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A comparative analysis of gene expression profiling by statistical and machine learning approaches

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Publications associées (31)

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Abstract IA02: Cancer-specific foundation models: Friend or foe in healthcare AI?

Maria Brbic

Foundation models have become a powerful tool in single-cell transcriptomics, enabling broad generalization across tasks such as cell type annotation, data integration, and drug response prediction. Yet, most current models are trained predominantly on hea ...

American Association for Cancer Research (AACR)2025

Learning to Reason with Neural Networks: Principles and Methods

Aryo Lotfi Jandaghi

This thesis focuses on understanding and improving the reasoning capabilities of neural networks. It develops theoretical results and empirical analyses to uncover reasoning potential and limitations, leveraging these insights to guide the design of improv ...

EPFL2025

Spectroscopy of two-dimensional interacting lattice electrons using symmetry-aware neural backflow transformations

Giuseppe Carleo, Jannes Willy E. Nys, Imelda Romero

Neural networks have shown to be a powerful tool to represent the ground state of quantum many-body systems, including fermionic systems. However, efficiently integrating lattice symmetries into neural representations remains a significant challenge. In th ...

NATURE PORTFOLIO2025

Explainable modeling for wind power forecasting: A Glass-Box model with high accuracy

Fernando Porté Agel, Jiannong Fang, Wenlong Liao

Machine learning models (e.g., neural networks) achieve high accuracy in wind power forecasting, but they are usually regarded as black boxes that lack interpretability. To address this issue, the paper proposes a glass-box model that combines high accurac ...

2025

Computational design of complex protein folds and soluble analogs of membrane proteins

Casper Alexander Goverde

Proteins are the molecular machines of life, driving essential biological processes such as enzymatic catalysis, cellular signaling, and immune responses. The ability to design entirely new proteins with desired structures and functions has immense implica ...

EPFL2025

Exploiting Representation Similarities in Self-Supervised Learning for Vision Tasks

Thomas Grégoire Stegmüller

Recent progress in computer vision has been driven by a simple yet transformative observation: the potential of 30-year-old neural networks can be unlocked by massively scaling their parameters and the amount of human-labeled training data. This breakthrou ...

EPFL2025

Modelleyen: Continual Learning and Planning via Structured Modelling of Environment Dynamics

Boi Faltings, Zeki Doruk Erden

The current machine learning paradigm relies on continuous representations and fixed neural network architectures to approximate environmental structures, leading to challenges with continual learning, internal structure design, and goal-directed behavior ...

Springer Science and Business Media Deutschland GmbH2025

Sequential Reasoning with Socially Caused Beliefs

Mert Kayaalp

Machine learning and artificial intelligence methods have achieved remarkable success, matching and even surpassing human capabilities in various complex tasks. However, many demonstrations have generally neglected a critical part of the intelligence that ...

EPFL2025

Search for Pair Production of Heavy Particles Decaying to a Top Quark and a Gluon in the Lepton Plus Jets Final State in Proton-proton Collisions at √s=13 Tev

Jan Steggemann, Anna Mascellani, Joanna Malgorzata Wanczyk

A search is presented for the pair production of new heavy resonances, each decaying into a top quark (t) or antiquark and a gluon (g). The analysis uses data recorded with the CMS detector from proton-proton collisions at a center-of-mass energy of 13 TeV ...

SPRINGER2025

On the Perspectives of Image-to-Lidar Constraints in Dynamic Network Optimisation

Thibaut Stoltz, Jan Skaloud, Davide Antonio Cucci, Laurent Valentin Jospin, Kyriaki Mouzakidou

The evolution of airborne mapping witnesses the introduction of hybrid lidar-camera systems to enhance data collection, i.e. to obtain simultaneously high-density point-cloud and texture. Yet, the common adjustment of both optical data streams is a nontriv ...

International Society for Photogrammetry and Remote Sensing2025

SaliencyMix plus : Noise-Minimized Image Mixing Method With Saliency Map in Data Augmentation

Zhixiong Jin

Data augmentation is vital in deep learning for enhancing model robustness by artificially expanding training datasets. However, advanced methods like CutMix blend images and assign labels based on pixel ratios, often introducing label noise by neglecting ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2025

Overcoming Distribution Shifts and Imbalance Challenges in Representation Learning for Deep Regression Models

Ismail Nejjar

Deep learning has shown remarkable potential for industrial applications, particularly in predictive maintenance and condition monitoring. A key challenge in this domain is prognostics, specifically predicting the Remaining Useful Life (RUL) of assets - a ...

EPFL2025

Plasma state monitoring and disruption characterization using multimodal VAEs

Giulio Romanelli, Olivier Sauter, Alessandro Pau, Yoeri Renier Johannes Poels, Cristina Venturini

When a plasma disrupts in a tokamak, significant heat and electromagnetic loads are deposited onto the surrounding device components. These forces scale with plasma current and magnetic field strength, making disruptions one of the key challenges for futur ...

IOP Publishing Ltd2025

Weighting Pseudo-labels via High-Activation Feature Index Similarity and Object Detection for Semi-supervised Segmentation

Minh Hieu Lê

Semi-supervised semantic segmentation methods leverage unlabeled data by pseudo-labeling them. Thus the success of these methods hinges on the reliability of the pseudo-labels. Existing methods mostly choose high-confidence pixels in an effort to avoid err ...

Springer Science and Business Media Deutschland GmbH2025

Cost-Efficiency Trade-offs for Neural Cascade Rankers in Web Search

Ekaterina Trimbach

Web search engines process billions of queries daily, making the balance between computational efficiency and ranking quality crucial. While neural ranking models have shown impressive performance, their computational costs, particularly in feature extract ...

ACM2025

Person Re-Identification and its Application to Multi-Object Tracking

Vladimir Dominic K. Somers

Multi-Object Tracking (MOT) is a fundamental computer vision task that involves detecting objects of interest in video frames and associating detections of the same object across time to form trajectories. For association, appearance cues, extracted throug ...

EPFL2025

Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Giorgia Benegiamo

Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

2025

HPV16-Expressing Tumors Release Multiple IL-1 Ligands to Orchestrate Systemic Immunosuppression Whose Disruption Enables Efficacy of a Therapeutic Vaccine

Marjorie Gabrielle Marie Cayatte, Dilara Selin Ozdoganlar, Douglas Hanahan, Krisztian Homicsko, Morgane Marie Lecointre, Jeremy Gilles Louis Guillot

It is well-established that symptomatic cancers evade immune destruction by coalescing tumor microenvironments to suppress adaptive immunity. Additionally, mouse models of cervical and other cancers have revealed a capability of tumors to systemically indu ...

American Association for Cancer Research (AACR)2025

Boosting Resource-Constrained Federated Learning Systems with Guessed Updates

Mohamed Yassine Boukhari, Anne-Marie Kermarrec, Rafael Pereira Pires, Rishi Sharma, Akash Balasaheb Dhasade

Federated learning (FL) enables a set of client devices to collaboratively train a model without sharing raw data. This process, though, operates under the constrained computation and communication resources of edge devices. These constraints combined with ...

Institute of Electrical and Electronics Engineers (IEEE)2025

Segmenting Object Affordances: Reproducibility and Sensitivity to Scale

Andrea Cavallaro

Visual affordance segmentation identifies image regions of an object an agent can interact with. Existing methods re-use and adapt learning-based architectures for semantic segmentation to the affordance segmentation task and evaluate on small-size dataset ...

Springer Science and Business Media Deutschland GmbH2025