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Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…

Genomics · Quantitative Biology 2025-04-18 Shuo Shuo Liu , Shikun Wang , Yuxuan Chen , Anil K. Rustgi , Ming Yuan , Jianhua Hu

The Matrix Element Method (MEM) is a powerful method to extract information from measured events at collider experiments. Compared to multivariate techniques built on large sets of experimental data, the MEM does not rely on an…

High Energy Physics - Experiment · Physics 2021-04-07 Florian Bury , Christophe Delaere

A novel approach is proposed, where energy filtered electrons, carrying both chemical identity and electrical information, serve as fine and flexible electrodes in direct electrical measurements. The method, termed 'chemically resolved…

Materials Science · Physics 2009-11-10 Hagai Cohen

Scanning Transmission Electron Microscopy (STEM) offers high-resolution images that are used to quantify the nanoscale atomic structure and composition of materials and biological specimens. In many cases, however, the resolution is limited…

Signal Processing · Electrical Eng. & Systems 2021-12-23 Daniel Nicholls , Alex Robinson , Jack Wells , Amirafshar Moshtaghpour , Mounib Bahri , Angus Kirkland , Nigel Browning

We propose a novel method to train deep convolutional neural networks which learn from multiple data sets of varying input sizes through weight sharing. This is an advantage in chemometrics where individual measurements represent exact…

Machine Learning · Statistics 2019-11-11 Jacob Søgaard Larsen , Line Clemmensen

The chemical master equation (CME), which describes the discrete and stochastic molecule number dynamics associated with biological processes like transcription, is difficult to solve analytically. It is particularly hard to solve for…

Subcellular Processes · Quantitative Biology 2021-03-23 John J. Vastola , Gennady Gorin , Lior Pachter , William R. Holmes

Deep learning (DL) based channel estimation (CE) and multiple input and multiple output detection (MIMODet), as two separate research topics, have provided convinced evidence to demonstrate the effectiveness and robustness of artificial…

Signal Processing · Electrical Eng. & Systems 2024-01-30 Xiangzhao Qin , Sha Hu , Jiankun Zhang , Jing Qian , Hao Wang

This study presents an innovative approach to predicting VCSEL emission characteristics using transformer neural networks. We demonstrate how to modify the transformer neural network for applications in physics. Our model achieved high…

Disordered Systems and Neural Networks · Physics 2025-09-17 Aleksei V. Belonovskii , Elizaveta I. Girshova , Erkki Lähderanta , Mikhail Kaliteevski

Neural methods of molecule property prediction require efficient encoding of structure and property relationship to be accurate. Recent work using graph algorithms shows limited generalization in the latent molecule encoding space. We build…

Quantitative Methods · Quantitative Biology 2020-11-26 Prateeth Nayak , Andrew Silberfarb , Ran Chen , Tulay Muezzinoglu , John Byrnes

Electron Cryo-Tomography (ECT) enables 3D visualization of macromolecule structure inside single cells. Macromolecule classification approaches based on convolutional neural networks (CNN) were developed to separate millions of…

Quantitative Methods · Quantitative Biology 2018-03-28 Jialiang Guo , Bo Zhou , Xiangrui Zeng , Zachary Freyberg , Min Xu

We report on the design, commissioning, and initial measurements of a Transition-edge Sensor (TES) x-ray spectrometer for the Electron Beam Ion Trap (EBIT) at the National Institute of Standards and Technology (NIST). Over the past few…

Objective: This paper investigates how generative models, trained on ground-truth images, can be used \changes{as} priors for inverse problems, penalizing reconstructions far from images the generator can produce. The aim is that learned…

Image and Video Processing · Electrical Eng. & Systems 2023-08-07 Margaret Duff , Ivor J. A. Simpson , Matthias J. Ehrhardt , Neill D. F. Campbell

Partial Differential Equations (PDEs) are fundamental for modeling physical systems, yet solving them in a generic and efficient manner using machine learning-based approaches remains challenging due to limited multi-input and multi-scale…

Machine Learning · Computer Science 2025-08-12 Yichen Luo , Jia Wang , Dapeng Lan , Yu Liu , Zhibo Pang

Indirect structural health monitoring (iSHM) for broken rail detection using onboard sensors presents a cost-effective paradigm for railway track assessment, yet reliably detecting small, transient anomalies (2-10 cm) remains a significant…

Machine Learning · Computer Science 2025-10-10 Sizhe Ma , Katherine A. Flanigan , Mario Bergés , James D. Brooks

Dynamic Contrast Enhanced Magnetic Resonance Imaging aids in the detection and assessment of tumor aggressiveness by using a Gadolinium-based contrast agent (GBCA). However, GBCA is known to have potential toxic effects. This risk can be…

Image and Video Processing · Electrical Eng. & Systems 2024-02-06 Sadhana S , Sriprabha Ramanarayanan , Arunima Sarkar , Matcha Naga Gayathri , Keerthi Ram , Mohanasankar Sivaprakasam

Editing model parameters directly in Transformers makes updating open-source transformer-based models possible without re-training (Meng et al., 2023). However, these editing methods have only been evaluated on statements about encyclopedic…

Computation and Language · Computer Science 2023-10-27 Anshita Gupta , Debanjan Mondal , Akshay Krishna Sheshadri , Wenlong Zhao , Xiang Lorraine Li , Sarah Wiegreffe , Niket Tandon

Medical image segmentation have drawn massive attention as it is important in biomedical image analysis. Good segmentation results can assist doctors with their judgement and further improve patients' experience. Among many available…

Image and Video Processing · Electrical Eng. & Systems 2021-09-20 Youyang Sha , Yonghong Zhang , Xuquan Ji , Lei Hu

Magnetic Resonance Imaging (MRI) is one of the most flexible and powerful medical imaging modalities. This flexibility does however come at a cost; MRI images acquired at different sites and with different parameters exhibit significant…

Emotion recognition in conversations (ERC), the task of recognizing the emotion of each utterance in a conversation, is crucial for building empathetic machines. Existing studies focus mainly on capturing context- and speaker-sensitive…

Artificial Intelligence · Computer Science 2023-11-01 Hui Ma , Jian Wang , Hongfei Lin , Bo Zhang , Yijia Zhang , Bo Xu

A propagator-based approach is investigated for Monte-Carlo (MC) modeling of neutral particles transport in fusion boundary plasmas. The propagator is essentially a Green function for the neutral kinetic equation, which depends on the…

Plasma Physics · Physics 2026-02-03 M. V. Umansky , G. J. Parker , R. D. Smirnov