4,566 results on '"P. Mattson"'
Search Results
2. Federated Discrete Denoising Diffusion Model for Molecular Generation with OpenFL
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Ta, Kevin, Foley, Patrick, Thieme, Mattson, Pandey, Abhishek, and Shah, Prashant
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Computer Science - Machine Learning ,Computer Science - Cryptography and Security - Abstract
Generating unique molecules with biochemically desired properties to serve as viable drug candidates is a difficult task that requires specialized domain expertise. In recent years, diffusion models have shown promising results in accelerating the drug design process through AI-driven molecular generation. However, training these models requires massive amounts of data, which are often isolated in proprietary silos. OpenFL is a federated learning framework that enables privacy-preserving collaborative training across these decentralized data sites. In this work, we present a federated discrete denoising diffusion model that was trained using OpenFL. The federated model achieves comparable performance with a model trained on centralized data when evaluating the uniqueness and validity of the generated molecules. This demonstrates the utility of federated learning in the drug design process. OpenFL is available at: https://github.com/securefederatedai/openfl, Comment: 10 pages, 5 figures
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- 2025
3. Toward Zero-Shot User Intent Recognition in Shared Autonomy
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Belsare, Atharv, Karimi, Zohre, Mattson, Connor, and Brown, Daniel S.
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Computer Science - Robotics ,Computer Science - Human-Computer Interaction - Abstract
A fundamental challenge of shared autonomy is to use high-DoF robots to assist, rather than hinder, humans by first inferring user intent and then empowering the user to achieve their intent. Although successful, prior methods either rely heavily on a priori knowledge of all possible human intents or require many demonstrations and interactions with the human to learn these intents before being able to assist the user. We propose and study a zero-shot, vision-only shared autonomy (VOSA) framework designed to allow robots to use end-effector vision to estimate zero-shot human intents in conjunction with blended control to help humans accomplish manipulation tasks with unknown and dynamically changing object locations. To demonstrate the effectiveness of our VOSA framework, we instantiate a simple version of VOSA on a Kinova Gen3 manipulator and evaluate our system by conducting a user study on three tabletop manipulation tasks. The performance of VOSA matches that of an oracle baseline model that receives privileged knowledge of possible human intents while also requiring significantly less effort than unassisted teleoperation. In more realistic settings, where the set of possible human intents is fully or partially unknown, we demonstrate that VOSA requires less human effort and time than baseline approaches while being preferred by a majority of the participants. Our results demonstrate the efficacy and efficiency of using off-the-shelf vision algorithms to enable flexible and beneficial shared control of a robot manipulator. Code and videos available here: https://sites.google.com/view/zeroshot-sharedautonomy/home., Comment: 10 pages, 6 figures, Accepted to IEEE/ACM International Conference on Human-Robot Interaction (HRI), 2025. Equal Contribution from the first three authors
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- 2025
4. Targeted Adversarial Denoising Autoencoders (TADA) for Neural Time Series Filtration
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Choi, Benjamin J., Milsap, Griffin, Scholl, Clara A., Tenore, Francesco, and Ogg, Mattson
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Computer Science - Machine Learning - Abstract
Current machine learning (ML)-based algorithms for filtering electroencephalography (EEG) time series data face challenges related to cumbersome training times, regularization, and accurate reconstruction. To address these shortcomings, we present an ML filtration algorithm driven by a logistic covariance-targeted adversarial denoising autoencoder (TADA). We hypothesize that the expressivity of a targeted, correlation-driven convolutional autoencoder will enable effective time series filtration while minimizing compute requirements (e.g., runtime, model size). Furthermore, we expect that adversarial training with covariance rescaling will minimize signal degradation. To test this hypothesis, a TADA system prototype was trained and evaluated on the task of removing electromyographic (EMG) noise from EEG data in the EEGdenoiseNet dataset, which includes EMG and EEG data from 67 subjects. The TADA filter surpasses conventional signal filtration algorithms across quantitative metrics (Correlation Coefficient, Temporal RRMSE, Spectral RRMSE), and performs competitively against other deep learning architectures at a reduced model size of less than 400,000 trainable parameters. Further experimentation will be necessary to assess the viability of TADA on a wider range of deployment cases., Comment: [Accepted] Artificial Intelligence for Time Series Analysis (AI4TS): Theory, Algorithms, and Applications @ AAAI 2025, Philadelphia, PA, USA
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- 2025
5. The EGS Collab project: Outcomes and lessons learned from hydraulic fracture stimulations in crystalline rock at 1.25 and 1.5 km depth
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Kneafsey, Tim, Dobson, Pat, Blankenship, Doug, Schwering, Paul, White, Mark, Morris, Joseph P, Huang, Lianjie, Johnson, Tim, Burghardt, Jeff, Mattson, Earl, Neupane, Ghanashyam, Strickland, Chris, Knox, Hunter, Vermuel, Vince, Ajo-Franklin, Jonathan, Fu, Pengcheng, Roggenthen, William, Doe, Tom, Schoenball, Martin, Hopp, Chet, Tribaldos, Verónica Rodríguez, Ingraham, Mathew, Guglielmi, Yves, Ulrich, Craig, Wood, Todd, Frash, Luke, Pyatina, Tatiana, Vandine, George, Smith, Megan, Horne, Roland, McClure, Mark, Singh, Ankush, Weers, Jon, Robertson, Michelle, and Team, the EGS Collab
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Earth Sciences ,Engineering ,Geology ,Geophysics ,Resources Engineering and Extractive Metallurgy ,Geochemistry & Geophysics ,Resources engineering and extractive metallurgy - Abstract
With the goal of better understanding stimulation in crystalline rock for improving enhanced geothermal systems (EGS), the EGS Collab Project performed a series of stimulations and flow tests at 1.25 and 1.5 km depths. The tests were performed in two well-instrumented testbeds in the Sanford Underground Research Facility in Lead, South Dakota, United States. The testbed for Experiment 1 at 1.5 km depth contained two open wells for injection and production and six instrumented monitoring wells surrounding the targeted stimulation zone. Four multi-step stimulation tests targeting hydraulic fracturing and nearly year-long ambient temperature and chilled water flow tests were performed in Experiment 1. The testbed for Experiments 2 and 3 was at 1.25 km depth and contained five open wells in an outwardly fanning five-spot pattern and two fans of well-instrumented monitoring wells surrounding the targeted stimulation zone. Experiment 2 targeted shear stimulation, and Experiment 3 targeted low-flow, high-flow, and oscillating pressure stimulation strategies. Hydraulic fracturing was successful in Experiments 1 and 3 in generating a connected system wherein injected water could be collected. However, the resulting flow was distributed dynamically, and not entirely collected at the anticipated production well. Thermal breakthrough was not observed in the production well, but that could have been masked by the Joule-Thomson effect. Shear stimulation in Experiment 2 did not occur – despite attempting to pressurize the fractures most likely to shear – because of the inability to inject water into a mostly-healed fracture, and the low shear-to-normal stress ratio. The EGS Collab experiments are described to provide a background for lessons learned on topics including induced seismicity, the correlation between seismicity and permeability, distributed and dynamic flow systems, thermoelastic and pressure effects, shear stimulation, local geology, thermal breakthrough, monitoring stimulation, grouting boreholes, modeling, and system management.
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- 2025
6. Integrating priorities at the intersection of cancer and neuroscience
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Hwang, William L, Perrault, Ella N, Birbrair, Alexander, Mattson, Brandi J, Gutmann, David H, Mabbott, Donald J, Cukierman, Edna, Repasky, Elizabeth A, Sloan, Erica K, Zong, Hui, Demir, Ihsan Ekin, Saloman, Jami L, Borniger, Jeremy C, Hu, Jian, Dietrich, Jorg, Breunig, Joshua J, Çifcibaşı, Kaan, Ahmad Kasm, Khalil Ali, Valiente, Manuel, Wintermark, Max, Acharya, Munjal M, Scheff, Nicole N, D'Silva, Nisha J, Vermeer, Paola D, Wong, Richard J, Talbot, Sebastien, Hervey-Jumper, Shawn L, Wang, Timothy C, Ye, Yi, Pan, Yuan, Bunimovich, Yuri L, and Amit, Moran
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Cancer ,Humans ,Neurosciences ,Neoplasms ,Translational Research ,Biomedical ,Animals ,Oncology & Carcinogenesis ,Biochemistry and cell biology ,Oncology and carcinogenesis - Abstract
Cancer neuroscience is a rapidly growing multidisciplinary field that conceptualizes tumors as tissues fully integrated into the nervous system. Recognizing the complexity and challenges in this field is of fundamental importance to achieving the goal of translational impact for cancer patients. Our commentary highlights key scientific priorities, optimal training settings, and roadblocks to translating scientific findings to the clinic in this emerging field, aiming to formulate a transformative and cohesive path forward.
