using deep learning

Related publications (50)

DEMO: Dielectric elastomer actuators (DEAs) for the restoration of facial movements

Yves Perriard, Yoan René Cyrille Civet, Stefania Maria Aliki Konstantinidi, Simon Holzer, Andres Osorio Salazar, Marc Michel Charles Favier

Facial paralysis is a highly burdening condition, resulting in a patient's inability to move his musculature on one or both sides of the mouth. The restoration of facial movement is crucial for enhancing the overall patients' quality of life. The use of DE ...

SPIE2025

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

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

Mspo: a Machine Learning Hyperparameter Optimization Method for Enhanced Breast Cancer Image Classification

Zaffar Ahmed Shaikh

As one of the major threats to women's health worldwide, breast cancer requires early diagnosis and accurate classification, since they are key to optimizing therapeutic interventions and ensuring precise prognosis. Recently, deep learning has demonstrated ...

SAGE PUBLICATIONS LTD2025

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Interact with Earth Observation Images using AI: Transparent Methods and Evaluation for Visual Question Answering

Christel Marie Tartini-Chappuis

Now is an exciting time for the domain of Earth observation (EO), with a multitude of diverse sensors looking at the planet from satellites, airplanes or drones. The volume of imagery acquired is massive, and hold great potential for a variety of applicati ...

EPFL2025

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Posterior-Based Analysis of Spatio-Temporal Features for Sign Language Assessment

Neha Tarigopula

Sign Language conveys information through multiple channels composed of manual (handshape, hand movement) and non-manual (facial expression, mouthing, body posture) components. Sign language assessment involves giving granular feedback to a learner, in ter ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2025

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

Learning to Assemble with Alternative Plans

Gabriel Rémi Vallat, Maryam Kamgarpour, Stefana Parascho, Ziqi Wang, Jingwen Wang

We present a reinforcement learning framework for constructing assemblies composed of rigid parts, which are commonly seen in many historical masonry buildings and bridges. Traditional construction methods for such structures often depend on dense scaffold ...

Association for Computing Machinery (ACM)2025

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

Foundations of a New Learning Paradigm in AI Grounded in the Principles of Evolutionary Developmental Biology

Zeki Doruk Erden

Contemporary AI faces important limitations that remain unresolved despite significant successes. Chief among these are the inability to acquire new knowledge without destroying old, the incomprehensible and nonengineerable nature of internal representatio ...

EPFL2025

Probing the latent hierarchical structure of data via diffusion models

Noam Itzhak Levi, Alessandro Favero, Antonio Sclocchi

High-dimensional data must be highly structured to be learnable. Although the compositional and hierarchical nature of data is often put forward to explain learnability, quantitative measurements establishing these properties are scarce. Likewise, accessin ...

2025

How Gradient Descent Balances Features: A Dynamical Analysis For Two-Layer Neural Networks

Volkan Cevher, Fanghui Liu, Zhenyu Zhu

This paper investigates the fundamental regression task of learning k neurons (a.k.a. teachers) from Gaussian input, using two-layer ReLU neural networks with width m (a.k.a. students) and m, k = O(1), trained via gradient descent under proper initializati ...

2025

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

Multi-scale and multi-energy non-destructive X-ray analysis of the European Retrievable Carrier (EURECA)

Grégoire Gabriel Germain Bourban, Volker Gass, Tobias Bandi

The reduction in costs for space travel and scientific experiments in microgravity raises the question of equipment reusability. This goal can only be achieved if the space travel associated system degradations are fully understood. Non-destructive analysi ...

2025

Computational drug development for membrane protein targets

Pierre Vogel, Henning Paul-Julius Stahlberg, Shuguang Yuan, Dongchun Ni, Babatunde Edukpe Ekundayo

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

2024

Eflop: a Sparsity-aware Metric for Evaluating Computational Cost in Spiking and Non-spiking Neural Networks

Liza Carol Andrea Dunbar

Deploying energy-efficient deep neural networks on energy-constrained edge devices is an important research topic in both machine learning and circuit design communities. Both artificial neural networks (ANNs) and spiking neural networks (SNNs) have been p ...

IOP Publishing Ltd2025

Recording physiological history of cells with chemical labeling

Kai Johnsson, Julien Hiblot

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

American Association for the Advancement of Science2024

Domain shift, domain adaptation, and generalization: A focus on MRI

Tobias Kober, Meritxell Bach Cuadra, Veronica Lily Ravano, Jonas Richiardi

Differences in acquisition protocols or hardware result in measurable changes in image characteristics. These differences affect distributional properties and can also affect the spatial and temporal characteristics of the images. Likewise, the distributio ...

Academic Press2025

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024