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Neuronal morphology encodes critical information about circuit function, development, and disease, yet current methods analyze topology or graph structure in isolation. We introduce GraPHFormer, a multimodal architecture that unifies these…

Computer Vision and Pattern Recognition · Computer Science 2026-03-24 Uzair Shah , Marco Agus , Mahmoud Gamal , Mahmood Alzubaidi , Corrado Cali , Pierre J. Magistretti , Abdesselam Bouzerdoum , Mowafa Househ

Advances in large-scale recording technologies now enable simultaneous measurements from multiple brain areas, offering new opportunities to study signal transmission across interacting components of neural circuits. However, neural…

Neurons and Cognition · Quantitative Biology 2025-10-27 Qi Xin , Robert E. Kass

Detailed mobile sensing data from phones, watches, and fitness trackers offer an unparalleled opportunity to quantify and act upon previously unmeasurable behavioral changes in order to improve individual health and accelerate responses to…

Machine Learning · Computer Science 2022-06-06 Mike A. Merrill , Tim Althoff

Electroencephalography signals (EEGs) contain rich multi-scale information crucial for understanding brain states, with potential applications in diagnosing and advancing the drug development landscape. However, extracting meaningful…

Machine Learning · Computer Science 2025-09-26 D. Darankoum , C. Habermacher , J. Volle , S. Grudinin

Single-cell RNA sequencing (scRNA-seq) enables single-cell transcriptomic profiling, revealing cellular heterogeneity and rare populations. Recent deep learning models like Geneformer and Mouse-Geneformer perform well on tasks such as…

Genomics · Quantitative Biology 2025-07-11 Yuki Nishio , Takayoshi Yamashita , Keita Ito , Tsubasa Hirakawa , Hironobu Fujiyoshi

Brain-Machine Interfacing (BMI) has greatly benefited from adopting machine learning methods for feature learning that require extensive data for training, which are often unavailable from a single dataset. Yet, it is difficult to combine…

Signal Processing · Electrical Eng. & Systems 2024-05-27 Jinpei Han , Xiaoxi Wei , A. Aldo Faisal

We propose a novel deep neural network architecture to integrate imaging and genetics data, as guided by diagnosis, that provides interpretable biomarkers. Our model consists of an encoder, a decoder and a classifier. The encoder learns a…

Classes, as fundamental elements of Computer Vision, have been extensively studied within incremental learning frameworks. In contrast, tokens, which play essential roles in many research fields, exhibit similar characteristics of growth,…

Machine Learning · Computer Science 2025-11-19 Jiaxin Qi , Yan Cui , Jianqiang Huang , Gaogang Xie

Cell type identification from single-cell transcriptomic data is a common goal of single-cell RNA sequencing (scRNAseq) data analysis. Neural networks have been employed to identify cell types from scRNAseq data with high performance.…

Genomics · Quantitative Biology 2020-05-11 Xishuang Dong , Shanta Chowdhury , Uboho Victor , Xiangfang Li , Lijun Qian

The voxelized Allen Atlas of the adult mouse brain (at a resolution of 200 microns) has been used in [arXiv:1303.0013] to estimate the region-specificity of 64 cell types whose transcriptional profile in the mouse brain has been measured in…

Neurons and Cognition · Quantitative Biology 2014-02-19 Pascal Grange , Jason W. Bohland , Benjamin Okaty , Ken Sugino , Hemant Bokil , Sacha Nelson , Lydia Ng , Michael Hawrylycz , Partha P. Mitra

Datasets from single-molecule experiments often reflect a large variety of molecular behaviour. The exploration of such datasets can be challenging, especially if knowledge about the data is limited and a priori assumptions about expected…

Data Analysis, Statistics and Probability · Physics 2020-04-06 Anton Vladyka , Tim Albrecht

We present a novel graph-based learning of EEG representations with gradient alignment (GEEGA) that leverages multi-domain information to learn EEG representations for brain-computer interfaces. Our model leverages graph convolutional…

Human-Computer Interaction · Computer Science 2025-12-09 Prithila Angkan , Amin Jalali , Paul Hungler , Ali Etemad

Deep learning has been widely applied in neuroimaging, including predicting brain-phenotype relationships from magnetic resonance imaging (MRI) volumes. MRI data usually requires extensive preprocessing prior to modeling, but variation…

Machine Learning · Computer Science 2023-10-17 Xinhui Li , Alex Fedorov , Mrinal Mathur , Anees Abrol , Gregory Kiar , Sergey Plis , Vince Calhoun

Phenotypic drug discovery has attracted widespread attention because of its potential to identify bioactive molecules. Transcriptomic profiling provides a comprehensive reflection of phenotypic changes in cellular responses to external…

Machine Learning · Computer Science 2025-01-16 Hui Liu , Shikai Jin

Objective: Electroencephalography (EEG) and electromyography (EMG) are two non-invasive bio-signals, which are widely used in human machine interface (HMI) technologies (EEG-HMI and EMG-HMI paradigm) for the rehabilitation of physically…

Neurons and Cognition · Quantitative Biology 2022-06-23 Omair Ali , Muhammad Saif-ur-Rehman , Tobias Glasmachers , Ioannis Iossifidis , Christian Klaes

This study introduces a specialized pipeline designed to classify the concentration state of an individual student during online learning sessions by training a custom-tailored machine learning model. Detailed protocols for acquiring and…

Machine Learning · Computer Science 2025-02-24 Zewen Zhuo , Mohamad Najafi , Hazem Zein , Amine Nait-Ali

Studying the neurological, genetic and evolutionary basis of human vocal communication mechanisms using animal vocalization models is an important field of neuroscience. The data sets typically comprise structured sequences of syllables or…

Previous electroencephalogram (EEG) emotion recognition relies on single-task learning, which may lead to overfitting and learned emotion features lacking generalization. In this paper, a graph-based multi-task self-supervised learning…

Signal Processing · Electrical Eng. & Systems 2022-05-03 Yang Li , Ji Chen , Fu Li , Boxun Fu , Hao Wu , Youshuo Ji , Yijin Zhou , Yi Niu , Guangming Shi , Wenming Zheng

There is increasing interest in using deep learning approach for EEG analysis as there are still rooms for the improvement of EEG analysis in its accuracy. Convolutional long short-term (CNNLSTM) has been successfully applied in time series…

Signal Processing · Electrical Eng. & Systems 2019-12-20 Lingling Yang , Leanne Lai Hang Chan , Yao Lu

We consider the problem of how many samples from a Gaussian multi-index model are required to weakly reconstruct the relevant index subspace. Despite its increasing popularity as a testbed for investigating the computational complexity of…

Machine Learning · Computer Science 2025-06-11 Leonardo Defilippis , Yatin Dandi , Pierre Mergny , Florent Krzakala , Bruno Loureiro