14,597 results on '"Hayden P"'
Search Results
2. Long term declines in the functional diversity of sharks in the coastal oceans of eastern Australia
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Christopher J. Henderson, Ben L. Gilby, Mischa P. Turschwell, Lucy A. Goodridge Gaines, Jesse D. Mosman, Thomas A. Schlacher, Hayden P. Borland, and Andrew D. Olds
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Biology (General) ,QH301-705.5 - Abstract
Abstract Human impacts lead to widespread changes in the abundance, diversity and traits of shark assemblages, altering the functioning of coastal ecosystems. The functional consequences of shark declines are often poorly understood due to the absence of empirical data describing long-term change. We use data from the Queensland Shark Control Program in eastern Australia, which has deployed mesh nets and baited hooks across 80 beaches using standardised methodologies since 1962. We illustrate consistent declines in shark functional richness quantified using both ecological (e.g., feeding, habitat and movement) and morphological (e.g., size, morphology) traits, and this corresponds with declining ecological functioning. We demonstrate a community shift from targeted apex sharks to a greater functional richness of non-target species. Declines in apex shark functional richness and corresponding changes in non-target species may lead to an anthropogenically induced trophic cascade. We suggest that repairing diminished shark populations is crucial for the stability of coastal ecosystems.
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- 2024
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3. Preventing Respiratory Viral Illness Invisibly (PRiVII): protocol for a pragmatic cluster randomized trial evaluating far-UVC light devices in long-term care facilities to reduce infections
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Hayden P. Nix, Samantha Meeker, Caroline E. King, Melissa Andrew, Ian R. C. Davis, Prosper S. Koto, Meaghan Sim, Jennifer Murdoch, Glenn Patriquin, Chris Theriault, Stephanie Reidy, Michael Rockwood, Tara Sampalli, Samuel D. Searle, and Kenneth Rockwood
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Respiratory viral illness ,Long-term care ,Cluster randomized controlled trial ,Geriatrics ,Medicine (General) ,R5-920 - Abstract
Abstract Background Respiratory viral illness (RVI)—e.g., influenza, COVID-19—is a serious threat in long-term care (LTC) facilities. Standard infection control measures are suboptimal in LTC facilities because of residents’ cognitive impairments, care needs, and susceptibility to loneliness and mental illness. Further, LTC residents living with high degrees of frailty who contract RVIs often develop the so-called atypical symptoms (e.g., delirium, worse mobility) instead of typical cough and fever, delaying infection diagnosis and treatment. Although far-UVC (222 nm) light devices have shown potent antiviral activity in vitro, clinical efficacy remains unproven. Methods Following a study to assay acceptability at each site, this multicenter, double-blinded, cluster-randomized, placebo-controlled trial aims to assess whether far-UVC light devices impact the incidence of RVIs in LTC facilities. Neighborhoods within LTC facilities are randomized to receive far-UVC light devices (222 nm) or identical placebo light devices that emit only visible spectrum light (400–700 nm) in common areas. All residents are monitored for RVIs using both a standard screening protocol and a novel screening protocol that target atypical symptoms. The 3-year incidence of RVIs will be compared using intention-to-treat analysis. A cost-consequence analysis will follow. Discussion This trial aims to inform decisions about whether to implement far-UVC light in LTC facilities for RVI prevention. The trial design features align with this pragmatic intent. Appropriate additional ethical protections have been implemented to mitigate participant vulnerabilities that arise from conducting this study. Knowledge dissemination will be supported through media engagement, peer-reviewed presentations, and publications. Trial registration ClinicalTrials.gov NCT05084898. October 20, 2021.
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- 2024
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4. The New Media Landscape and Its Effects on Skin Cancer Diagnostics, Prognostics, and Prevention: Scoping Review
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Priscilla L Haff, Alli Jacobson, Madison M Taylor, Hayden P Schandua, David P Farris, Hung Q Doan, and Kelly C Nelson
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Dermatology ,RL1-803 - Abstract
BackgroundThe wide availability of web-based sources, including social media (SM), has supported rapid, widespread dissemination of health information. This dissemination can be an asset during public health emergencies; however, it can also present challenges when the information is inaccurate or ill-informed. Of interest, many SM sources discuss cancer, specifically cutaneous melanoma and keratinocyte cancers (basal cell and squamous cell carcinoma). ObjectiveThrough a comprehensive and scoping review of the literature, this study aims to gain an actionable perspective of the state of SM information regarding skin cancer diagnostics, prognostics, and prevention. MethodsWe performed a scoping literature review to establish the relationship between SM and skin cancer. A literature search was conducted across MEDLINE, Embase, Cochrane Library, Web of Science, and Scopus from January 2000 to June 2023. The included studies discussed SM and its relationship to and effect on skin cancer. ResultsThrough the search, 1009 abstracts were initially identified, 188 received full-text review, and 112 met inclusion criteria. The included studies were divided into 7 groupings based on a publication’s primary objective: misinformation (n=40, 36%), prevention campaign (n=19, 17%), engagement (n=16, 14%), research (n=12, 11%), education (n=11, 10%), demographics (n=10, 9%), and patient support (n=4, 3%), which were the most common identified themes. ConclusionsThrough this review, we gained a better understanding of the SM environment addressing skin cancer information, and we gained insight into the best practices by which SM could be used to positively influence the health care information ecosystem.