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- 2025
7. Turing Representational Similarity Analysis (RSA): A Flexible Method for Measuring Alignment Between Human and Artificial Intelligence
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Ogg, Mattson, Bose, Ritwik, Scharf, Jamie, Ratto, Christopher, and Wolmetz, Michael
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Computer Science - Artificial Intelligence - Abstract
As we consider entrusting Large Language Models (LLMs) with key societal and decision-making roles, measuring their alignment with human cognition becomes critical. This requires methods that can assess how these systems represent information and facilitate comparisons to human understanding across diverse tasks. To meet this need, we developed Turing Representational Similarity Analysis (RSA), a method that uses pairwise similarity ratings to quantify alignment between AIs and humans. We tested this approach on semantic alignment across text and image modalities, measuring how different Large Language and Vision Language Model (LLM and VLM) similarity judgments aligned with human responses at both group and individual levels. GPT-4o showed the strongest alignment with human performance among the models we tested, particularly when leveraging its text processing capabilities rather than image processing, regardless of the input modality. However, no model we studied adequately captured the inter-individual variability observed among human participants. This method helped uncover certain hyperparameters and prompts that could steer model behavior to have more or less human-like qualities at an inter-individual or group level. Turing RSA enables the efficient and flexible quantification of human-AI alignment and complements existing accuracy-based benchmark tasks. We demonstrate its utility across multiple modalities (words, sentences, images) for understanding how LLMs encode knowledge and for examining representational alignment with human cognition.
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- 2024
8. Agent-Based Emulation for Deploying Robot Swarm Behaviors
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Vega, Ricardo, Zhu, Kevin, Mattson, Connor, Brown, Daniel S., and Nowzari, Cameron
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Computer Science - Robotics ,Electrical Engineering and Systems Science - Systems and Control - Abstract
Despite significant research, robotic swarms have yet to be useful in solving real-world problems, largely due to the difficulty of creating and controlling swarming behaviors in multi-agent systems. Traditional top-down approaches in which a desired emergent behavior is produced often require complex, resource-heavy robots, limiting their practicality. This paper introduces a bottom-up approach by employing an Embodied Agent-Based Modeling and Simulation approach, emphasizing the use of simple robots and identifying conditions that naturally lead to self-organized collective behaviors. Using the Reality-to-Simulation-to-Reality for Swarms (RSRS) process, we tightly integrate real-world experiments with simulations to reproduce known swarm behaviors as well as discovering a novel emergent behavior without aiming to eliminate or even reduce the sim2real gap. This paper presents the development of an Agent-Based Embodiment and Emulation process that balances the importance of running physical swarming experiments and the prohibitively time-consuming process of even setting up and running a single experiment with 20+ robots by leveraging low-fidelity lightweight simulations to enable hypothesis-formation to guide physical experiments. We demonstrate the usefulness of our methods by emulating two known behaviors from the literature and show a third behavior `discovered' by accident., Comment: 8 pages, 6 figures, submitted to ICRA 2025
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- 2024
9. Spiking Neural Networks as a Controller for Emergent Swarm Agents
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Zhu, Kevin, Mattson, Connor, Snyder, Shay, Vega, Ricardo, Brown, Daniel S., Parsa, Maryam, and Nowzari, Cameron
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Computer Science - Neural and Evolutionary Computing ,Computer Science - Multiagent Systems ,Electrical Engineering and Systems Science - Systems and Control - Abstract
Drones which can swarm and loiter in a certain area cost hundreds of dollars, but mosquitos can do the same and are essentially worthless. To control swarms of low-cost robots, researchers may end up spending countless hours brainstorming robot configurations and policies to ``organically" create behaviors which do not need expensive sensors and perception. Existing research explores the possible emergent behaviors in swarms of robots with only a binary sensor and a simple but hand-picked controller structure. Even agents in this highly limited sensing, actuation, and computational capability class can exhibit relatively complex global behaviors such as aggregation, milling, and dispersal, but finding the local interaction rules that enable more collective behaviors remains a significant challenge. This paper investigates the feasibility of training spiking neural networks to find those local interaction rules that result in particular emergent behaviors. In this paper, we focus on simulating a specific milling behavior already known to be producible using very simple binary sensing and acting agents. To do this, we use evolutionary algorithms to evolve not only the parameters (the weights, biases, and delays) of a spiking neural network, but also its structure. To create a baseline, we also show an evolutionary search strategy over the parameters for the incumbent hand-picked binary controller structure. Our simulations show that spiking neural networks can be evolved in binary sensing agents to form a mill., Comment: 8 pages, 7 figures, presented at the 2024 International Conference on Neuromorphic Systems
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- 2024
10. Math Abilities among Children with Neurodevelopmental Difficulties: Understanding Cognitive Factors and Evaluating a Pilot Intervention
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Danielle Mattson, Kathryn Kryska, Jacqueline Pei, Claire Coles, Julie Kable, Molly Millians, Gail Andrew, Damien Cormier, and Carmen Rasmussen
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Math development in children relies on several underlying cognitive functions, including executive functions (EF), working memory (WM), and visual-motor abilities, such as visual-motor integration (VMI). Understanding how these cognitive factors contribute to children's math performance is critical to supporting math learning and long-term math success. The present quasi-experimental waitlist control study (N = 28) aimed to (a) examine the unique contributions of EF, WM, and VMI to math abilities among children ages 5-8 years old with neurodevelopmental difficulties; (b) determine whether a math intervention (the Mathematics Interactive Learning Experience; MILE) that supports these cognitive processes was effective when modified to be delivered to small groups in a school setting, and (c) examine whether any participant characteristics, such as age or IQ, were correlated with post-intervention math score changes. At baseline, participants' math scores were significantly below the normative mean in all math content areas (ps < 0.01). EF, WM, and VMI were highly correlated with math ability; however, verbal WM was the only unique predictor of math ability in regressions analysis. Compared to a waitlist control group, children in the immediate MILE intervention group achieved significantly greater math gains overall. When all children who ultimately completed the intervention were considered together, significant improvement was observed in more than half of math content areas. Furthermore, at the individual level, 85.7% of participants showed reliable change in at least one math content area. Implications for supporting math learning in children with neurodevelopmental difficulties are discussed.
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- 2024
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11. Reduction of APOE accounts for neurobehavioral deficits in fetal alcohol spectrum disorders.
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Hwang, Hye, Yamashita, Satoshi, Matsumoto, Yu, Ito, Mariko, Edwards, Alex, Sasaki, Junko, Dutta, Dipankar, Mohammad, Shahid, Yamashita, Chiho, Wetherill, Leah, Schwantes-An, Tae-Hwi, Abreu, Marco, Mahnke, Amanda, Mattson, Sarah, Foroud, Tatiana, Miranda, Rajesh, Chambers, Christina, Torii, Masaaki, and Hashimoto-Torii, Kazue
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Fetal Alcohol Spectrum Disorders ,Animals ,Mice ,Female ,Humans ,Pregnancy ,Apolipoproteins E ,Prenatal Exposure Delayed Effects ,Male ,Brain ,Genome-Wide Association Study ,Polymorphism ,Single Nucleotide ,Disease Models ,Animal ,Child ,Mice ,Inbred C57BL ,Ethanol - Abstract
A hallmark of fetal alcohol spectrum disorders (FASD) is neurobehavioral deficits that still do not have effective treatment. Here, we present that reduction of Apolipoprotein E (APOE) is critically involved in neurobehavioral deficits in FASD. We show that prenatal alcohol exposure (PAE) changes chromatin accessibility of Apoe locus, and causes reduction of APOE levels in both the brain and peripheral blood in postnatal mice. Of note, postnatal administration of an APOE receptor agonist (APOE-RA) mitigates motor learning deficits and anxiety in those mice. Several molecular and electrophysiological properties essential for learning, which are altered by PAE, are restored by APOE-RA. Our human genome-wide association study further reveals that the interaction of PAE and a single nucleotide polymorphism in the APOE enhancer which chromatin is closed by PAE in mice is associated with lower scores in the delayed matching-to-sample task in children. APOE in the plasma is also reduced in PAE children, and the reduced level is associated with their lower cognitive performance. These findings suggest that controlling the APOE level can serve as an effective treatment for neurobehavioral deficits in FASD.
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- 2024
12. Representation Alignment from Human Feedback for Cross-Embodiment Reward Learning from Mixed-Quality Demonstrations
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Mattson, Connor, Aribandi, Anurag, and Brown, Daniel S.
