Publications related to Track: Machine Learning in Protein Science De Novo Design of Viral Epitope Mimetics with Non-Regular Structural Features

Related publications (22)

Do You Trust Your Model? Emerging Malware Threats in the Deep Learning Ecosystem

Training high-quality deep learning models is a challenging task due to computational and technical requirements. A growing number of individuals, institutions, and companies increasingly rely on pre-trained, third-party models made available in public rep ...

2025

Helmet material design for mitigating traumatic axonal injuries through AI-driven constitutive law enhancement

Dominique Pioletti, Pierre-Etienne Bourban, Naser Nasrollahzadeh Mamaghani, Vincent Marc Varanges, Pezhman Eghbalishamsabadi

Sports helmets provide incomplete protection against brain injuries. Here we aim to improve helmet liner efficiency by employing a novel approach that optimizes their properties. By exploiting a finite element model that simulates head impacts, we develope ...

2025

Uncertainty-aware diabetic retinopathy detection using deep learning enhanced by Bayesian approaches

Zaffar Ahmed Shaikh

Deep learning-based medical image analysis has shown strong potential in disease categorization, segmentation, detection, and even prediction. However, in high-stakes and complex domains like healthcare, the opaque nature of these models makes it challengi ...

2025

Sim-to-Real Causal Transfer: A Metric Learning Approach to Causally-Aware Interaction Representations

Alexandre Massoud Alahi, Yuejiang Liu, Po-Chien Luan, Ahmad Rahimi

Modeling spatial-temporal interactions among neighboring agents is at the heart of multi-agent problems such as motion forecasting and crowd navigation. Despite notable progress, it remains unclear to which extent modern representations can capture the cau ...

2025

Adversarial Training For Defense Against Label Poisoning Attacks

Volkan Cevher

As machine learning models grow in complexity and increasingly rely on publicly sourced data, such as the human-annotated labels used in training large language models, they become more vulnerable to label poisoning attacks. These attacks, in which adversa ...

2025

Fine-tuning protein language models to understand the functional impact of missense variants

Jacques Fellay

Elucidating the functional effects of missense variants is crucial yet challenging. To investigate their impact, we fine-tuned protein language models, including ESM2 and ProtT5, to classify 20 protein features at amino acid resolution. In addition, we tra ...

2025

A two-level resolution neural network with enhanced interpretability for freeway traffic forecasting

Nikolaos Geroliminis, Semin Kwak, Danya Li

© The Author(s) 2024.Deep learning models are widely used for traffic forecasting on freeways due to their ability to learn complex temporal and spatial relationships. In particular, graph neural networks, which integrate graph theory into deep learning, h ...

Nature Research2024

Stripping the Swiss discount curve using kernel ridge regression

Nicolas Etienne Camenzind, Damir Filipovic

We analyze and implement the kernel ridge regression (KR) method developed in Filipovic et al. (Stripping the discount curve-a robust machine learning approach. Swiss Finance Institute Research Paper No. 22-24. SSRN. https://ssrn.com/abstract=4058150, 2022 ...

Springer Heidelberg2024

Qualify-as-you-go: sensor fusion of optical and acoustic signatures with contrastive deep learning for multi-material composition monitoring in laser powder bed fusion process

Christian Leinenbach, Antonios Nikolaos Baganis

Growing demand for multi-material Laser Powder Bed Fusion (LPBF) faces process control and quality monitoring challenges, particularly in ensuring precise material composition. This study explores optical and acoustic emission signals during LPBF processes ...

Taylor & Francis Ltd2024

A prediction rigidity formalism for low-cost uncertainties in trained neural networks

Michele Ceriotti, Federico Grasselli, Sanggyu Chong, Filippo Bigi

Quantifying the uncertainty of regression models is essential to ensure their reliability, particularly since their application often extends beyond their training domain. Based on the solution of a constrained optimization problem, this work proposes ‘pre ...