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- 2024
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5. Interplay in galectin expression predicts patient outcomes in a spatially restricted manner in PDAC
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Oladimeji Abudu, Duy Nguyen, Isabel Millward, Julia E. Manning, Mussarat Wahid, Abbey Lightfoot, Francesca Marcon, Reena Merard, Sandra Margielewska-Davies, Keith Roberts, Rachel Brown, Sarah Powell-Brett, Samantha M. Nicol, Fouzia Zayou, Wayne D. Croft, Hayden Pearce, Paul Moss, Asif J. Iqbal, and Helen M. McGettrick
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galectins ,cancer ,pancreas ,PDAC ,stromal ,ductal ,Therapeutics. Pharmacology ,RM1-950 - Abstract
Background: Galectins (Gal’s) are a family of carbohydrate-binding proteins that are known to support the tumour microenvironment through their immunosuppressive activity and ability to promote metastasis. As such they are attractive therapeutic targets, but little is known about the cellular expression pattern of galectins within the tumour and its neighbouring stromal microenvironment. Here we investigated the cellular expression pattern of Gals within pancreatic ductal adenocarcinoma (PDAC). Methods: Galectin gene and protein expression were analysed by scRNAseq (n=4) and immunofluorescence imaging (n=19) in fibroblasts and epithelial cells of pancreatic biopsies from PDAC patients. Galectin surface expression was also assessed on tumour adjacent normal fibroblasts and cancer associated primary fibroblasts from PDAC biopsies using flow cytometry. Results: scRNAseq revealed higher Gal-1 expression in fibroblasts and higher Gal-3 and −4 expression in epithelial cells. Both podoplanin (PDPN+, stromal/fibroblast) cells and EpCAM+ epithelial cells expressed Gal-1 protein, with highest expression seen in the stromal compartment. By contrast, significantly more Gal-3 and −4 protein was expressed in ductal cells expressing either EpCAM or PDPN, when compared to the stroma. Ductal Gal-4 cellular expression negatively correlated with ductal Gal-1, but not Gal-3 expression. Higher ductal cellular expression of Gal-1 correlated with smaller tumour size and better patient survival. Conclusions: In summary, the intricate interplay and cell-specific expression patterns of galectins within the PDAC tissue, particularly the inverse correlation between Gal-1 and Gal-4 in ducts and its significant association with patient survival, highlights the complex molecular landscape underlying PDAC and provides valuable insights for future therapeutic interventions.
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- 2024
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6. Metalloborospherene Analogs to Metallofullerene
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Jordan Burkhardt, Hayden Prescott, and Wan-Lu Li
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fullerene ,borospherene ,metal-containing cages ,analogs ,clusters ,Inorganic chemistry ,QD146-197 - Abstract
Boron, the neighbor element to carbon in the periodic table, is characterized by unique electron deficiency that fosters multicenter delocalized bonding, contributing to its diverse chemistry. Unlike carbon cages (fullerenes), which preserve their structural integrity under endohedral or exohedral doping, larger boron cages (borospherenes) exhibit diverse structural configurations. These configurations can differ from those of pure boron cages and are stabilized by various metals through unique metal–boron bonding, resulting in a variety of metalloborospherenes. Due to boron’s electron deficiency, metalloborospherenes exhibit fascinating chemical bonding patterns that vary with cluster size and the type of metal dopants. This review paper highlights recent advancements in metalloborospherene research, drawing comparisons with metallofullerenes, and focuses on the use of transition metals, lanthanides, and actinides as dopants across various cage dimensions.
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- 2024
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7. Disruptive lysosomal-metabolic signaling and neurodevelopmental deficits that precede Purkinje cell loss in a mouse model of Niemann-Pick Type-C disease
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Sarah Kim, Kathleen Ochoa, Sierra E. Melli, Fawad A. K. Yousufzai, Zerian D. Barrera, Aela A. Williams, Gianna McIntyre, Esteban Delgado, James N. Bolish, Collin M. Macleod, Mary Boghos, Hayden P. Lens, Alex G. Ramos, Vincent B. Wilson, Kelly Maloney, Zachary M. Padron, Amaal H. Khan, Rosa E. Blanco, and Ileana Soto
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Medicine ,Science - Abstract
Abstract Purkinje cell (PC) loss occurs at an early age in patients and animal models of Niemann-Pick Type C (NPC), a lysosomal storage disease caused by mutations in the Npc1 or Npc2 genes. Although degeneration of PCs occurs early in NPC, little is known about how NPC1 deficiency affects the postnatal development of PCs. Using the Npc1 nmf164 mouse model, we found that NPC1 deficiency significantly affected the postnatal development of PC dendrites and synapses. The developing dendrites of Npc1 nmf164 PCs were significantly deficient in mitochondria and lysosomes. Furthermore, anabolic (mTORC1) and catabolic (TFEB) signaling pathways were not only perturbed but simultaneously activated in NPC1-deficient PCs, suggesting a loss of metabolic balance. We also found that mice with conditional heterozygous deletion of the Phosphatase and Tensin Homolog Deleted on Chromosome 10 gene (Pten-cHet), an inhibitor of mTORC1, showed similar early dendritic alterations in PCs to those found in Npc1-deficient mice. However, in contrast to Npc1 nmf164 mice, Pten-cHet mice exhibited the overactivation of the mTORC1 pathway but with a strong inhibition of TFEB signaling, along with no dendritic mitochondrial reductions by the end of their postnatal development. Our data suggest that disruption of the lysosomal-metabolic signaling in PCs causes dendritic and synaptic developmental deficits that precede and promote their early degeneration in NPC.
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- 2023
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8. Data Analytics Position Description Analysis: Skills Review and Implications for Data Analytics Curricula
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Queen E. Booker, Carl M. Rebman, Hayden Wimmer, Steve B. Levkoff, Loreen Powell, and Jennifer L. Breese
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The focus of this study was to assess the skill requirements for data analytics positions and to understand data analysis employment expectations for new graduates. Furthermore, this work seeks to highlight issues relevant to curriculum management in university degree programs. 786 job postings were analyzed for domain-related, soft skills, as well as degree requirements. Soft skills, often referred to as people skills, comprised the largest part of the results (11 of the top 21 skills). Results revealed the most frequent soft skills were related to communication and teams or teamwork. The most frequent domain skills were related to visualization, data cleaning, data extraction and programming. Implications for curriculum based on results are discussed, and suggestions for future research are provided.