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Computer Science - Robotics ,Computer Science - Artificial Intelligence - Abstract
We study the problem of cross-embodiment inverse reinforcement learning, where we wish to learn a reward function from video demonstrations in one or more embodiments and then transfer the learned reward to a different embodiment (e.g., different action space, dynamics, size, shape, etc.). Learning reward functions that transfer across embodiments is important in settings such as teaching a robot a policy via human video demonstrations or teaching a robot to imitate a policy from another robot with a different embodiment. However, prior work has only focused on cases where near-optimal demonstrations are available, which is often difficult to ensure. By contrast, we study the setting of cross-embodiment reward learning from mixed-quality demonstrations. We demonstrate that prior work struggles to learn generalizable reward representations when learning from mixed-quality data. We then analyze several techniques that leverage human feedback for representation learning and alignment to enable effective cross-embodiment learning. Our results give insight into how different representation learning techniques lead to qualitatively different reward shaping behaviors and the importance of human feedback when learning from mixed-quality, mixed-embodiment data., Comment: First Two Authors Share Equal Contribution. 19 Pages, 4 Figures
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- 2024
13. Qualitative Exploration and Proof of Concept Toward the Development of the Burnout Assessment for Developmental Disability Settings (BADDS) for Behavioral Health Providers
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Bottini, Summer, Gillis Mattson, Jennifer, Herrod, Jessica, Sinha, Cynthia, Scheithauer, Mindy, Mevers, Joanna Lomas, and Scahill, Lawrence
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- 2025
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14. A multilineage screen identifies actionable synthetic lethal interactions in human cancers
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Fong, Samson H., Kuenzi, Brent M., Mattson, Nicole M., Lee, John, Sanchez, Kyle, Bojorquez-Gomez, Ana, Ford, Kyle, Munson, Brenton P., Licon, Katherine, Bergendahl, Sarah, Shen, John Paul, Kreisberg, Jason F., Mali, Prashant, Hager, Jeffrey H., White, Michael A., and Ideker, Trey
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- 2025
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15. Effects of vaginal estrogen on serum estradiol during aromatase inhibitor therapy in breast cancer patients with vulvovaginal atrophy: a prospective trial
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Faltinová, Mária, Vehmanen, Leena, Lyytinen, Heli, Savolainen-Peltonen, Hanna, Virtanen, Anni, Haanpää, Mikko, Hämäläinen, Esa, Tiitinen, Aila, and Mattson, Johanna
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- 2024
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16. Exploring Differences in Leadership Behaviors and in the Perceived Work Environment Between Younger and Older Managers in a Swedish Mining Company
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Lööw, Joel, Vinberg, Stig, Johansson, Jan, Jakobsson, Mats, Mattson Molnar, Malin, and Larsson, Johan
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- 2024
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17. Effects of an Activity Schedule Intervention Package on Cooperative Vocal Exchanges During Learning Centers
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Mattson, Stephanie L., Higbee, Thomas S., Nichols, Beverly, Aguilar, Juliana, and Campbell, Vincent E.
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- 2024
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18. Distributed Ranges: A Model for Distributed Data Structures, Algorithms, and Views
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Brock, Benjamin, Cohn, Robert, Bakshi, Suyash, Karna, Tuomas, Kim, Jeongnim, Nowak, Mateusz, Ślusarczyk, Łukasz, Stefanski, Kacper, and Mattson, Timothy G.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Data structures and algorithms are essential building blocks for programs, and \emph{distributed data structures}, which automatically partition data across multiple memory locales, are essential to writing high-level parallel programs. While many projects have designed and implemented C++ distributed data structures and algorithms, there has not been widespread adoption of an interoperable model allowing algorithms and data structures from different libraries to work together. This paper introduces distributed ranges, which is a model for building generic data structures, views, and algorithms. A distributed range extends a C++ range, which is an iterable sequence of values, with a concept of segmentation, thus exposing how the distributed range is partitioned over multiple memory locales. Distributed data structures provide this distributed range interface, which allows them to be used with a collection of generic algorithms implemented using the distributed range interface. The modular nature of the model allows for the straightforward implementation of \textit{distributed views}, which are lightweight objects that provide a lazily evaluated view of another range. Views can be composed together recursively and combined with algorithms to implement computational kernels using efficient, flexible, and high-level standard C++ primitives. We evaluate the distributed ranges model by implementing a set of standard concepts and views as well as two execution runtimes, a multi-node, MPI-based runtime and a single-process, multi-GPU runtime. We demonstrate that high-level algorithms implemented using generic, high-level distributed ranges can achieve performance competitive with highly-tuned, expert-written code., Comment: To appear in ACM International Conference on Supercomputing (ICS) 2024
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- 2024
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19. An Abstraction Hierarchy Toward Productive Quantum Programming
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Di Matteo, Olivia, Núñez-Corrales, Santiago, Stęchły, Michał, Reinhardt, Steven P., and Mattson, Tim
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Quantum Physics - Abstract
Experience from seven decades of classical computing suggests that a sustainable computer industry depends on a community of software engineers writing programs to address a wide variety of specific end-user needs, achieving both performance and utility in the process. Quantum computing is an emerging technology, and we do not yet have the insight to understand what quantum software tools and practices will best support researchers, software engineers, or applications specialists. Developers for today's quantum computers are grappling with the low-level details of the hardware, and progress towards scalable devices does not yet suggest what higher-level abstractions may look like. In this paper, we analyze and reframe the current state of the quantum software stack using the language of programming models. We propose an abstraction hierarchy to support quantum software engineering and discuss the consequences of overlaps across the programming, execution, and hardware models found in current technologies. We exercise this hierarchy for solving the eigenvalue estimation problem in two ways (a variational algorithm with error mitigation, and phase estimation with error correction) and pinpoint key differences in these approaches in terms of these layered models and their overlaps. While our work points to concrete conceptual challenges and gaps in quantum programming and proposes some specific steps forward, our primary thesis is that progress hinges on thinking about the abstraction hierarchy holistically, and not just about its components., Comment: 11 pages, 3 figures. Submitted to IEEE QCE 24
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- 2024
20. Introducing v0.5 of the AI Safety Benchmark from MLCommons
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Vidgen, Bertie, Agrawal, Adarsh, Ahmed, Ahmed M., Akinwande, Victor, Al-Nuaimi, Namir, Alfaraj, Najla, Alhajjar, Elie, Aroyo, Lora, Bavalatti, Trupti, Bartolo, Max, Blili-Hamelin, Borhane, Bollacker, Kurt, Bomassani, Rishi, Boston, Marisa Ferrara, Campos, Siméon, Chakra, Kal, Chen, Canyu, Coleman, Cody, Coudert, Zacharie Delpierre, Derczynski, Leon, Dutta, Debojyoti, Eisenberg, Ian, Ezick, James, Frase, Heather, Fuller, Brian, Gandikota, Ram, Gangavarapu, Agasthya, Gangavarapu, Ananya, Gealy, James, Ghosh, Rajat, Goel, James, Gohar, Usman, Goswami, Sujata, Hale, Scott A., Hutiri, Wiebke, Imperial, Joseph Marvin, Jandial, Surgan, Judd, Nick, Juefei-Xu, Felix, Khomh, Foutse, Kailkhura, Bhavya, Kirk, Hannah Rose, Klyman, Kevin, Knotz, Chris, Kuchnik, Michael, Kumar, Shachi H., Kumar, Srijan, Lengerich, Chris, Li, Bo, Liao, Zeyi, Long, Eileen Peters, Lu, Victor, Luger, Sarah, Mai, Yifan, Mammen, Priyanka Mary, Manyeki, Kelvin, McGregor, Sean, Mehta, Virendra, Mohammed, Shafee, Moss, Emanuel, Nachman, Lama, Naganna, Dinesh Jinenhally, Nikanjam, Amin, Nushi, Besmira, Oala, Luis, Orr, Iftach, Parrish, Alicia, Patlak, Cigdem, Pietri, William, Poursabzi-Sangdeh, Forough, Presani, Eleonora, Puletti, Fabrizio, Röttger, Paul, Sahay, Saurav, Santos, Tim, Scherrer, Nino, Sebag, Alice Schoenauer, Schramowski, Patrick, Shahbazi, Abolfazl, Sharma, Vin, Shen, Xudong, Sistla, Vamsi, Tang, Leonard, Testuggine, Davide, Thangarasa, Vithursan, Watkins, Elizabeth Anne, Weiss, Rebecca, Welty, Chris, Wilbers, Tyler, Williams, Adina, Wu, Carole-Jean, Yadav, Poonam, Yang, Xianjun, Zeng, Yi, Zhang, Wenhui, Zhdanov, Fedor, Zhu, Jiacheng, Liang, Percy, Mattson, Peter, and Vanschoren, Joaquin
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
This paper introduces v0.5 of the AI Safety Benchmark, which has been created by the MLCommons AI Safety Working Group. The AI Safety Benchmark has been designed to assess the safety risks of AI systems that use chat-tuned language models. We introduce a principled approach to specifying and constructing the benchmark, which for v0.5 covers only a single use case (an adult chatting to a general-purpose assistant in English), and a limited set of personas (i.e., typical users, malicious users, and vulnerable users). We created a new taxonomy of 13 hazard categories, of which 7 have tests in the v0.5 benchmark. We plan to release version 1.0 of the AI Safety Benchmark by the end of 2024. The v1.0 benchmark will provide meaningful insights into the safety of AI systems. However, the v0.5 benchmark should not be used to assess the safety of AI systems. We have sought to fully document the limitations, flaws, and challenges of v0.5. This release of v0.5 of the AI Safety Benchmark includes (1) a principled approach to specifying and constructing the benchmark, which comprises use cases, types of systems under test (SUTs), language and context, personas, tests, and test items; (2) a taxonomy of 13 hazard categories with definitions and subcategories; (3) tests for seven of the hazard categories, each comprising a unique set of test items, i.e., prompts. There are 43,090 test items in total, which we created with templates; (4) a grading system for AI systems against the benchmark; (5) an openly available platform, and downloadable tool, called ModelBench that can be used to evaluate the safety of AI systems on the benchmark; (6) an example evaluation report which benchmarks the performance of over a dozen openly available chat-tuned language models; (7) a test specification for the benchmark.
