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Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

Computational Engineering, Finance, and Science · Computer Science 2023-01-10 Fang Wu , Stan Z. Li

Medical imaging segmentation is a highly active area of research, with deep learning-based methods achieving state-of-the-art results in several benchmarks. However, the lack of standardized tools for training, testing, and evaluating new…

Image and Video Processing · Electrical Eng. & Systems 2024-11-19 Adrian Celaya , Evan Lim , Rachel Glenn , Brayden Mi , Alex Balsells , Dawid Schellingerhout , Tucker Netherton , Caroline Chung , Beatrice Riviere , David Fuentes

Quantitative magnetization transfer (qMT) imaging provides myelin-sensitive biomarkers, such as the pool size ratio (PSR), which is valuable for multiple sclerosis (MS) assessment. However, qMT requires specialized 20-30 minute scans. We…

Image and Video Processing · Electrical Eng. & Systems 2025-11-27 Jiacheng Wang , Hao Li , Xing Yao , Ahmad Toubasi , Taegan Vinarsky , Caroline Gheen , Joy Derwenskus , Chaoyang Jin , Richard Dortch , Junzhong Xu , Francesca Bagnato , Ipek Oguz

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in…

Driven by advances in recording technology, large-scale high-dimensional datasets have emerged across many scientific disciplines. Especially in biology, clustering is often used to gain insights into the structure of such datasets, for…

Machine Learning · Computer Science 2024-10-22 Polina Turishcheva , Laura Hansel , Martin Ritzert , Marissa A. Weis , Alexander S. Ecker

We present MedMNIST, a collection of 10 pre-processed medical open datasets. MedMNIST is standardized to perform classification tasks on lightweight 28x28 images, which requires no background knowledge. Covering the primary data modalities…

Computer Vision and Pattern Recognition · Computer Science 2021-06-08 Jiancheng Yang , Rui Shi , Bingbing Ni

The NuSeC dataset is created by selecting 4 images with the size of 1024*1024 pixels from the slides of each patient among 25 patients. Therefore, there are a total of 100 images in the NuSeC dataset. To carry out a consistent comparative…

Image and Video Processing · Electrical Eng. & Systems 2025-07-22 Refik Samet , Nooshin Nemati , Emrah Hancer , Serpil Sak , Bilge Ayca Kirmizi

Like many scientific fields, new chemistry literature has grown at a staggering pace, with thousands of papers released every month. A large portion of chemistry literature focuses on new molecules and reactions between molecules. Most…

Quantitative Methods · Quantitative Biology 2021-09-10 Daniel Campos , Heng Ji

The size, diversity, and quality of pretraining datasets critically determine the generalization ability of foundation models. Despite their growing importance in chemoinformatics, the effectiveness of molecular representation learning has…

Machine Learning · Computer Science 2025-09-26 Jakub Adamczyk , Jakub Poziemski , Franciszek Job , Mateusz Król , Maciej Makowski

The research presents an overhead view of 10 important objects and follows the general formatting requirements of the most popular machine learning task: digit recognition with MNIST. This dataset offers a public benchmark extracted from…

Computer Vision and Pattern Recognition · Computer Science 2021-02-09 David Noever , Samantha E. Miller Noever

With the development of the medical image field, researchers seek to develop a class of datasets to block the need for medical knowledge, such as \text{MedMNIST} (v2). MedMNIST (v2) includes a large number of small-sized (28 $\times$ 28 or…

Computer Vision and Pattern Recognition · Computer Science 2023-04-21 Zhuoran Zheng , Xiuyi Jia

Benchmarks and datasets have important role in evaluation of machine learning algorithms and neural network implementations. Traditional dataset for images such as MNIST is applied to evaluate efficiency of different training algorithms in…

Neural and Evolutionary Computing · Computer Science 2016-04-25 Mazdak Fatahi , Mahmood Ahmadi , Mahyar Shahsavari , Arash Ahmadi , Philippe Devienne

Magnetic Particle Imaging (MPI) is an emerging imaging modality based on the magnetic response of superparamagnetic iron oxide nanoparticles to achieve high-resolution and real-time imaging without harmful radiation. One key challenge in…

Numerical Analysis · Mathematics 2025-01-13 Meira Iske , Hannes Albers , Tobias Knopp , Tobias Kluth

We propose a unified cross-domain transfer learning framework that leverages knowledge from multiple heterogeneous medical imaging datasets to improve performance across segmentation, classification, and object detection tasks. Our approach…

Computer Vision and Pattern Recognition · Computer Science 2026-05-05 Ceausescu Ciprian-Mihai , Anghelina Ion-Marian , Alexe Dumitru-Bogdan

This paper presents a new concept formation approach that supports the ability to incrementally learn and predict labels for visual images. This work integrates the idea of convolutional image processing, from computer vision research, with…

Computer Vision and Pattern Recognition · Computer Science 2022-01-19 Christopher J. MacLellan , Harshil Thakur

Ultrafast diffraction imaging is a powerful tool to retrieve the geometric structure of gas-phase molecules with combined picometre spatial and attosecond temporal resolution. However, structural retrieval becomes progressively difficult…

Chemical Physics · Physics 2021-10-13 Xinyao Liu , Kasra Amini , Aurelien Sanchez , Blanca Belsa , Tobias Steinle , Jens Biegert

The characterization and analysis of microstructure is the foundation of microstructural science, connecting the materials structure to its composition, process history, and properties. Microstructural quantification traditionally involves…

Computer Vision and Pattern Recognition · Computer Science 2020-10-28 Elizabeth A. Holm , Ryan Cohn , Nan Gao , Andrew R. Kitahara , Thomas P. Matson , Bo Lei , Srujana Rao Yarasi

Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts…

Machine Learning · Computer Science 2022-03-29 Yuanqi Du , Tianfan Fu , Jimeng Sun , Shengchao Liu

Small molecules in biological samples are studied to provide information about disease states, environmental toxins, natural product drug discovery, and many other applications. The primary window into the composition of small molecule…

Machine Learning · Computer Science 2023-05-08 Gennady Voronov , Rose Lightheart , Joe Davison , Christoph A. Krettler , David Healey , Thomas Butler

The integration of deep learning based systems in clinical practice is often impeded by challenges rooted in limited and heterogeneous medical datasets. In addition, the field has increasingly prioritized marginal performance gains on a…

Image and Video Processing · Electrical Eng. & Systems 2025-03-18 Sebastian Doerrich , Francesco Di Salvo , Julius Brockmann , Christian Ledig