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- 2024
9. A high‐resolution 3D atlas of the spectrum of tuberculous and COVID‐19 lung lesions
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Gordon Wells, Joel N Glasgow, Kievershen Nargan, Kapongo Lumamba, Rajhmun Madansein, Kameel Maharaj, Leon Y Perumal, Malcolm Matthew, Robert L Hunter, Hayden Pacl, Jacelyn E Peabody Lever, Denise D Stanford, Satinder P Singh, Prachi Bajpai, Upender Manne, Paul V Benson, Steven M Rowe, Stephan le Roux, Alex Sigal, Muofhe Tshibalanganda, Carlyn Wells, Anton du Plessis, Mpumelelo Msimang, Threnesan Naidoo, and Adrie J C Steyn
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calcification ,COVID‐19 ,granuloma ,thrombosis ,tuberculosis ,Medicine (General) ,R5-920 ,Genetics ,QH426-470 - Abstract
Abstract Our current understanding of the spectrum of TB and COVID‐19 lesions in the human lung is limited by a reliance on low‐resolution imaging platforms that cannot provide accurate 3D representations of lesion types within the context of the whole lung. To characterize TB and COVID‐19 lesions in 3D, we applied micro/nanocomputed tomography to surgically resected, postmortem, and paraffin‐embedded human lung tissue. We define a spectrum of TB pathologies, including cavitary lesions, calcium deposits outside and inside necrotic granulomas and mycetomas, and vascular rearrangement. We identified an unusual spatial arrangement of vasculature within an entire COVID‐19 lobe, and 3D segmentation of blood vessels revealed microangiopathy associated with hemorrhage. Notably, segmentation of pathological anomalies reveals hidden pathological structures that might otherwise be disregarded, demonstrating a powerful method to visualize pathologies in 3D in TB lung tissue and whole COVID‐19 lobes. These findings provide unexpected new insight into the spatial organization of the spectrum of TB and COVID‐19 lesions within the framework of the entire lung.
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- 2022
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10. The single cell transcriptional landscape of esophageal adenocarcinoma and its modulation by neoadjuvant chemotherapy
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Wayne Croft, Richard P. T. Evans, Hayden Pearce, Mona Elshafie, Ewen A. Griffiths, and Paul Moss
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Esophageal adenocarcinoma ,scRNA-Seq ,Regulatory T cell ,Cancer-associated fibroblast ,Plasmacytoid dendritic cell ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Immune checkpoint blockade has recently proven effective in subsets of patients with esophageal adenocarcinoma (EAC) but little is known regarding the EAC immune microenvironment. We determined the single cell transcriptional profile of EAC in 8 patients who were treatment-naive (n = 4) or had received neoadjuvant chemotherapy (n = 4). Analysis of 52,387 cells revealed 10 major cell subsets of tumor, immune and stromal cells. Prior to chemotherapy tumors were heavy infiltrated by T regulatory cells and exhausted effector T cells whilst plasmacytoid dendritic cells were markedly expanded. Two dominant cancer-associated fibroblast populations were also observed whilst endothelial populations were suppressed. Pathological remission following chemotherapy associated with broad reversal of immune abnormalities together with fibroblast transition and an increase in endothelial cells whilst a chemoresistant epithelial stem cell population correlated with poor response. These findings reveal features that underlie and limit the response to current immunotherapy and identify a range of novel opportunities for targeted therapy.
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- 2022
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11. Spatial determination and prognostic impact of the fibroblast transcriptome in pancreatic ductal adenocarcinoma
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Wayne Croft, Hayden Pearce, Sandra Margielewska-Davies, Lindsay Lim, Samantha M Nicol, Fouzia Zayou, Daniel Blakeway, Francesca Marcon, Sarah Powell-Brett, Brinder Mahon, Reena Merard, Jianmin Zuo, Gary Middleton, Keith Roberts, Rachel M Brown, and Paul Moss
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pancreatic cancer ,PDAC ,cancer-associated fibroblasts ,NanoString GeoMx ,tumour microenvironment ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Pancreatic ductal adenocarcinoma has a poor clinical outcome and responses to immunotherapy are suboptimal. Stromal fibroblasts are a dominant but heterogenous population within the tumor microenvironment and therapeutic targeting of stromal subsets may have therapeutic utility. Here, we combine spatial transcriptomics and scRNA-Seq datasets to define the transcriptome of tumor-proximal and tumor-distal cancer-associated fibroblasts (CAFs) and link this to clinical outcome. Tumor-proximal fibroblasts comprise large populations of myofibroblasts, strongly expressed podoplanin, and were enriched for Wnt ligand signaling. In contrast, inflammatory CAFs were dominant within tumor-distal subsets and expressed complement components and the Wnt-inhibitor SFRP2. Poor clinical outcome was correlated with elevated HIF-1α and podoplanin expression whilst expression of inflammatory and complement genes was predictive of extended survival. These findings demonstrate the extreme transcriptional heterogeneity of CAFs and its determination by apposition to tumor. Selective targeting of tumor-proximal subsets, potentially combined with HIF-1α inhibition and immune stimulation, may offer a multi-modal therapeutic approach for this disease.