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- 2024
21. Croissant: A Metadata Format for ML-Ready Datasets
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Akhtar, Mubashara, Benjelloun, Omar, Conforti, Costanza, Foschini, Luca, Giner-Miguelez, Joan, Gijsbers, Pieter, Goswami, Sujata, Jain, Nitisha, Karamousadakis, Michalis, Kuchnik, Michael, Krishna, Satyapriya, Lesage, Sylvain, Lhoest, Quentin, Marcenac, Pierre, Maskey, Manil, Mattson, Peter, Oala, Luis, Oderinwale, Hamidah, Ruyssen, Pierre, Santos, Tim, Shinde, Rajat, Simperl, Elena, Suresh, Arjun, Thomas, Goeffry, Tykhonov, Slava, Vanschoren, Joaquin, Varma, Susheel, van der Velde, Jos, Vogler, Steffen, Wu, Carole-Jean, and Zhang, Luyao
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Databases ,Computer Science - Information Retrieval - Abstract
Data is a critical resource for machine learning (ML), yet working with data remains a key friction point. This paper introduces Croissant, a metadata format for datasets that creates a shared representation across ML tools, frameworks, and platforms. Croissant makes datasets more discoverable, portable, and interoperable, thereby addressing significant challenges in ML data management. Croissant is already supported by several popular dataset repositories, spanning hundreds of thousands of datasets, enabling easy loading into the most commonly-used ML frameworks, regardless of where the data is stored. Our initial evaluation by human raters shows that Croissant metadata is readable, understandable, complete, yet concise., Comment: Published at the NeurIPS 2024 Datasets and Benchmark Track. A shorter version appeared earlier in Proceedings of ACM SIGMOD/PODS'24 Data Management for End-to-End Machine Learning (DEEM) Workshop https://dl.acm.org/doi/10.1145/3650203.3663326
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- 2024
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22. Behavioral Skills Training with Adult Interventionists: A Systematic Review
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Sandra G. Smith, Stephanie L. Mattson, Juliana Aguilar, Nicole Pyle, and Thomas S. Higbee
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Behavioral skills training (BST) is a performance- and competency-based training package composed of instructions, modeling, rehearsal, and feedback. Previous reviews have demonstrated that BST is an effective training package to teach interventionists to implement behavior analytic interventions (Kirkpatrick et al. in "Journal of Behavioral Education," 28, 344-361, Kirkpatrick et al., "Journal of Behavioral Education" 28344-361, 2019). The purpose of this review was to examine the characteristics of BST for training adult interventionists to implement behavior analytic procedures with children with autism spectrum disorder (ASD). Also, we investigated various factors that may lead to efficient BST delivery, compiled the external validity indicators included in BST research, and investigated the methodological quality of BST research studies. In this systematic review of 30 studies from 2004 to 2019, we found that trainers consistently taught the four BST components, yet implementation varied substantially across studies. Inconsistent reporting of factors affecting efficiency limited our ability to analyze which components and delivery methods was most efficient. External validity measures, such as generalization and outcome measures for children receiving the behavior analytic intervention, were often reported. The evidence quality and design quality were mixed. BST is generally accepted as an effective intervention for training a wide range of interventions; however, more high-quality research studies are needed including evaluation of explicit descriptions for all BST components.
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- 2024
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23. Systems Reviews: An Approach to Building Coherence, Increasing Efficiency, and Improving Workflow at State Education Agencies
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Region 15 Comprehensive Center, WestEd, Mattson, Heather, Zoffel, Jennifer, and McCormick, Malachy
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The challenges state education agencies (SEAs) must address are exceedingly complex, requiring sophisticated levels of thinking and problem-solving as well as the ability to leverage disparate points of view in finding impactful solutions. These challenges are technical, requiring specific and known solutions to achieve desired results. To provide more coherent, integrated services to the field in the face of complex challenges, SEAs need to engage in systems change. This brief from the Region 15 Comprehensive Center shares its iterative Systems Review approach that assists SEAs in considering new and more effective ways to build coherence, increase efficiency, and improve workflow--all in the service of effectively supporting local education agencies (LEAs) in implementing state priorities.
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- 2023
24. Akt-activated GSK3β inhibitory peptide effectively blocks tau hyperphosphorylation
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Lee, Eunjin, Lee, Yujeong, Yang, Seonguk, Gong, Eun Ji, Kim, Jaehoon, Ha, Nam-Chul, Jo, Dong-Gyu, Mattson, Mark P., and Lee, Jaewon
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- 2024
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25. Development of a checklist for evaluation of shared decision-making in consultation for extremely preterm delivery
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Guindon, Michael, Feltman, Dalia M., Litke-Wager, Carrie, Okonek, Elizabeth, Mullin, Kaitlyn T., Anani, Uchenna E., Murray II, Peter D., Mattson, Christopher, and Krick, Jeanne
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- 2024
- Full Text
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26. Targeting the peripheral neural-tumour microenvironment for cancer therapy
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Yaniv, Dan, Mattson, Brandi, Talbot, Sebastien, Gleber-Netto, Frederico O., and Amit, Moran
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- 2024
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27. Neural response to vocal emotional intensity in youth
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Morningstar, M., Billetdeaux, K. A., Mattson, W. I., Gilbert, A. C., Nelson, E. E., and Hoskinson, K. R.
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- 2024
- Full Text
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28. Young Children of Mothers with a History of Depression Show Attention Bias to Sad Faces: An Eye-tracking Study
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Fu, Xiaoxue, Bolton, Scout H., Morningstar, Michele, Mattson, Whitney I., Feng, Xin, and Nelson, Eric E.
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- 2024
- Full Text
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29. MPIrigen: MPI Code Generation through Domain-Specific Language Models
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Schneider, Nadav, Hasabnis, Niranjan, Vo, Vy A., Kadosh, Tal, Krien, Neva, Capotă, Mihai, Tamir, Guy, Willke, Ted, Ahmed, Nesreen, Pinter, Yuval, Mattson, Timothy, and Oren, Gal
- Subjects
Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Artificial Intelligence ,Computer Science - Computation and Language ,Computer Science - Machine Learning ,Computer Science - Software Engineering - Abstract
The imperative need to scale computation across numerous nodes highlights the significance of efficient parallel computing, particularly in the realm of Message Passing Interface (MPI) integration. The challenging parallel programming task of generating MPI-based parallel programs has remained unexplored. This study first investigates the performance of state-of-the-art language models in generating MPI-based parallel programs. Findings reveal that widely used models such as GPT-3.5 and PolyCoder (specialized multi-lingual code models) exhibit notable performance degradation, when generating MPI-based programs compared to general-purpose programs. In contrast, domain-specific models such as MonoCoder, which are pretrained on MPI-related programming languages of C and C++, outperform larger models. Subsequently, we introduce a dedicated downstream task of MPI-based program generation by fine-tuning MonoCoder on HPCorpusMPI. We call the resulting model as MPIrigen. We propose an innovative preprocessing for completion only after observing the whole code, thus enabling better completion with a wider context. Comparative analysis against GPT-3.5 zero-shot performance, using a novel HPC-oriented evaluation method, demonstrates that MPIrigen excels in generating accurate MPI functions up to 0.8 accuracy in location and function predictions, and with more than 0.9 accuracy for argument predictions. The success of this tailored solution underscores the importance of domain-specific fine-tuning in optimizing language models for parallel computing code generation, paving the way for a new generation of automatic parallelization tools. The sources of this work are available at our GitHub MPIrigen repository: https://github.com/Scientific-Computing-Lab-NRCN/MPI-rigen
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- 2024
30. The Landscape and Challenges of HPC Research and LLMs
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Chen, Le, Ahmed, Nesreen K., Dutta, Akash, Bhattacharjee, Arijit, Yu, Sixing, Mahmud, Quazi Ishtiaque, Abebe, Waqwoya, Phan, Hung, Sarkar, Aishwarya, Butler, Branden, Hasabnis, Niranjan, Oren, Gal, Vo, Vy A., Munoz, Juan Pablo, Willke, Theodore L., Mattson, Tim, and Jannesari, Ali
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Computer Science - Machine Learning - Abstract
Recently, language models (LMs), especially large language models (LLMs), have revolutionized the field of deep learning. Both encoder-decoder models and prompt-based techniques have shown immense potential for natural language processing and code-based tasks. Over the past several years, many research labs and institutions have invested heavily in high-performance computing, approaching or breaching exascale performance levels. In this paper, we posit that adapting and utilizing such language model-based techniques for tasks in high-performance computing (HPC) would be very beneficial. This study presents our reasoning behind the aforementioned position and highlights how existing ideas can be improved and adapted for HPC tasks.