2024

Unravelling the components of diffuse scattering using deep learning

Lucas Sebastian Powell-Rudden

Many technologically important material properties are underpinned by disorder and short-range structural correlations; therefore, elucidating structure-property relationships in functional materials requires understanding both the average and the local st ...

Int Union Crystallography2024

Enhancing Peer Review with AI-Powered Suggestion Generation Assistance: Investigating the Design Dynamics

Xiaotian Su, Seyed Parsa Neshaei

While writing peer reviews resembles an important task in science, education, and large organizations, providing fruitful suggestions to peers is not a straightforward task, as different user interaction designs of text suggestion interfaces can have diver ...

Association for Computing Machinery2024

Reaction-Agnostic Featurization of Bidentate Ligands for Bayesian Ridge Regression of Enantioselectivity

Jérôme Waser, Anne-Clémence Corminboeuf, Matthew Wodrich, Rubén Laplaza Solanas, Alexandre Alain Schöpfer

Chiral ligands are important components in asymmetric homogeneous catalysis, but their synthesis and screening can be both time-consuming and resource-intensive. Data-driven approaches, in contrast to screening procedures based on intuition, have the poten ...

Amer Chemical Soc2024

FVLLMONTI: The 3D Neural Network Compute Cube (N2C2) Concept for Efficient Transformer Architectures Towards Speech-to-Speech Translation

David Atienza Alonso, Giovanni Ansaloni, Alireza Amirshahi

This multi-partner-project contribution introduces the midway results of the Horizon 2020 FVLLMONTI project. In this project we develop a new and ultra-efficient class of ANN accelerators, the neural network compute cube (N2C2), which is specifically desig ...

Institute of Electrical and Electronics Engineers Inc.2024

Impact of phylogeny on inference from protein sequences: from models to natural data

Nicola Dietler

Proteins are macromolecules considered as the building blocks of cells because they are at the heart of almost every cellular task, ranging from chemical to mechanical processes. For instance, proteins play a role as enzymes for digestion, transporters of ...

EPFL2024

Point-process-based Representation Learning for Electronic Health Records

David Atienza Alonso, Anisoara Ionescu, Hojjat Karami

Irregular sampling of time series in electronic health records (EHRs) presents a challenge for the development of machine learning models. Additionally, the pattern of missing data in certain clinical variables is not random, but depends on the decisions o ...

IEEE2023

Machine Learning for Optical Motion Capture-Driven Musculoskeletal Modelling from Inertial Motion Capture Data

Rahul Sharma

Marker-based Optical Motion Capture (OMC) systems and associated musculoskeletal (MSK) modelling predictions offer non-invasively obtainable insights into muscle and joint loading at an in vivo level, aiding clinical decision-making. However, an OMC system ...

MDPI2023

Enhancing argumentative writing with automated feedback and social comparison nudging

Thiemo Wambsganss

The advantages offered by natural language processing (NLP) and machine learning enable students to receive automated feedback on their argumentation skills, independent of educator, time, and location. Although there is a growing amount of literature on f ...

PERGAMON-ELSEVIER SCIENCE LTD2022

Fluctuations, Bias, Variance & Ensemble of Learners: Exact Asymptotics for Convex Losses in High-Dimension

Florent Gérard Krzakala, Bruno Loureiro

From the sampling of data to the initialisation of parameters, randomness is ubiquitous in modern Machine Learning practice. Understanding the statistical fluctuations engendered by the different sources of randomness in prediction is therefore key to unde ...

JMLR-JOURNAL MACHINE LEARNING RESEARCH2022

Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors

Pierre Vogel, Florence Pojer, Somi Reddy Majjigapu, Aline Emma Christine Reynaud

The haem enzyme indoleamine 2,3-dioxygenase 1 (IDO1) catalyses the rate-limiting step in the kynurenine pathway of tryptophan metabolism and plays an essential role in immunity, neuronal function, and ageing. Expression of IDO1 in cancer cells results in t ...

TAYLOR & FRANCIS LTD2022