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- 2023
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12. Uses of equipoise in discussions of the ethics of randomized controlled trials of COVID-19 therapies
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Hayden P. Nix and Charles Weijer
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Research ethics ,COVID-19 ,Equipoise ,Randomised controlled trial ,Medical philosophy. Medical ethics ,R723-726 - Abstract
Abstract Background Early in the COVID-19 pandemic, the urgent need to discover effective therapies for COVID-19 prompted questions about the ethical problem of randomization along with its widely accepted solution: equipoise. In this scoping review, uses of equipoise in discussions of randomized controlled trials (RCT) of COVID-19 therapies are evaluated to answer three questions. First, how has equipoise been applied to COVID-19 research? Second, has equipoise been employed accurately? And third, do concerns about equipoise pose a barrier to the ethical conduct of COVID-19 RCTs? Methods Google Scholar and Pubmed were searched for articles containing substantial discussion about equipoise and COVID-19 RCTs. 347 article titles were screened, 91 full text articles were assessed, and 48 articles were included. Uses of equipoise were analyzed and abstracted into seven categories. Results and discussion Approximately two-thirds of articles (33/48 articles) used equipoise in a way that is consistent with the concept. They invoked equipoise to support (1) RCTs of specific therapies, (2) RCTs in general, and (3) the early termination of RCTs after achieving the primary outcome. Approximately one-third of articles (15/48 articles) used equipoise in a manner that is inconsistent with the concept. These articles argued that physician preference, widespread use of unproven therapies, patient preference, or expectation of therapeutic benefit may undermine equipoise and render RCTs unethical. In each case, the purported ethical problem can be resolved by correcting the use of equipoise. Conclusions Our findings highlight the continued relevance of equipoise as it supports the conduct of well-conceived RCTs and provides moral guidance to physicians and researchers as they search for effective therapies for COVID-19.
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- 2021
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13. GPU Sharing with Triples Mode
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Byun, Chansup, Reuther, Albert, Anderson, LaToya, Arcand, William, Bergeron, Bill, Bestor, David, Bonn, Alexander, Burrill, Daniel, Gadepally, Vijay, Houle, Michael, Hubbell, Matthew, Jananthan, Hayden, Jones, Michael, Luszczek, Piotr, Michaleas, Peter, Milechin, Lauren, Morales, Guillermo, Mullen, Julie, Prout, Andrew, Rosa, Antonio, Yee, Charles, and Kepner, Jeremy
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
There is a tremendous amount of interest in AI/ML technologies due to the proliferation of generative AI applications such as ChatGPT. This trend has significantly increased demand on GPUs, which are the workhorses for training AI models. Due to the high costs of GPUs and lacking supply, it has become of interest to optimize GPU usage in HPC centers. MIT Lincoln Laboratory Supercomputing Center (LLSC) has developed an easy-to-use GPU sharing feature supported by LLSC-developed tools including LLsub and LLMapReduce. This approach overcomes some of the limitations with the existing methods for GPU sharing. This allows users to apply GPU sharing whenever possible while they are developing their AI/ML models and/or doing parametric study on their AI models or executing other GPU applications. Based on our initial experimental results with GPU sharing, GPU sharing with triples mode is easy to use and achieved significant improvement in GPU usage and throughput performance for certain types of AI applications.
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- 2024
14. LLload: An Easy-to-Use HPC Utilization Tool
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Byun, Chansup, Reuther, Albert, Mullen, Julie, Anderson, LaToya, Arcand, William, Bergeron, Bill, Bestor, David, Bonn, Alexander, Burrill, Daniel, Gadepally, Vijay, Houle, Michael, Hubbell, Matthew, Jananthan, Hayden, Jones, Michael, Luszczek, Piotr, Michaleas, Peter, Milechin, Lauren, Morales, Guillermo, Prout, Andrew, Rosa, Antonio, Yee, Charles, and Kepner, Jeremy
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Computer Science - Performance - Abstract
The increasing use and cost of high performance computing (HPC) requires new easy-to-use tools to enable HPC users and HPC systems engineers to transparently understand the utilization of resources. The MIT Lincoln Laboratory Supercomputing Center (LLSC) has developed a simple command, LLload, to monitor and characterize HPC workloads. LLload plays an important role in identifying opportunities for better utilization of compute resources. LLload can be used to monitor jobs both programmatically and interactively. LLload can characterize users' jobs using various LLload options to achieve better efficiency. This information can be used to inform the user to optimize HPC workloads and improve both CPU and GPU utilization. This includes improvements using judicious oversubscription of the computing resources. Preliminary results suggest significant improvement in GPU utilization and overall throughput performance with GPU overloading in some cases. By enabling users to observe and fix incorrect job submission and/or inappropriate execution setups, LLload can increase the resource usage and improve the overall throughput performance. LLload is a light-weight, easy-to-use tool for both HPC users and HPC systems engineers to monitor HPC workloads to improve system utilization and efficiency.
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- 2024
15. Kinematic Flow for Cosmological Loop Integrands
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Baumann, Daniel, Goodhew, Harry, and Lee, Hayden
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High Energy Physics - Theory ,Astrophysics - Cosmology and Nongalactic Astrophysics ,General Relativity and Quantum Cosmology - Abstract
Recently, an interesting pattern was found in the differential equations satisfied by the Feynman integrals describing tree-level correlators of conformally coupled scalars in a power-law FRW cosmology [1,2]. It was proven that simple and universal graphical rules predict the equations for arbitrary graphs as a flow in kinematic space. In this note, we show that the same rules$\unicode{x2013}$with one small addition$\unicode{x2013}$also determine the differential equations for loop integrands. We explain that both the basis of master integrals and the singularities of the differential equations can be represented by tubings of marked graphs. An important novelty in the case of loops is that some basis functions can vanish, and we present a graphical rule to identify these vanishing functions. Taking this into account, we then demonstrate that the kinematic flow correctly predicts the differential equations for all loop integrands., Comment: 32 pages
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- 2024
16. Analysis of Parallel Boarding Methods in a Multi-Aisle Flying Wing Aircraft
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Ryd, Emil, Khandelwal, Vihaan, So, Hayden, and Steffen, Jason H.