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- 2024
31. High-statistics measurement of Collins and Sivers asymmetries for transversely polarised deuterons
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Alexeev, G. D., Alexeev, M. G., Alice, C., Amoroso, A., Andrieux, V., Anosov, V., Asatryan, S., Augsten, K., Augustyniak, W., Azevedo, C. D. R., Badelek, B., Barth, J., Beck, R., Beckers, J., Bedfer, Y., Bernhard, J., Bodlak, M., Bradamante, F., Bressan, A., Chang, W. -C., Chatterjee, C., Chiosso, M., Chumakov, A. G., Chung, S. -U., Cicuttin, A., Correia, P. M. M., Crespo, M. L., D'Ago, D., Torre, S. Dalla, Dasgupta, S. S., Dasgupta, S., Delcarro, F., Denisenko, I., Denisov, O. Yu., Donskov, S. V., Doshita, N., Dreisbach, Ch., Dunnweber, W., Dusaev, R. R., Ecker, D., Eremeev, D., Faccioli, P., Faessler, M., Finger, M., Finger jr., M., Fischer, H., Flothner, K. J., Florian, W., Friedrich, J. M., Frolov, V., Ordonez, L. G. Garcia, Gautheron, F., Gavrichtchouk, O. P., Gerassimov, S., Giarra, J., Giordano, D., Grasso, A., Gridin, A., Perdekamp, M. Grosse, Grube, B., Gruner, M., Guskov, A., Haas, P., von Harrach, D., Hoffmann, M., Hoghmrtsyan, A., d'Hose, N., Hsieh, C. -Y., Huber, S., Ishimoto, S., Ivanov, A., Iwata, T., Jary, V., Joosten, R., Kabuss, E., Kaspar, F., Kerbizi, A., Ketzer, B., Khatun, A., Khaustov, G. V., Klasek, T., Klein, F., Koivuniemi, J. H., Kolosov, V. N., Horikawa, K. Kondo, Konorov, I., Konstantinov, V. F., Korzenev, A. Yu., Kotzinian, A. M., Kouznetsov, O. M., Koval, A., Kral, Z., Krinner, F., Kunne, F., Kurek, K., Kurjata, R. P., Kveton, A., Lavickova, K., Levorato, S., Lian, Y. -S., Lichtenstadt, J., Lin, P. -J., Longo, R., Lyubovitskij, V. E., Maggiora, A., Magnon, A., Makke, N., Mallot, G. K., Maltsev, A., Martin, A., Marzec, J., Matousek, J., Matsuda, T., Mattson, G., Pires, C. Menezes, Metzger, F., Meyer, M., Meyer, W., Mikhailov, Yu. V., Mikhasenko, M., Mitrofanov, E., Miura, D., Miyachi, Y., Molina, R., Moretti, A., Movsisyan, A., Nagaytsev, A., Neyret, D., Niemiec, M., Novy, J., Nowak, W. -D., Nukazuka, G., Olshevsky, A. G., Ostrick, M., Panzieri, D., Parsamyan, B., Paul, S., Pekeler, H., Peng, J. -C., Pesek, M., Peshekhonov, D. V., Peskova, M., Platchkov, S., Pochodzalla, J., Polyakov, V. A., Quaresma, M., Quintans, C., Reicherz, G., Riedl, C., Ryabchikov, D. I., Rychter, A., Rymbekova, A., Samoylenko, V. D., Sandacz, A., Sarkar, S., Savin, I. A., Sbrizzai, G., Schmieden, H., Selyunin, A., Sharko, K., Sinha, L., Spulbeck, D., Srnka, A., Stolarski, M., Sulc, M., Suzuki, H., Takanashi, Y., Tessaro, S., Tessarotto, F., Thiel, A., Tosello, F., Townsend, A., Triloki, T., Tskhay, V., Valinoti, B., Veit, B. M., Veloso, J. F. C. A., Ventura, B., Vijayakumar, A., Virius, M., Wagner, M., Wallner, S., Zaremba, K., Zavertyaev, M., Zemko, M., Zemlyanichkina, E., and Ziembicki, M.
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High Energy Physics - Experiment ,High Energy Physics - Phenomenology - Abstract
New results are presented on a high-statistics measurement of Collins and Sivers asymmetries of charged hadrons produced in deep inelastic scattering of muons on a transversely polarised $^6$LiD target. The data were taken in 2022 with the COMPASS spectrometer using the 160 \gevv\ muon beam at CERN, balancing the existing data on transversely polarised proton targets. The first results from about two-thirds of the new data have total uncertainties smaller by up to a factor of three compared to the previous deuteron measurements. Using all the COMPASS proton and deuteron results, both the transversity and the Sivers distribution functions of the $u$ and $d$ quark, as well as the tensor charge in the measured $x$-range are extracted. In particular, the accuracy of the $d$ quark results is significantly improved.
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- 2023
32. Final COMPASS results on the transverse-spin-dependent azimuthal asymmetries in the pion-induced Drell-Yan process
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Alexeev, G. D., Alexeev, M. G., Alice, C., Amoroso, A., Andrieux, V., Anosov, V., Augsten, K., Augustyniak, W., Azevedo, C. D. R., Badelek, B., Barth, J., Beck, R., Beckers, J., Bedfer, Y., Bernhard, J., Bodlak, M., Bradamante, F., Bressan, A., Chang, W. -C., Chatterjee, C., Chiosso, M., Chumakov, A. G., Chung, S. -U., Cicuttin, A., Correia, P. M. M., Crespo, M. L., D'Ago, D., Torre, S. Dalla, Dasgupta, S. S., Dasgupta, S., Delcarro, F., Denisenko, I., Denisov, O. Yu., Donskov, S. V., Doshita, N., Dreisbach, Ch., Dunnweber, W., Dusaev, R. R., Ecker, D., Eremeev, D., Faccioli, P., Faessler, M., Finger, M., Finger jr., M., Fischer, H., Flothner, K. J., Florian, W., Friedrich, J. M., Frolov, V., Ordonez, L. G. Garcia, Gautheron, F., Gavrichtchouk, O. P., Gerassimov, S., Giarra, J., Giordano, D., Grasso, A., Gridin, A., Perdekamp, M. Grosse, Grube, B., Gruner, M., Guskov, A., Haas, P., von Harrach, D., Heitz, R., Hoffmann, M., d'Hose, N., Hsieh, C. -Y., Huber, S., Ishimoto, S., Ivanov, A., Iwata, T., Jary, V., Joosten, R., Kabuss, E., Kaspar, F., Kerbizi, A., Ketzer, B., Khatun, A., Khaustov, G. V., Klein, F., Koivuniemi, J. H., Kolosov, V. N., Horikawa, K. Kondo, Konorov, I., Konstantinov, V. F., Korzenev, A. Yu., Kotzinian, A. M., Kouznetsov, O. M., Koval, A., Kral, Z., Krinner, F., Kunne, F., Kurek, K., Kurjata, R. P., Kveton, A., Lavickova, K., Levorato, S., Lian, Y. -S., Lichtenstadt, J., Lin, P. -J., Longo, R., Lyubovitskij, V. E., Maggiora, A., Magnon, A., Makke, N., Mallot, G. K., Maltsev, A., Martin, A., Marzec, J., Matousek, J., Matsuda, T., Mattson, G., Pires, C. Menezes, Metzger, F., Meyer, M., Meyer, W., Mikhailov, Yu. V., Mikhasenko, M., Mitrofanov, E., Miura, D., Miyachi, Y., Molina, R., Moretti, A., Nagaytsev, A., Neyret, D., Niemiec, M., Novy, J., Nowak, W. -D., Nukazuka, G., Olshevsky, A. G., Ostrick, M., Panzieri, D., Parsamyan, B., Paul, S., Pekeler, H., Peng, J. -C., Pesek, M., Peshekhonov, D. V., Peskova, M., Platchkov, S., Pochodzalla, J., Polyakov, V. A., Quaresma, M., Quintans, C., Reicherz, G., Riedl, C., Ryabchikov, D. I., Rychter, A., Rymbekova, A., Samoylenko, V. D., Sandacz, A., Sarkar, S., Savada, T., Savin, I. A., Sbrizzai, G., Schmieden, H., Selyunin, A., Sharko, K., Sinha, L., Spulbeck, D., Srnka, A., Stolarski, M., Sulc, M., Suzuki, H., Tessaro, S., Tessarotto, F., Thiel, A., Tosello, F., Townsend, A., Triloki, T., Tskhay, V., Valinoti, B., Veit, B. M., Veloso, J. F. C. A., Ventura, B., Vijayakumar, A., Virius, M., Wagner, M., Wallner, S., Zaremba, K., Zavertyaev, M., Zemko, M., Zemlyanichkina, E., and Ziembicki, M.
- Subjects
High Energy Physics - Experiment ,High Energy Physics - Phenomenology - Abstract
The COMPASS Collaboration performed measurements of the Drell-Yan process in 2015 and 2018 using a 190 GeV/c $\pi^{-}$ beam impinging on a transversely polarised ammonia target. Combining the data of both years, we present final results on the amplitudes of the five azimuthal modulations in the dimuon production cross section. Three of these transverse-spin-dependent azimuthal asymmetries (TSAs) probe the nucleon leading-twist Sivers, transversity, and pretzelosity transverse-momentum dependent (TMD) parton distribution functions (PDFs). The other two are induced by subleading effects. These TSAs provide unique new inputs for the study of the nucleon TMD PDFs and their universality properties. In particular, the Sivers TSA observed in this measurement is consistent with the fundamental QCD prediction of a sign change of naive time-reversal-odd TMD PDFs when comparing the Drell-Yan process with semi-inclusive measurements of deep inelastic scattering. Also, within the context of model predictions, the observed transversity TSA is consistent with the expectation of a sign change for the Boer-Mulders function.
