Search Results for author: Geoffrey Fox

Found 30 papers, 5 papers with code

Surrogate modeling of Cellular-Potts Agent-Based Models as a segmentation task using the U-Net neural network architecture

no code implementations1 May 2025 Tien Comlekoglu, J. Quetzalcóatl Toledo-Marín, Tina Comlekoglu, Douglas W. DeSimone, Shayn M. Peirce, Geoffrey Fox, James A. Glazier

The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems.

Building Machine Learning Challenges for Anomaly Detection in Science

no code implementations3 Mar 2025 Elizabeth G. Campolongo, Yuan-Tang Chou, Ekaterina Govorkova, Wahid Bhimji, Wei-Lun Chao, Chris Harris, Shih-Chieh Hsu, Hilmar Lapp, Mark S. Neubauer, Josephine Namayanja, Aneesh Subramanian, Philip Harris, Advaith Anand, David E. Carlyn, Subhankar Ghosh, Christopher Lawrence, Eric Moreno, Ryan Raikman, Jiaman Wu, Ziheng Zhang, Bayu Adhi, Mohammad Ahmadi Gharehtoragh, Saúl Alonso Monsalve, Marta Babicz, Furqan Baig, Namrata Banerji, William Bardon, Tyler Barna, Tanya Berger-Wolf, Adji Bousso Dieng, Micah Brachman, Quentin Buat, David C. Y. Hui, Phuong Cao, Franco Cerino, Yi-Chun Chang, Shivaji Chaulagain, An-Kai Chen, Deming Chen, Eric Chen, Chia-Jui Chou, Zih-Chen Ciou, Miles Cochran-Branson, Artur Cordeiro Oudot Choi, Michael Coughlin, Matteo Cremonesi, Maria Dadarlat, Peter Darch, Malina Desai, Daniel Diaz, Steven Dillmann, Javier Duarte, Isla Duporge, Urbas Ekka, Saba Entezari Heravi, Hao Fang, Rian Flynn, Geoffrey Fox, Emily Freed, Hang Gao, Jing Gao, Julia Gonski, Matthew Graham, Abolfazl Hashemi, Scott Hauck, James Hazelden, Joshua Henry Peterson, Duc Hoang, Wei Hu, Mirco Huennefeld, David Hyde, Vandana Janeja, Nattapon Jaroenchai, Haoyi Jia, Yunfan Kang, Maksim Kholiavchenko, Elham E. Khoda, Sangin Kim, Aditya Kumar, Bo-Cheng Lai, Trung Le, Chi-Wei Lee, Janghyeon Lee, Shaocheng Lee, Suzan van der Lee, Charles Lewis, Haitong Li, Haoyang Li, Henry Liao, Mia Liu, Xiaolin Liu, Xiulong Liu, Vladimir Loncar, Fangzheng Lyu, Ilya Makarov, Abhishikth Mallampalli Chen-Yu Mao, Alexander Michels, Alexander Migala, Farouk Mokhtar, Mathieu Morlighem, Min Namgung, Andrzej Novak, Andrew Novick, Amy Orsborn, Anand Padmanabhan, Jia-Cheng Pan, Sneh Pandya, Zhiyuan Pei, Ana Peixoto, George Percivall, Alex Po Leung, Sanjay Purushotham, Zhiqiang Que, Melissa Quinnan, Arghya Ranjan, Dylan Rankin, Christina Reissel, Benedikt Riedel, Dan Rubenstein, Argyro Sasli, Eli Shlizerman, Arushi Singh, Kim Singh, Eric R. Sokol, Arturo Sorensen, Yu Su, Mitra Taheri, Vaibhav Thakkar, Ann Mariam Thomas, Eric Toberer, Chenghan Tsai, Rebecca Vandewalle, Arjun Verma, Ricco C. Venterea, He Wang, Jianwu Wang, Sam Wang, Shaowen Wang, Gordon Watts, Jason Weitz, Andrew Wildridge, Rebecca Williams, Scott Wolf, Yue Xu, Jianqi Yan, Jai Yu, Yulei Zhang, Haoran Zhao, Ying Zhao, Yibo Zhong

We present the different datasets along with a scheme to make machine learning challenges around the three datasets findable, accessible, interoperable, and reusable (FAIR).