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Physics - Physics and Society - Abstract
We examine the speed of different boarding methods in a proposed Flying Wing aircraft design with four aisles using an agent-based model. We study the effect of various passenger movement variables on the boarding process. We evaluate the impact of these factors on the boarding time when the boarding process runs sequentially and in parallel with the aisles of the Flying Wing layout. Then, we analyze the impact of an increase in the number of aisles on the relative speed of all boarding methods and conclude that methods utilizing boarding of the separate aisles simultaneously (parallel boarding) converge to the fastest boarding time given by the Steffen method. With parallel boarding of the aisles the relative advantage of the Steffen method compared to Windows-Middle-Aisle (WMA) or Back-to-front boarding decreases, from being 1.6-2.1 times as fast to being approximately equal for our fiducial Flying Wing seating arrangement. Standard methods such as Back-to-front or WMA are about twice as fast to board a four-aisle Flying Wing plane, compared to a single-aisle aircraft with the same number of passengers. We also investigate the difference between the optimal approach to parallel boarding, where consecutive passengers always enter separate aisles, and a less optimal but more practical approach. The practical approach is only up to 1.06 times slower than the optimal, meaning that the advantages of parallel boarding can be utilized without resorting to impractical boarding methods. Hence, the introduction of multiple aisles into aircraft seating design offers the prospect of significantly decreasing the boarding time for passengers, without the introduction of inconvenient boarding methods., Comment: 25 pages, 9 figures
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- 2024
17. Tensor Integrals in the Large-Scale Structure
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Lee, Hayden
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Astrophysics - Cosmology and Nongalactic Astrophysics ,High Energy Physics - Phenomenology ,High Energy Physics - Theory - Abstract
We present a new method for evaluating tensor integrals in the large-scale structure. Decomposing a $\Lambda$CDM-like universe into a finite sum of scaling universes using the FFTLog, we can recast loop integrals for biased tracers in the large-scale structure as certain tensor integrals in quantum field theory. While rotational symmetry is spontaneously broken by the fixed reference frame in which biased tracers are observed, the tensor structures can still be organized to respect the underlying symmetry. Projecting the loop integrands for scaling universes onto spherical harmonics, the problem effectively reduces to the evaluation of one-dimensional radial integrals, which can be solved analytically. Using this method, we derive analytic expressions for the one-loop power spectrum, bispectrum, and trispectrum for arbitrary multipole moments in the basis of scaling universes., Comment: 5+7 pages
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- 2024
18. OAH-Net: A Deep Neural Network for Hologram Reconstruction of Off-axis Digital Holographic Microscope
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Liu, Wei, Delikoyun, Kerem, Chen, Qianyu, Yildiz, Alperen, Myo, Si Ko, Kuan, Win Sen, Soong, John Tshon Yit, Cove, Matthew Edward, Hayden, Oliver, and Lee, Hweekuan
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Physics - Optics ,Computer Science - Artificial Intelligence - Abstract
Off-axis digital holographic microscopy is a high-throughput, label-free imaging technology that provides three-dimensional, high-resolution information about samples, particularly useful in large-scale cellular imaging. However, the hologram reconstruction process poses a significant bottleneck for timely data analysis. To address this challenge, we propose a novel reconstruction approach that integrates deep learning with the physical principles of off-axis holography. We initialized part of the network weights based on the physical principle and then fine-tuned them via weakly supersized learning. Our off-axis hologram network (OAH-Net) retrieves phase and amplitude images with errors that fall within the measurement error range attributable to hardware, and its reconstruction speed significantly surpasses the microscope's acquisition rate. Crucially, OAH-Net demonstrates remarkable external generalization capabilities on unseen samples with distinct patterns and can be seamlessly integrated with other models for downstream tasks to achieve end-to-end real-time hologram analysis. This capability further expands off-axis holography's applications in both biological and medical studies., Comment: 11 pages, 4 figures
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- 2024
19. SeerAttention: Learning Intrinsic Sparse Attention in Your LLMs
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Gao, Yizhao, Zeng, Zhichen, Du, Dayou, Cao, Shijie, So, Hayden Kwok-Hay, Cao, Ting, Yang, Fan, and Yang, Mao
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Computer Science - Computation and Language - Abstract
Attention is the cornerstone of modern Large Language Models (LLMs). Yet its quadratic complexity limits the efficiency and scalability of LLMs, especially for those with a long-context window. A promising approach addressing this limitation is to leverage the sparsity in attention. However, existing sparsity-based solutions predominantly rely on predefined patterns or heuristics to approximate sparsity. This practice falls short to fully capture the dynamic nature of attention sparsity in language-based tasks. This paper argues that attention sparsity should be learned rather than predefined. To this end, we design SeerAttention, a new Attention mechanism that augments the conventional attention with a learnable gate that adaptively selects significant blocks in an attention map and deems the rest blocks sparse. Such block-level sparsity effectively balances accuracy and speedup. To enable efficient learning of the gating network, we develop a customized FlashAttention implementation that extracts the block-level ground truth of attention map with minimum overhead. SeerAttention not only applies to post-training, but also excels in long-context fine-tuning. Our results show that at post-training stages, SeerAttention significantly outperforms state-of-the-art static or heuristic-based sparse attention methods, while also being more versatile and flexible to adapt to varying context lengths and sparsity ratios. When applied to long-context fine-tuning with YaRN, SeerAttention can achieve a remarkable 90% sparsity ratio at a 32k context length with minimal perplexity loss, offering a 5.67x speedup over FlashAttention-2.