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- 2023
33. Beyond PID Controllers: PPO with Neuralized PID Policy for Proton Beam Intensity Control in Mu2e
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Xu, Chenwei, Hu, Jerry Yao-Chieh, Narayanan, Aakaash, Thieme, Mattson, Nagaslaev, Vladimir, Austin, Mark, Arnold, Jeremy, Berlioz, Jose, Hanlet, Pierrick, Ibrahim, Aisha, Nicklaus, Dennis, Mitrevski, Jovan, John, Jason Michael St., Pradhan, Gauri, Saewert, Andrea, Seiya, Kiyomi, Schupbach, Brian, Thurman-Keup, Randy, Tran, Nhan, Shi, Rui, Ogrenci, Seda, Shuping, Alexis Maya-Isabelle, Hazelwood, Kyle, and Liu, Han
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Physics - Accelerator Physics - Abstract
We introduce a novel Proximal Policy Optimization (PPO) algorithm aimed at addressing the challenge of maintaining a uniform proton beam intensity delivery in the Muon to Electron Conversion Experiment (Mu2e) at Fermi National Accelerator Laboratory (Fermilab). Our primary objective is to regulate the spill process to ensure a consistent intensity profile, with the ultimate goal of creating an automated controller capable of providing real-time feedback and calibration of the Spill Regulation System (SRS) parameters on a millisecond timescale. We treat the Mu2e accelerator system as a Markov Decision Process suitable for Reinforcement Learning (RL), utilizing PPO to reduce bias and enhance training stability. A key innovation in our approach is the integration of a neuralized Proportional-Integral-Derivative (PID) controller into the policy function, resulting in a significant improvement in the Spill Duty Factor (SDF) by 13.6%, surpassing the performance of the current PID controller baseline by an additional 1.6%. This paper presents the preliminary offline results based on a differentiable simulator of the Mu2e accelerator. It paves the groundwork for real-time implementations and applications, representing a crucial step towards automated proton beam intensity control for the Mu2e experiment., Comment: 10 pages, accepted at NeurIPS 2023 ML4Phy Workshop
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- 2023
34. MonoCoder: Domain-Specific Code Language Model for HPC Codes and Tasks
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Kadosh, Tal, Hasabnis, Niranjan, Vo, Vy A., Schneider, Nadav, Krien, Neva, Capota, Mihai, Wasay, Abdul, Ahmed, Nesreen, Willke, Ted, Tamir, Guy, Pinter, Yuval, Mattson, Timothy, and Oren, Gal
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Computer Science - Programming Languages ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Computer Science - Software Engineering - Abstract
With easier access to powerful compute resources, there is a growing trend in AI for software development to develop large language models (LLMs) to address a variety of programming tasks. Even LLMs applied to tasks from the high-performance computing (HPC) domain are huge in size and demand expensive compute resources for training. This is partly because LLMs for HPC tasks are obtained by finetuning existing LLMs that support several natural and/or programming languages. We found this design choice confusing - why do we need LLMs trained on natural languages and programming languages unrelated to HPC for HPC-specific tasks? In this line of work, we aim to question choices made by existing LLMs by developing smaller language models (LMs) for specific domains - we call them domain-specific LMs. Specifically, we start with HPC as a domain and build an HPC-specific LM, named MonoCoder, which is orders of magnitude smaller than existing LMs but delivers better performance on non-HPC and HPC codes. Specifically, we pre-trained MonoCoder on an HPC-specific dataset (named HPCorpus) of C and C++ programs mined from GitHub. We evaluated the performance of MonoCoder against state-of-the-art multi-lingual LLMs. Results demonstrate that MonoCoder, although much smaller than existing LMs, outperforms other LLMs on normalized-perplexity tests (in relation to model size) while also delivering competing CodeBLEU scores for high-performance and parallel code generations. In other words, results suggest that MonoCoder understands HPC code better than state-of-the-art LLMs.
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- 2023
35. Prognostic immune markers in esophageal cancer patients managed with trimodal therapy
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Farrugia, Mark K., Repasky, Elizabeth A., Chen, Minhui, Attwood, Kristopher, Catalfamo, Kayla, Rosenheck, Hanna, Yao, Song, Mattson, David M., Mukherjee, Sarbajit, Kukar, Moshim, Witkiewicz, Agnieszka K., and Singh, Anurag K.
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- 2025
- Full Text
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36. PragFormer: Data-Driven Parallel Source Code Classification with Transformers
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Harel, Re’em, Kadosh, Tal, Hasabnis, Niranjan, Mattson, Timothy, Pinter, Yuval, and Oren, Gal
- Published
- 2025
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37. Respiratory complex I regulates dendritic cell maturation in explant model of human tumor immune microenvironment.
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Turpin, Rita, Liu, Ruixian, Munne, Pauliina, Peura, Aino, Rannikko, Jenna, Philips, Gino, Boeckx, Bram, Salmelin, Natasha, Hurskainen, Elina, Suleymanova, Ilida, Aung, July, Vuorinen, Elisa, Lehtinen, Laura, Mutka, Minna, Kovanen, Panu, Niinikoski, Laura, Meretoja, Tuomo, Mattson, Johanna, Mustjoki, Satu, Saavalainen, Päivi, Goga, Andrei, Lambrechts, Diether, Pouwels, Jeroen, Hollmén, Maija, and Klefström, Juha
- Subjects
Breast Neoplasms ,Dendritic Cells ,Drug Evaluation ,Preclinical ,Immunity ,Innate ,Immunomodulation ,Humans ,Female ,Electron Transport Complex I ,Antineoplastic Agents ,Breast Neoplasms ,Dendritic Cells ,Metformin ,Tumor Microenvironment ,Sulfonamides ,Bridged Bicyclo Compounds ,Heterocyclic - Abstract
BACKGROUND: Combining cytotoxic chemotherapy or novel anticancer drugs with T-cell modulators holds great promise in treating advanced cancers. However, the response varies depending on the tumor immune microenvironment (TIME). Therefore, there is a clear need for pharmacologically tractable models of the TIME to dissect its influence on mono- and combination treatment response at the individual level. METHODS: Here we establish a patient-derived explant culture (PDEC) model of breast cancer, which retains the immune contexture of the primary tumor, recapitulating cytokine profiles and CD8+T cell cytotoxic activity. RESULTS: We explored the immunomodulatory action of a synthetic lethal BCL2 inhibitor venetoclax+metformin drug combination ex vivo, discovering metformin cannot overcome the lymphocyte-depleting action of venetoclax. Instead, metformin promotes dendritic cell maturation through inhibition of mitochondrial complex I, increasing their capacity to co-stimulate CD4+T cells and thus facilitating antitumor immunity. CONCLUSIONS: Our results establish PDECs as a feasible model to identify immunomodulatory functions of anticancer drugs in the context of patient-specific TIME.
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- 2024
38. A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens
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Mattson, Nicole M, Chan, Anthony KN, Miyashita, Kazuya, Mukhaleva, Elizaveta, Chang, Wen-Han, Yang, Lu, Ma, Ning, Wang, Yingyu, Pokharel, Sheela Pangeni, Li, Mingli, Liu, Qiao, Xu, Xiaobao, Chen, Renee, Singh, Priyanka, Zhang, Leisi, Elsayed, Zeinab, Chen, Bryan, Keen, Denise, Pirrotte, Patrick, Rosen, Steven T, Chen, Jianjun, LaBarge, Mark A, Shively, John E, Vaidehi, Nagarajan, Rockne, Russell C, Feng, Mingye, and Chen, Chun-Wei
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Cancer ,Genetics ,5.1 Pharmaceuticals ,Humans ,Clustered Regularly Interspaced Short Palindromic Repeats ,Cell Membrane ,Chemical Sciences ,Medical and Health Sciences ,Biophysics ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences ,Chemical sciences - Abstract
The plasma membrane is enriched for receptors and signaling proteins that are accessible from the extracellular space for pharmacological intervention. Here we conducted a series of CRISPR screens using human cell surface proteome and integrin family libraries in multiple cancer models. Our results identified ITGAV (integrin αV) and its heterodimer partner ITGB5 (integrin β5) as the essential integrin α/β pair for cancer cell expansion. High-density CRISPR gene tiling further pinpointed the integral pocket within the β-propeller domain of ITGAV for integrin αVβ5 dimerization. Combined with in silico compound docking, we developed a CRISPR-Tiling-Instructed Computer-Aided (CRISPR-TICA) pipeline for drug discovery and identified Cpd_AV2 as a lead inhibitor targeting the β-propeller central pocket of ITGAV. Cpd_AV2 treatment led to rapid uncoupling of integrin αVβ5 and cellular apoptosis, providing a unique class of therapeutic action that eliminates the integrin signaling via heterodimer dissociation. We also foresee the CRISPR-TICA approach to be an accessible method for future drug discovery studies.
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- 2024
39. A dataset of paired head and eye movements during visual tasks in virtual environments
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Rubow, Colin, Tsai, Chia-Hsuan, Brewer, Eric, Mattson, Connor, Brown, Daniel S., and Zhang, Haohan
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- 2024
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40. Toward generalizable phenotype prediction from single-cell morphology representations
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Tomkinson, Jenna, Kern, Roshan, Mattson, Cameron, and Way, Gregory P.
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- 2024
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41. NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes
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Chang, Michael, Sherief, Mohamed, Ioannou, Maria, Chinnasamy, Viveka, Chen, Lucy, Frost, Michael, Mattson-Hoss, Michelle, Sarnoff, Herb, Kamson, David O., Holdhoff, Matthias, Mukherjee, Debraj, Bettegowda, Chetan, Rincon-Torroella, Jordina, Croog, Victoria, Huang, Peng, Rodriguez, Fausto J., Lucas, Calixto-Hope G., and Schreck, Karisa C.