Anomaly Detection scientific discovery

Scalable Cosmic AI Inference using Cloud Serverless Computing with FMI

1 code implementation8 Jan 2025 Mills Staylor, Amirreza Dolatpour Fathkouhi, Md Khairul Islam, Kaleigh O'Hara, Ryan Ghiles Goudjil, Geoffrey Fox, Judy Fox

Large-scale astronomical image data processing and prediction is essential for astronomers, providing crucial insights into celestial objects, the universe's history, and its evolution.

Astronomy

Zephyr quantum-assisted hierarchical Calo4pQVAE for particle-calorimeter interactions

no code implementations6 Dec 2024 Ian Lu, Hao Jia, Sebastian Gonzalez, Deniz Sogutlu, J. Quetzalcoatl Toledo-Marin, Sehmimul Hoque, Abhishek Abhishek, Colin Gay, Roger Melko, Eric Paquet, Geoffrey Fox, Maximilian Swiatlowski, Wojciech Fedorko

Through the integration of classical computation and quantum simulation, this hybrid framework paves way for utilizing large-scale quantum simulations as priors in deep generative models.

Science Time Series: Deep Learning in Hydrology

no code implementations19 Oct 2024 Junyang He, Ying-Jung Chen, Anushka Idamekorala, Geoffrey Fox

This analysis is fully open source with a Jupyter Notebook running on Google Colab for both an LSTM-based analysis and the data engineering preprocessing.

Deep Learning Time Series

Study of Dropout in PointPillars with 3D Object Detection

no code implementations1 Sep 2024 Xiaoxiang Sun, Geoffrey Fox

3D object detection is critical for autonomous driving, leveraging deep learning techniques to interpret LiDAR data.

3D Object Detection Autonomous Driving +1

Time Series Foundation Models and Deep Learning Architectures for Earthquake Temporal and Spatial Nowcasting

no code implementations21 Aug 2024 Alireza Jafari, Geoffrey Fox, John B. Rundle, Andrea Donnellan, Lisa Grant Ludwig

Despite significant advancements, existing literature on earthquake nowcasting lacks comprehensive evaluations of pre-trained foundation models and modern deep learning architectures.

Time Series Time Series Forecasting

Feasibility Study on Active Learning of Smart Surrogates for Scientific Simulations

no code implementations10 Jul 2024 Pradeep Bajracharya, Javier Quetzalcóatl Toledo-Marín, Geoffrey Fox, Shantenu Jha, Linwei Wang

High-performance scientific simulations, important for comprehension of complex systems, encounter computational challenges especially when exploring extensive parameter spaces.

Active Learning Diversity

A Comprehensive Evaluation of Generative Models in Calorimeter Shower Simulation

no code implementations8 Jun 2024 Farzana Yasmin Ahmad, Vanamala Venkataswamy, Geoffrey Fox

Our evaluation revealed that the CaloDiffusion and CaloScore generative models demonstrate the most accurate simulation of particle showers, yet there remains substantial room for improvement.

RINAS: Training with Dataset Shuffling Can Be General and Fast

no code implementations4 Dec 2023 Tianle Zhong, Jiechen Zhao, Xindi Guo, Qiang Su, Geoffrey Fox

However, loading shuffled data for large datasets incurs significant overhead in the deep learning pipeline and severely impacts the end-to-end training throughput.

Deep Learning Language Modeling +1

RTP: Rethinking Tensor Parallelism with Memory Deduplication

1 code implementation2 Nov 2023 Cheng Luo, Tianle Zhong, Geoffrey Fox

In the evolving landscape of neural network models, one prominent challenge stand out: the significant memory overheads associated with training expansive models.

Analyzing the Performance of Deep Encoder-Decoder Networks as Surrogates for a Diffusion Equation

no code implementations7 Feb 2023 J. Quetzalcoatl Toledo-Marin, James A. Glazier, Geoffrey Fox

Our results indicate that increasing the size of the training set has a substantial effect on reducing performance fluctuations and overall error.

Decoder

GTrans: Spatiotemporal Autoregressive Transformer with Graph Embeddings for Nowcasting Extreme Events

no code implementations18 Jan 2022 Bo Feng, Geoffrey Fox

In contrast, applications in social networks, road traffic, physics, and chemical property prediction where data features can be organized with nodes and edges of graphs.