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- 2024
20. The GALAH Survey: Stellar parameters and abundances for 800,000 Gaia RVS spectra using GALAH DR4 and The Cannon
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Das, Pradosh Barun, Zucker, Daniel B., De Silva, Gayandhi M., Borsato, Nicholas W., Mura-Guzmán, Aldo, Buder, Sven, Ness, Melissa, Nordlander, Thomas, Casey, Andrew R., Martell, Sarah L., Bland-Hawthorn, Joss, de Grijs, Richard, Freeman, Ken C., Kos, Janez, Stello, Dennis, Lewis, Geraint F., Hayden, Michael R., and Sharma, Sanjib
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Solar and Stellar Astrophysics - Abstract
Analysing stellar parameters and abundances from nearly one million Gaia DR3 Radial Velocity Spectrometer (RVS) spectra poses challenges due to the limited spectral coverage (restricted to the infrared Ca II triplet) and variable signal-to-noise ratios of the data. To address this, we use The Cannon, a data-driven method, to transfer stellar parameters and abundances from the GALAH Data Release 4 (DR4; R ~ 28,000) catalogue to the lower resolution Gaia DR3 RVS spectra (R ~ 11,500). Our model, trained on 14,484 common targets, predicts parameters such as Teff, log g, and [Fe/H], along with several other elements across approximately 800,000 Gaia RVS spectra. We utilise stars from open and globular clusters present in the Gaia RVS catalogue to validate our predicted mean [Fe/H] with high precision (~0.02-0.10 dex). Additionally, we recover the bimodal distribution of [Ti/Fe] versus [Fe/H], reflecting the high and low alpha-components of Milky Way disk stars, demonstrating The Cannon's capability for accurate stellar abundance determination from medium-resolution Gaia RVS spectra. The methodologies and resultant catalogue presented in this work highlight the remarkable potential of the RVS dataset, which by the end of the Gaia mission will comprise spectra of over 200 million stars., Comment: Submitted to MNRAS, 16 pages, 15 figures
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- 2024
21. A Framework for SLO, Carbon, and Wastewater-Aware Sustainable FaaS Cloud Platform Management
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Qi, Sirui, Moore, Hayden, Hogade, Ninad, Milojicic, Dejan, Bash, Cullen, and Pasricha, Sudeep
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Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Function-as-a-Service (FaaS) is a growing cloud computing paradigm that is expected to reduce the user cost of service over traditional serverful approaches. However, the environmental impact of FaaS has not received much attention. We investigate FaaS scheduling and scaling from a sustainability perspective in this work. We find that the service-level objectives (SLOs) of FaaS and carbon emissions conflict with each other. We also find that SLO-focused FaaS scheduling can exacerbate water use in a datacenter. We propose a novel sustainability-focused FaaS scheduling and scaling framework to co-optimize SLO performance, carbon emissions, and wastewater generation.
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- 2024
22. Supercomputer 3D Digital Twin for User Focused Real-Time Monitoring
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Bergeron, William, Hubbell, Matthew, Mojica, Daniel, Reuther, Albert, Arcand, William, Bestor, David, Burrill, Daniel, Chansup, Byun, Gadepally, Vijay, Houle, Michael, Jananthan, Hayden, Jones, Michael, Luszczek, Piotr, Michaleas, Peter, Milechin, Lauren, Prout, Julie Mullen Andrew, Rosa, Antonio, Yee, Charles, and Kepner, Jeremy
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Real-time supercomputing performance analysis is a critical aspect of evaluating and optimizing computational systems in a dynamic user environment. The operation of supercomputers produce vast quantities of analytic data from multiple sources and of varying types so compiling this data in an efficient matter is critical to the process. MIT Lincoln Laboratory Supercomputing Center has been utilizing the Unity 3D game engine to create a Digital Twin of our supercomputing systems for several years to perform system monitoring. Unity offers robust visualization capabilities making it ideal for creating a sophisticated representation of the computational processes. As we scale the systems to include a diversity of resources such as accelerators and the addition of more users, we need to implement new analysis tools for the monitoring system. The workloads in research continuously change, as does the capability of Unity, and this allows us to adapt our monitoring tools to scale and incorporate features enabling efficient replay of system wide events, user isolation, and machine level granularity. Our system fully takes advantage of the modern capabilities of the Unity Engine in a way that intuitively represents the real time workload performed on a supercomputer. It allows HPC system engineers to quickly diagnose usage related errors with its responsive user interface which scales efficiently with large data sets.
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- 2024
23. The DECam Ecliptic Exploration Project (DEEP). VII. The Strengths of Three Superfast Rotating Main-belt Asteroids from a Preliminary Search of DEEP Data
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Strauss, Ryder, McNeill, Andrew, Trilling, David E., Valdes, Francisco, Bernardinell, Pedro H., Fuentes, Cesar, Gerdes, David W., Holman, Matthew J., Juric, Mario, Lin, Hsing Wen, Markwardt, Larissa, Mommert, Michael, Napier, Kevin J., Oldroyd, William J., Payne, Matthew J., Rivkin, Andrew S., Schlichting, Hilke E., Sheppard, Scott S., Smotherman, Hayden, Trujillo, Chadwick A, Adams, Fred C., and Chandler, Colin Orion
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Astrophysics - Earth and Planetary Astrophysics - Abstract
Superfast rotators (SFRs) are small solar system objects that rotate faster than generally possible for a cohesionless rubble pile. Their rotational characteristics allow us to make inferences about their interior structure and composition. Here, we present the methods and results from a preliminary search for SFRs in the DECam Ecliptic Exploration Project (DEEP) data set. We find three SFRs from a sample of 686 main-belt asteroids, implying an occurrence rate of 0.4 -0.3/+0.1 percent - a higher incidence rate than has been measured by previous studies. We suggest that this high occurrence rate is due to the small sub-kilometer size regime to which DEEP has access: the objects searched here were as small as 500 m. We compute the minimum required cohesive strength for each of these SFRs and discuss the implications of these strengths in the context of likely evolution mechanisms. We find that all three of these SFRs require strengths that are more than that of weak regolith but consistent with many cohesive asteroid strengths reported in the literature. Across the full DEEP data set, we have identified ~70,000 Main-Belt Asteroids and expect ~300 SFRs - a result that will be assessed in a future paper.
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- 2024
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24. Embedding-based statistical inference on generative models
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Helm, Hayden, Acharyya, Aranyak, Duderstadt, Brandon, Park, Youngser, and Priebe, Carey E.