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- 2024
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42. Analytical microscopy techniques using coaxial and oblique illuminations to detect thin glass particulates generated from glass vials for parenteral drug products
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Sanni, Adedayo M., Opalade, Adedamola A., Shamirian, Armen, Mattson, Spencer, Driscoll, Eric, St. Martin, Michael, Mohan, Shikhar, Trimmer, Brooke, Bunch, Tarq, Ovadia, Robert, Yoon, Jungjoo, Ma, Sarina, and Foti, Chris
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- 2024
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43. Human biomonitoring without in-person interaction: public health engagements during the COVID-19 pandemic and future implications
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Mattson, Alyssa J., Yu, Jiali, Miller, Elizabeth M., Schueller, Michael, Pentella, Michael, and Dai, Susie Y.
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- 2024
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44. DMLR: Data-centric Machine Learning Research -- Past, Present and Future
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Oala, Luis, Maskey, Manil, Bat-Leah, Lilith, Parrish, Alicia, Gürel, Nezihe Merve, Kuo, Tzu-Sheng, Liu, Yang, Dror, Rotem, Brajovic, Danilo, Yao, Xiaozhe, Bartolo, Max, Rojas, William A Gaviria, Hileman, Ryan, Aliment, Rainier, Mahoney, Michael W., Risdal, Meg, Lease, Matthew, Samek, Wojciech, Dutta, Debojyoti, Northcutt, Curtis G, Coleman, Cody, Hancock, Braden, Koch, Bernard, Tadesse, Girmaw Abebe, Karlaš, Bojan, Alaa, Ahmed, Dieng, Adji Bousso, Noy, Natasha, Reddi, Vijay Janapa, Zou, James, Paritosh, Praveen, van der Schaar, Mihaela, Bollacker, Kurt, Aroyo, Lora, Zhang, Ce, Vanschoren, Joaquin, Guyon, Isabelle, and Mattson, Peter
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Distributed, Parallel, and Cluster Computing ,Electrical Engineering and Systems Science - Signal Processing - Abstract
Drawing from discussions at the inaugural DMLR workshop at ICML 2023 and meetings prior, in this report we outline the relevance of community engagement and infrastructure development for the creation of next-generation public datasets that will advance machine learning science. We chart a path forward as a collective effort to sustain the creation and maintenance of these datasets and methods towards positive scientific, societal and business impact., Comment: Published in the Journal of Data-centric Machine Learning Research (DMLR) at https://data.mlr.press/assets/pdf/v01-5.pdf
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- 2023
45. Exploring Behavior Discovery Methods for Heterogeneous Swarms of Limited-Capability Robots
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Mattson, Connor, Clark, Jeremy C., and Brown, Daniel S.
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Computer Science - Robotics ,Computer Science - Machine Learning ,Computer Science - Multiagent Systems - Abstract
We study the problem of determining the emergent behaviors that are possible given a functionally heterogeneous swarm of robots with limited capabilities. Prior work has considered behavior search for homogeneous swarms and proposed the use of novelty search over either a hand-specified or learned behavior space followed by clustering to return a taxonomy of emergent behaviors to the user. In this paper, we seek to better understand the role of novelty search and the efficacy of using clustering to discover novel emergent behaviors. Through a large set of experiments and ablations, we analyze the effect of representations, evolutionary search, and various clustering methods in the search for novel behaviors in a heterogeneous swarm. Our results indicate that prior methods fail to discover many interesting behaviors and that an iterative human-in-the-loop discovery process discovers more behaviors than random search, swarm chemistry, and automated behavior discovery. The combined discoveries of our experiments uncover 23 emergent behaviors, 18 of which are novel discoveries. To the best of our knowledge, these are the first known emergent behaviors for heterogeneous swarms of computation-free agents. Videos, code, and appendix are available at the project website: https://sites.google.com/view/heterogeneous-bd-methods, Comment: 11 pages, 9 figures, To be published in Proceedings IEEE International Symposium on Multi-Robot & Multi-Agent Systems (MRS 2023)
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- 2023
46. Indirect Swarm Control: Characterization and Analysis of Emergent Swarm Behaviors
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Vega, Ricardo, Mattson, Connor, Brown, Daniel S., and Nowzari, Cameron
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Computer Science - Robotics ,Electrical Engineering and Systems Science - Systems and Control - Abstract
Emergence and emergent behaviors are often defined as cases where changes in local interactions between agents at a lower level effectively changes what occurs in the higher level of the system (i.e., the whole swarm) and its properties. However, the manner in which these collective emergent behaviors self-organize is less understood. The focus of this paper is in presenting a new framework for characterizing the conditions that lead to different macrostates and how to predict/analyze their macroscopic properties, allowing us to indirectly engineer the same behaviors from the bottom up by tuning their environmental conditions rather than local interaction rules. We then apply this framework to a simple system of binary sensing and acting agents as an example to see if a re-framing of this swarms problem can help us push the state of the art forward. By first creating some working definitions of macrostates in a particular swarm system, we show how agent-based modeling may be combined with control theory to enable a generalized understanding of controllable emergent processes without needing to simulate everything. Whereas phase diagrams can generally only be created through Monte Carlo simulations or sweeping through ranges of parameters in a simulator, we develop closed-form functions that can immediately produce them revealing an infinite set of swarm parameter combinations that can lead to a specifically chosen self-organized behavior. While the exact methods are still under development, we believe simply laying out a potential path towards solutions that have evaded our traditional methods using a novel method is worth considering. Our results are characterized through both simulations and real experiments on ground robots., Comment: 8 pages, 13 figures, submitted to IROS 2024 conference
- Published
- 2023
47. Comparing recent PTA results on the nanohertz stochastic gravitational wave background
- Author
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The International Pulsar Timing Array Collaboration, Agazie, G., Antoniadis, J., Anumarlapudi, A., Archibald, A. M., Arumugam, P., Arumugam, S., Arzoumanian, Z., Askew, J., Babak, S., Bagchi, M., Bailes, M., Nielsen, A. -S. Bak, Baker, P. T., Bassa, C. G., Bathula, A., Bécsy, B., Berthereau, A., Bhat, N. D. R., Blecha, L., Bonetti, M., Bortolas, E., Brazier, A., Brook, P. R., Burgay, M., Burke-Spolaor, S., Burnette, R., Caballero, R. N., Cameron, A., Case, R., Chalumeau, A., Champion, D. J., Chanlaridis, S., Charisi, M., Chatterjee, S., Chatziioannou, K., Cheeseboro, B. D., Chen, S., Chen, Z. -C., Cognard, I., Cohen, T., Coles, W. A., Cordes, J. M., Cornish, N. J., Crawford, F., Cromartie, H. T., Crowter, K., Curyło, M., Cutler, C. J., Dai, S., Dandapat, S., Deb, D., DeCesar, M. E., DeGan, D., Demorest, P. B., Deng, H., Desai, S., Desvignes, G., Dey, L., Dhanda-Batra, N., Di Marco, V., Dolch, T., Drachler, B., Dwivedi, C., Ellis, J. A., Falxa, M., Feng, Y., Ferdman, R. D., Ferrara, E. C., Fiore, W., Fonseca, E., Franchini, A., Freedman, G. E., Gair, J. R., Garver-Daniels, N., Gentile, P. A., Gersbach, K. A., Glaser, J., Good, D. C., Goncharov, B., Gopakumar, A., Graikou, E., Grießmeier, J. -M., Guillemot, L., Gültekin, K., Guo, Y. J., Gupta, Y., Grunthal, K., Hazboun, J. S., Hisano, S., Hobbs, G. B., Hourihane, S., Hu, H., Iraci, F., Islo, K., Izquierdo-Villalba, D., Jang, J., Jawor, J., Janssen, G. H., Jennings, R. J., Jessner, A., Johnson, A. D., Jones, M. L., Joshi, B. C., Kaiser, A. R., Kaplan, D. L., Kapur, A., Kareem, F., Karuppusamy, R., Keane, E. F., Keith, M. J., Kelley, L. Z., Kerr, M., Key, J. S., Kharbanda, D., Kikunaga, T., Klein, T. C., Kolhe, N., Kramer, M., Krishnakumar, M. A., Kulkarni, A., Laal, N., Lackeos, K., Lam, M. T., Lamb, W. G., Larsen, B. B., Lazio, T. J. W., Lee, K. J., Levin, Y., Lewandowska, N., Littenberg, T. B., Liu, K., Liu, T., Liu, Y., Lommen, A., Lorimer, D. R., Lower, M. E., Luo, J., Luo, R., Lynch, R. S., Lyne, A. G., Ma, C. -P., Maan, Y., Madison, D. R., Main, R. A., Manchester, R. N., Mandow, R., Mattson, M. A., McEwen, A., McKee, J. W., McLaughlin, M. A., McMann, N., Meyers, B. W., Meyers, P. M., Mickaliger, M. B., Miles, M., Mingarelli, C. M. F., Mitridate, A., Natarajan, P., Nathan, R. S., Ng, C., Nice, D. J., Niţu, I. C., Nobleson, K., Ocker, S. K., Olum, K. D., Osłowski, S., Paladi, A. K., Parthasarathy, A., Pennucci, T. T., Perera, B. B. P., Perrodin, D., Petiteau, A., Petrov, P., Pol, N. S., Porayko, N. K., Possenti, A., Prabu, T., Leclere, H. Quelquejay, Radovan, H. A., Rana, P., Ransom, S. M., Ray, P. S., Reardon, D. J., Rogers, A. F., Romano, J. D., Russell, C. J., Samajdar, A., Sanidas, S. A., Sardesai, S. C., Schmiedekamp, A., Schmiedekamp, C., Schmitz, K., Schult, L., Sesana, A., Shaifullah, G., Shannon, R. M., Shapiro-Albert, B. J., Siemens, X., Simon, J., Singha, J., Siwek, M. S., Speri, L., Spiewak, R., Srivastava, A., Stairs, I. H., Stappers, B. W., Stinebring, D. R., Stovall, K., Sun, J. P., Surnis, M., Susarla, S. C., Susobhanan, A., Swiggum, J. K., Takahashi, K., Tarafdar, P., Taylor, J., Taylor, S. R., Theureau, G., Thrane, E., Thyagarajan, N., Tiburzi, C., Toomey, L., Turner, J. E., Unal, C., Vallisneri, M., van der Wateren, E., van Haasteren, R., Vecchio, A., Krishnan, V. Venkatraman, Verbiest, J. P. W., Vigeland, S. J., Wahl, H. M., Wang, S., Wang, Q., Witt, C. A., Wang, J., Wang, L., Wayt, K. E., Wu, Z., Young, O., Zhang, L., Zhang, S., Zhu, X. -J., and Zic, A.
