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Time-Varying Network Driver Estimation (TNDE) Quantifies Stage-Specific Regulatory Effects From Single-Cell Snapshots
Identifying key driver genes governing biological processes such as development and disease progression remains a challenge. While existing methods can reconstruct cellular trajectories or infer static gene regulatory networks (GRNs), they often fail to quantify time-resolved regulatory effects within specific temporal windows. Here, we present Time-varying Network Driver Estimation (TNDE), a computational framework quantifying dynamic gene driver effects from single-cell snapshot data under a linear Markov assumption. TNDE leverages a shared graph attention encoder to preserve the local topological structure of the data. Furthermore, by incorporating partial optimal transport, TNDE accounts for unmatched cells arising from proliferation or apoptosis, thereby enabling trajectory alignment in non-equilibrium processes. Benchmarking on simulated datasets demonstrates that TNDE outperforms existing baseline methods across diverse complex regulatory scenarios. Applied to mouse erythropoiesis data, TNDE identifies stage-specific driver genes, the functional relevance of which is corroborated by biological validation. TNDE offers an effective quantitative tool for dissecting dynamic regulatory mechanisms underlying complex biological processes.
The use of artificial intelligence in music creation: between interface and appropriation
Zeller, Arnaud, Pebayle, Emmanuelle Chevry
By observing the activities and relationships of musicians and sound designers to the activities of creation, performance, publishing and dissemination with artificial intelligence (AI), from two specialized forums between 2022 and 2024, this article proposes a lexicometric analysis of the representations linked to their use. Indeed, the machine, now equipped with artificial intelligences requiring new appropriations and enabling new mediations, constitutes new challenges for artists. To study these confrontations and new mediations, our approach mobilizes the theoretical framework of the Human-AI Musicking Framework, based on a lexicometric analysis of content. The aim is to clarify the present and future uses of AI from the interfaces, in the creation of sound and musical content, and to identify the obstacles, obstacles, brakes and limits to appropriation ``in the fact of making the content one's own and integrating it as a part of oneself'' (Bachimont and Crozat, 2004) in the context of a collaboration between musician and machine.
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Active Matter as a framework for living systems-inspired Robophysics
Janzen, Giulia, Maselli, Gaia, Jimenez, Juan F., Garcia-Perez, Lia, Fernandez, D A Matoz, Valeriani, Chantal
Robophysics investigates the physical principles that govern living-like robots operating in complex, realworld environments. Despite remarkable technological advances, robots continue to face fundamental efficiency limitations. At the level of individual units, locomotion remains a challenge, while at the collective level, robot swarms struggle to achieve shared purpose, coordination, communication, and cost efficiency. This perspective article examines the key challenges faced by bio-inspired robotic collectives and highlights recent research efforts that incorporate principles from active-matter physics and biology into the modeling and design of robot swarms.
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REVE: A Foundation Model for EEG -- Adapting to Any Setup with Large-Scale Pretraining on 25,000 Subjects
Ouahidi, Yassine El, Lys, Jonathan, Thölke, Philipp, Farrugia, Nicolas, Pasdeloup, Bastien, Gripon, Vincent, Jerbi, Karim, Lioi, Giulia
Foundation models have transformed AI by reducing reliance on task-specific data through large-scale pretraining. While successful in language and vision, their adoption in EEG has lagged due to the heterogeneity of public datasets, which are collected under varying protocols, devices, and electrode configurations. Existing EEG foundation models struggle to generalize across these variations, often restricting pretraining to a single setup, resulting in suboptimal performance, in particular under linear probing. We present REVE (Representation for EEG with Versatile Embeddings), a pretrained model explicitly designed to generalize across diverse EEG signals. REVE introduces a novel 4D positional encoding scheme that enables it to process signals of arbitrary length and electrode arrangement. Using a masked autoencoding objective, we pretrain REVE on over 60,000 hours of EEG data from 92 datasets spanning 25,000 subjects, representing the largest EEG pretraining effort to date. REVE achieves state-of-the-art results on 10 downstream EEG tasks, including motor imagery classification, seizure detection, sleep staging, cognitive load estimation, and emotion recognition. With little to no fine-tuning, it demonstrates strong generalization, and nuanced spatio-temporal modeling. We release code, pretrained weights, and tutorials to support standardized EEG research and accelerate progress in clinical neuroscience.
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