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
The recent cohort of publicly available generative models can produce human expert level content across a variety of topics and domains. Given a model in this cohort as a base model, methods such as parameter efficient fine-tuning, in-context learning, and constrained decoding have further increased generative capabilities and improved both computational and data efficiency. Entire collections of derivative models have emerged as a byproduct of these methods and each of these models has a set of associated covariates such as a score on a benchmark, an indicator for if the model has (or had) access to sensitive information, etc. that may or may not be available to the user. For some model-level covariates, it is possible to use "similar" models to predict an unknown covariate. In this paper we extend recent results related to embedding-based representations of generative models -- the data kernel perspective space -- to classical statistical inference settings. We demonstrate that using the perspective space as the basis of a notion of "similar" is effective for multiple model-level inference tasks.
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- 2024
25. Neural Scaling Laws of Deep ReLU and Deep Operator Network: A Theoretical Study
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Liu, Hao, Zhang, Zecheng, Liao, Wenjing, and Schaeffer, Hayden
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Neural scaling laws play a pivotal role in the performance of deep neural networks and have been observed in a wide range of tasks. However, a complete theoretical framework for understanding these scaling laws remains underdeveloped. In this paper, we explore the neural scaling laws for deep operator networks, which involve learning mappings between function spaces, with a focus on the Chen and Chen style architecture. These approaches, which include the popular Deep Operator Network (DeepONet), approximate the output functions using a linear combination of learnable basis functions and coefficients that depend on the input functions. We establish a theoretical framework to quantify the neural scaling laws by analyzing its approximation and generalization errors. We articulate the relationship between the approximation and generalization errors of deep operator networks and key factors such as network model size and training data size. Moreover, we address cases where input functions exhibit low-dimensional structures, allowing us to derive tighter error bounds. These results also hold for deep ReLU networks and other similar structures. Our results offer a partial explanation of the neural scaling laws in operator learning and provide a theoretical foundation for their applications.
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- 2024
26. The GALAH Survey: Data Release 4
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Buder, S., Kos, J., Wang, E. X., McKenzie, M., Howell, M., Martell, S. L., Hayden, M. R., Zucker, D. B., Nordlander, T., Montet, B. T., Traven, G., Bland-Hawthorn, J., De Silva, G. M., Freeman, K. C., Lewis, G. F., Lind, K., Sharma, S., Simpson, J. D., Stello, D., Zwitter, T., Amarsi, A. M., Armstrong, J. J., Banks, K., Beavis, M. A., Beeson, K., Chen, B., Ciucă, I., Da Costa, G. S., de Grijs, R., Martin, B., Nataf, D. M., Ness, M. K., Rains, A. D., Scarr, T., Vogrinčič, R., Wang, Z., Wittenmyer, R. A., Xie, Y., and Collaboration, The GALAH
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Astrophysics - Astrophysics of Galaxies ,Astrophysics - Solar and Stellar Astrophysics - Abstract
The stars of the Milky Way carry the chemical history of our Galaxy in their atmospheres as they journey through its vast expanse. Like barcodes, we can extract the chemical fingerprints of stars from high-resolution spectroscopy. The fourth data release (DR4) of the Galactic Archaeology with HERMES (GALAH) Survey, based on a decade of observations, provides the chemical abundances of up to 32 elements for 917 588 stars that also have exquisite astrometric data from the $Gaia$ satellite. For the first time, these elements include life-essential nitrogen to complement carbon, and oxygen as well as more measurements of rare-earth elements critical to modern-life electronics, offering unparalleled insights into the chemical composition of the Milky Way. For this release, we use neural networks to simultaneously fit stellar parameters and abundances across the full spectrum, leveraging synthetic grids computed with Spectroscopy Made Easy. These grids account for atomic line formation in non-local thermodynamic equilibrium for 14 elements. In a two-iteration process, we first fit stellar labels for all 1 085 520 spectra, then co-add repeated observations and refine these labels using astrometric data from $Gaia$ and 2MASS photometry, improving the accuracy and precision of stellar parameters and abundances. Our validation thoroughly assesses the reliability of spectroscopic measurements and highlights key caveats for catalogue users. GALAH DR4 represents yet another milestone in Galactic archaeology, combining detailed chemical compositions from multiple nucleosynthetic channels with kinematic information and age estimates. The resulting dataset, covering nearly a million stars, opens new avenues for understanding not only the chemical and dynamical history of the Milky Way, but also the broader questions of the origin of elements and the evolution of planets, stars, and galaxies., Comment: 43 pages, 38 figures to be submitted to PASA. Accompanying the GALAH Data Release 4, see https://www.galah-survey.org and https://cloud.datacentral.org.au/teamdata/GALAH/public/GALAH_DR4/. All code available on http://github.com/svenbuder/GALAH_DR4/ and https://github.com/svenbuder/galah_dr4_paper. Comments welcome
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- 2024
27. Consistent estimation of generative model representations in the data kernel perspective space
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Acharyya, Aranyak, Trosset, Michael W., Priebe, Carey E., and Helm, Hayden S.
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Computer Science - Machine Learning ,Mathematics - Statistics Theory - Abstract
Generative models, such as large language models and text-to-image diffusion models, produce relevant information when presented a query. Different models may produce different information when presented the same query. As the landscape of generative models evolves, it is important to develop techniques to study and analyze differences in model behaviour. In this paper we present novel theoretical results for embedding-based representations of generative models in the context of a set of queries. We establish sufficient conditions for the consistent estimation of the model embeddings in situations where the query set and the number of models grow.