Property Prediction Time Series +1

Earthquake Nowcasting with Deep Learning

no code implementations18 Dec 2021 Geoffrey Fox, John Rundle, Andrea Donnellan, Bo Feng

We review previous approaches to nowcasting earthquakes and introduce new approaches based on deep learning using three distinct models based on recurrent neural networks and transformers.

Deep Learning

Scientific Machine Learning Benchmarks

no code implementations25 Oct 2021 Jeyan Thiyagalingam, Mallikarjun Shankar, Geoffrey Fox, Tony Hey

In this paper, we describe our approach to the development of scientific machine learning benchmarks and review other approaches to benchmarking scientific machine learning.

Benchmarking BIG-bench Machine Learning

Multidimensional Scaling for Gene Sequence Data with Autoencoders

no code implementations19 Apr 2021 Pulasthi Wickramasinghe, Geoffrey Fox

Multidimensional scaling of gene sequence data has long played a vital role in analysing gene sequence data to identify clusters and patterns.

Dimensionality Reduction

Deep learning approaches to surrogates for solving the diffusion equation for mechanistic real-world simulations

1 code implementation10 Feb 2021 J. Quetzalcóatl Toledo-Marín, Geoffrey Fox, James P. Sluka, James A. Glazier

To improve convergence during training, we apply a training approach that uses roll-back to reject stochastic changes to the network that increase the loss function.

A Fast, Scalable, Universal Approach For Distributed Data Aggregations

no code implementations27 Oct 2020 Niranda Perera, Vibhatha Abeykoon, Chathura Widanage, Supun Kamburugamuve, Thejaka Amila Kanewala, Pulasthi Wickramasinghe, Ahmet Uyar, Hasara Maithree, Damitha Lenadora, Geoffrey Fox

But, we believe that there is an essential requirement for a data analytics tool that can universally integrate with existing frameworks, and thereby increase the productivity and efficiency of the entire data analytics pipeline.

Deep Tiered Image Segmentation For Detecting Internal Ice Layers in Radar Imagery

no code implementations8 Oct 2020 Yuchen Wang, Mingze Xu, John Paden, Lora Koenig, Geoffrey Fox, David Crandall

Understanding the structure of Earth's polar ice sheets is important for modeling how global warming will impact polar ice and, in turn, the Earth's climate.

Image Segmentation Semantic Segmentation

High Performance Data Engineering Everywhere

no code implementations19 Jul 2020 Chathura Widanage, Niranda Perera, Vibhatha Abeykoon, Supun Kamburugamuve, Thejaka Amila Kanewala, Hasara Maithree, Pulasthi Wickramasinghe, Ahmet Uyar, Gurhan Gunduz, Geoffrey Fox

In this paper we present Cylon, an open-source high performance distributed data processing library that can be seamlessly integrated with existing Big Data and AI/ML frameworks.

Distributed, Parallel, and Cluster Computing Databases

Scientific Image Restoration Anywhere

2 code implementations12 Nov 2019 Vibhatha Abeykoon, Zhengchun Liu, Rajkumar Kettimuthu, Geoffrey Fox, Ian Foster

We explore this question by evaluating the performance and accuracy of a scientific image restoration model, for which both model input and output are images, on edge computing devices.

Edge-computing Image Denoising +2

Learning Everywhere: A Taxonomy for the Integration of Machine Learning and Simulations

no code implementations29 Sep 2019 Geoffrey Fox, Shantenu Jha

We present a taxonomy of research on Machine Learning (ML) applied to enhance simulations together with a catalog of some activities.

BIG-bench Machine Learning

Understanding ML driven HPC: Applications and Infrastructure

no code implementations5 Sep 2019 Geoffrey Fox, Shantenu Jha

We recently outlined the vision of "Learning Everywhere" which captures the possibility and impact of how learning methods and traditional HPC methods can be coupled together.

Performance Optimization on Model Synchronization in Parallel Stochastic Gradient Descent Based SVM

no code implementations3 May 2019 Vibhatha Abeykoon, Geoffrey Fox, Minje Kim

In this research, we identify the bottlenecks in model synchronization in parallel stochastic gradient descent (PSGD)-based SVM algorithm with respect to the training model synchronization frequency (MSF).

Model Optimization

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