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Astrophysics - High Energy Astrophysical Phenomena ,General Relativity and Quantum Cosmology - Abstract
The Australian, Chinese, European, Indian, and North American pulsar timing array (PTA) collaborations recently reported, at varying levels, evidence for the presence of a nanohertz gravitational wave background (GWB). Given that each PTA made different choices in modeling their data, we perform a comparison of the GWB and individual pulsar noise parameters across the results reported from the PTAs that constitute the International Pulsar Timing Array (IPTA). We show that despite making different modeling choices, there is no significant difference in the GWB parameters that are measured by the different PTAs, agreeing within $1\sigma$. The pulsar noise parameters are also consistent between different PTAs for the majority of the pulsars included in these analyses. We bridge the differences in modeling choices by adopting a standardized noise model for all pulsars and PTAs, finding that under this model there is a reduction in the tension in the pulsar noise parameters. As part of this reanalysis, we "extended" each PTA's data set by adding extra pulsars that were not timed by that PTA. Under these extensions, we find better constraints on the GWB amplitude and a higher signal-to-noise ratio for the Hellings and Downs correlations. These extensions serve as a prelude to the benefits offered by a full combination of data across all pulsars in the IPTA, i.e., the IPTA's Data Release 3, which will involve not just adding in additional pulsars, but also including data from all three PTAs where any given pulsar is timed by more than as single PTA., Comment: 21 pages, 9 figures, submitted to ApJ
- Published
- 2023
48. Direct-to-Patient Mobile Teledermoscopy: Prospective Observational Study.
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Fan, Winnie, Mattson, Gunnar, and Twigg, Amanda
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dermatological ,dermatology ,dermoscopy ,diagnoses ,diagnosis ,diagnostic ,diagnostic concordance ,direct-to-patient ,eHealth ,full body skin exam ,image ,images ,imaging ,lesion ,lesions ,mHealth ,mobile health ,mobile teledermoscopy ,skin ,smartphone ,teledermatology ,telehealth ,telemedicine - Abstract
Direct-to-patient mobile teledermoscopy is a feasible and useful adjunct to smartphone imaging for monitoring patient-identified lesions of concern, achieving comparable diagnostic and management accuracy as in-office dermatology.
- Published
- 2024
49. The EGS Collab Project – Summaries of Experiments 2 and 3: Experiments at 1.25 km depth at the Sanford Underground Research Facility
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Kneafsey, Timothy, Johnson, Timothy, Burghardt, Jeff, Schwering, Paul, Frash, Luke, Roggenthen, William, Hopp, Chet, Neupane, Ghanashyam, Mattson, Earl, Ulrich, Craig, Soom, Florian, Doe, Thomas, Weers, Jon, Artz, Tyler, and Robertson, Michelle
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coupled process modeling ,crystalline rock ,EGS Collab ,Enhanced Geothermal Systems ,experimental ,field test ,flow test ,Sanford Underground Research Facility ,stimulation - Abstract
The EGS Collab project performed well-monitored rock stimulation and flow tests at the 10-m scale in an underground research laboratory to inform challenges in implementing enhanced geothermal system (EGS) technology. This project, supported by the US Department of Energy, gathered data and observations from the field tests and compared these to simulation results to understand processes and to build confidence in numerical modeling of the processes. The project consisted of 3 Experiments, each comprising test and testbed design, many individual tests, numerical simulation, and analysis. The Experiments were performed in two deep underground testbeds at the Sanford Underground Research Facility (SURF) in Lead, South Dakota. Field experiments are now complete, significant data sets have been collected and analyzed, and some analysis continues. Experiments using underground test facilities have many advantages in that they allow:•Three-dimensional characterization of the stimulated volume by complementary geophysical methods surrounding the experiment•Using techniques that are currently not applicable under geothermal condition to provide processes insight •Comprehensive tracer testing and detailed characterization of complex fluid movements•Understanding the geometry of the stimulated network at the meso-scale and its implications for effective fracture surface area, rock block size, and heat exchange.Underground testing has its own set of complications, however, which affect the ability to perform tests as desired and affect the experiment results. Included here are the inability to flow at desired injection rates due to stress gradients caused by drift cooling, and the need to strongly limit induced seismicity because the distance to people and equipment.Experiment 1 examined hydraulic fracturing at a depth of 1.5 km in a well-characterized phyllite. Eight subhorizontal boreholes were used in this Experiment. Geophysical monitoring instrumentation was deployed in six boreholes to monitor stimulation events and flow tests. The other two boreholes were used to perform and carefully measure water injection and production. More than a dozen stimulations and nearly one year of flow tests in the testbed were performed. Detailed observations of processes occurring during stimulation and dynamic flow tests were collected and analyzed. Flow tests using ambient-temperature and chilled water were performed with intermittent tracer tests to examine system behavior. We achieved adaptive control of the tests using close monitoring of rapidly disseminated data and near-real-time simulation. Numerical simulation was critical in answering key experimental design questions, forecasting fracture behavior, and analyzing results. We were successful in performing many simulations in near-real-time in conjunction with the field experiments, with more detailed simulations performed later. Experiment 2 was intended to examine hydraulic shearing of natural fractures at a depth of 1.25 km in amphibolite. The stresses, rock type, and fracture conditions are different than in Experiment 1. The testbed consists of 9 boreholes, in addition to 2 exploratory characterization boreholes. Four boreholes drilled as two fans of 2 monitoring holes contained grouted-in monitoring sensors. The remaining five open boreholes drilled in a five-spot pattern were adaptively used for injection, production, and monitoring. Approximately five fracture set orientations were encountered in the testbed along with a low-stress rhyolite sill at 35 m below the access drift in exploratory well TV4100. The testbed was designed to optimize the potential for shear stimulation while also avoiding the low-stress rhyolite. Experiment 2 focused on stimulating a fracture in the most likely orientation to shear, however shear stimulation did not occur probably due to cementation from natural secondary mineralization. Other fracture sets encountered were also cemented and had orientations less likely to shear.Experiment 3 consisted of several stimulations in the same testbed as Experiment 2 allowing different stimulation approaches including ramped-rate injection, rapid injection, and oscillating-pressure injection. Ultimately these methods created hydraulic fractures, one of which was used for a medium-duration cold water injection test. The major findings of the EGS Collab Project include: 1.Significant shear stimulation did not occur during our stimulation attempts. Shear stimulation may occur but under a limited set of conditions not encountered.2.Our stimulations resulted in hydraulic fractures that required hydraulic propping. Pumping at pressures exceeding the minimum principal stress may not be feasible in an enhanced geothermal system.3.The systems we generated were complex hydraulic fracture/natural fracture systems, and these systems changed over time in response to applied pressures and flowrates and to unknown stimuli.4.The project attempted alternative stimulation methods, which did not provide significant flow improvement. 5.Thermal breakthrough was not achieved as designed, most likely because flow to production boreholes was not adequate. 6.The combination of geophysical tools used provided excellent understanding of many important processes. 7.Microearthquakes (MEQs) didn’t necessarily identify flow paths.8.Engineering tools bounding expected seismicity are needed.This report provides a summary of tests and analyses performed for EGS Collab Experiment 2 (Shear Stimulation in Testbed 2) and Experiment 3 (Alternative Stimulation methods). Much of the EGS Collab work has been published in journals and conference papers, presented in conferences, included in written reports, and submitted in data sets to the Geothermal Data Repository (GDR). The entirety of these written works is included as an appendix to this report, and this report serves as a summary and framework pointing to these published papers, presentations, and reports.
- Published
- 2024
50. Ventricular Epicardial Adipose Distribution on Human Hearts: 3-Dimensional Reconstructions and Quantitative Assessments
- Author
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Brigham, Renee C., Mattson, Alexander R., and Iaizzo, Paul A.
- Published
- 2024
- Full Text
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