Publications associées à Transcriptional Regulatory Networks across Species : Evolution, Inference, and Refinement

Publications associées (57)

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

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

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

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Massimo Bourquin

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Cyril David Son-Tuyên Pulver

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

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

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

Improving the accuracy and interpretability of neural networks for wind power forecasting

Fernando Porté Agel, Jiannong Fang, Wenlong Liao

Deep neural networks (DNNs) are receiving increasing attention in wind power forecasting due to their ability to effectively capture complex patterns in wind data. However, their forecast errors are severely limited by the local optimal weight issue in opt ...

2025

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

A ride time-oriented scheduling algorithm for dial-a-ride problems

Nikolaos Geroliminis, Claudia Bongiovanni, Mor Kaspi

This paper offers a new algorithm to efficiently optimize scheduling decisions for dial-a-ride problems (DARPs), including problem variants considering electric and autonomous vehicles (e-ADARPs). The scheduling heuristic, based on linear programming theor ...

Pergamon-Elsevier Science Ltd2024

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

Dual Isotope Analysis Reveals Phylogenetic Patterns and Novel Insights Into Methoxy Group Synthesis of Structural Biomolecules in Leaf and Woody Plant Tissues

Philipp Schuler

Stable carbon and hydrogen isotopes of wood methoxy groups (δ2Hmeth, δ13Cmeth), mainly sourced by structural biomolecules like lignin and pectin, provide important insights into climatic, hydrological and physiological conditions. This study systematically ...

Wiley2025

Reach For the Arcs: Reconstructing Surfaces from SDFs via Tangent Points

Yingying Ren

We introduce an algorithm to reconstruct a mesh from discrete samples of a shape's Signed Distance Function (SDF). A simple geometric reinterpretation of the SDF lets us formulate the problem through a point cloud, from which a surface can be extracted wit ...

Association for Computing Machinery2024

Using deep reinforcement learning to investigate stretch feedback during swimming of the lamprey

Auke Ijspeert, Astha Gupta

Animals have to navigate complex environments and perform intricate swimming maneuvers in the real world. To conquer these challenges, animals evolved a variety of motion control strategies. While it is known that many factors contribute to motion control, ...

IOP Publishing Ltd2025

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

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

Context selectivity with dynamic availability enables lifelong continual learning

Wulfram Gerstner, Guillaume Emmanuel Fernand Bellec, Martin Louis Lucien Rémy Barry

“You never forget how to ride a bike”, – but how is that possible? The brain is able to learn complex skills, stop the practice for years, learn other skills in between, and still retrieve the original knowledge when necessary. The mechanisms of this capab ...

Elsevier BV2025

A phase transition between positional and semantic learning in a solvable model of dot-product attention

Lenka Zdeborová, Florent Gérard Krzakala, Hugo Chao Cui, Freya Behrens

Many empirical studies have provided evidence for the emergence of algorithmic mechanisms (abilities) in the learning of language models, that lead to qualitative improvements in the model capabilities. Yet, a theoretical characterization of how such mecha ...

2025

Infusing structured knowledge priors in neural models for sample-efficient symbolic reasoning

Mattia Atzeni

The ability to reason, plan and solve highly abstract problems is a hallmark of human intelligence. Recent advancements in artificial intelligence, propelled by deep neural networks, have revolutionized disciplines like computer vision and natural language ...

EPFL2024

Adaptive projected variational quantum dynamics

Giuseppe Carleo, Stefano Barison, David Linteau

We propose an adaptive quantum algorithm to prepare accurate variational time evolved wave functions. The method is based on the projected variational quantum dynamics (pVQD) algorithm, that performs a global optimization with linear scaling in the number ...

Amer Physical Soc2024

Training hybrid neural networks with multimode optical nonlinearities using digital twins

Demetri Psaltis, Christophe Moser, Niyazi Ulas Dinç, Ilker Oguz, Mustafa Yildirim, Jih-Liang Hsieh

The ability to train ever-larger neural networks brings artificial intelligence to the forefront of scientific and technical discoveries. However, their exponentially increasing size creates a proportionally greater demand for energy and computational hard ...

Walter de Gruyter GmbH2025