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- 2024
28. Sequential Learning in the Dense Associative Memory
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McAlister, Hayden, Robins, Anthony, and Szymanski, Lech
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Computer Science - Neural and Evolutionary Computing ,Computer Science - Artificial Intelligence - Abstract
Sequential learning involves learning tasks in a sequence, and proves challenging for most neural networks. Biological neural networks regularly conquer the sequential learning challenge and are even capable of transferring knowledge both forward and backwards between tasks. Artificial neural networks often totally fail to transfer performance between tasks, and regularly suffer from degraded performance or catastrophic forgetting on previous tasks. Models of associative memory have been used to investigate the discrepancy between biological and artificial neural networks due to their biological ties and inspirations, of which the Hopfield network is perhaps the most studied model. The Dense Associative Memory, or modern Hopfield network, generalizes the Hopfield network, allowing for greater capacities and prototype learning behaviors, while still retaining the associative memory structure. We investigate the performance of the Dense Associative Memory in sequential learning problems, and benchmark various sequential learning techniques in the network. We give a substantial review of the sequential learning space with particular respect to the Hopfield network and associative memories, as well as describe the techniques we implement in detail. We also draw parallels between the classical and Dense Associative Memory in the context of sequential learning, and discuss the departures from biological inspiration that may influence the utility of the Dense Associative Memory as a tool for studying biological neural networks. We present our findings, and show that existing sequential learning methods can be applied to the Dense Associative Memory to improve sequential learning performance.
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- 2024
29. Hypersparse Traffic Matrices from Suricata Network Flows using GraphBLAS
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Houle, Michael, Jones, Michael, Wallmeyer, Dan, Brodeur, Risa, Burr, Justin, Jananthan, Hayden, Merrell, Sam, Michaleas, Peter, Perez, Anthony, Prout, Andrew, and Kepner, Jeremy
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
Hypersparse traffic matrices constructed from network packet source and destination addresses is a powerful tool for gaining insights into network traffic. SuiteSparse: GraphBLAS, an open source package or building, manipulating, and analyzing large hypersparse matrices, is one approach to constructing these traffic matrices. Suricata is a widely used open source network intrusion detection software package. This work demonstrates how Suricata network flow records can be used to efficiently construct hypersparse matrices using GraphBLAS.
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- 2024
30. Time-Series Forecasting, Knowledge Distillation, and Refinement within a Multimodal PDE Foundation Model
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Jollie, Derek, Sun, Jingmin, Zhang, Zecheng, and Schaeffer, Hayden
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Computer Science - Machine Learning - Abstract
Symbolic encoding has been used in multi-operator learning as a way to embed additional information for distinct time-series data. For spatiotemporal systems described by time-dependent partial differential equations, the equation itself provides an additional modality to identify the system. The utilization of symbolic expressions along side time-series samples allows for the development of multimodal predictive neural networks. A key challenge with current approaches is that the symbolic information, i.e. the equations, must be manually preprocessed (simplified, rearranged, etc.) to match and relate to the existing token library, which increases costs and reduces flexibility, especially when dealing with new differential equations. We propose a new token library based on SymPy to encode differential equations as an additional modality for time-series models. The proposed approach incurs minimal cost, is automated, and maintains high prediction accuracy for forecasting tasks. Additionally, we include a Bayesian filtering module that connects the different modalities to refine the learned equation. This improves the accuracy of the learned symbolic representation and the predicted time-series.
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- 2024
31. HPC with Enhanced User Separation
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Prout, Andrew, Reuther, Albert, Houle, Michael, Jones, Michael, Michaleas, Peter, Anderson, LaToya, Arcand, William, Bergeron, Bill, Bestor, David, Bonn, Alex, Burrill, Daniel, Byun, Chansup, Gadepally, Vijay, Hubbell, Matthew, Jananthan, Hayden, Luszczek, Piotr, Milechin, Lauren, Morales, Guillermo, Mullen, Julie, Rosa, Antonio, Yee, Charles, and Kepner, Jeremy
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
HPC systems used for research run a wide variety of software and workflows. This software is often written or modified by users to meet the needs of their research projects, and rarely is built with security in mind. In this paper we explore several of the key techniques that MIT Lincoln Laboratory Supercomputing Center has deployed on its systems to manage the security implications of these workflows by providing enforced separation for processes, filesystem access, network traffic, and accelerators to make every user feel like they are running on a personal HPC.
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- 2024
32. PROSE-FD: A Multimodal PDE Foundation Model for Learning Multiple Operators for Forecasting Fluid Dynamics
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Liu, Yuxuan, Sun, Jingmin, He, Xinjie, Pinney, Griffin, Zhang, Zecheng, and Schaeffer, Hayden
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Computer Science - Machine Learning ,Mathematics - Numerical Analysis ,Physics - Fluid Dynamics - Abstract
We propose PROSE-FD, a zero-shot multimodal PDE foundational model for simultaneous prediction of heterogeneous two-dimensional physical systems related to distinct fluid dynamics settings. These systems include shallow water equations and the Navier-Stokes equations with incompressible and compressible flow, regular and complex geometries, and different buoyancy settings. This work presents a new transformer-based multi-operator learning approach that fuses symbolic information to perform operator-based data prediction, i.e. non-autoregressive. By incorporating multiple modalities in the inputs, the PDE foundation model builds in a pathway for including mathematical descriptions of the physical behavior. We pre-train our foundation model on 6 parametric families of equations collected from 13 datasets, including over 60K trajectories. Our model outperforms popular operator learning, computer vision, and multi-physics models, in benchmark forward prediction tasks. We test our architecture choices with ablation studies.
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- 2024
33. Anonymized Network Sensing Graph Challenge
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Jananthan, Hayden, Jones, Michael, Arcand, William, Bestor, David, Bergeron, William, Burrill, Daniel, Buluc, Aydin, Byun, Chansup, Davis, Timothy, Gadepally, Vijay, Grant, Daniel, Houle, Michael, Hubbell, Matthew, Luszczek, Piotr, Michaleas, Peter, Milechin, Lauren, Milner, Chasen, Morales, Guillermo, Morris, Andrew, Mullen, Julie, Patel, Ritesh, Pentland, Alex, Pisharody, Sandeep, Prout, Andrew, Reuther, Albert, Rosa, Antonio, Wachman, Gabriel, Yee, Charles, and Kepner, Jeremy
- Subjects
Computer Science - Networking and Internet Architecture ,Computer Science - Discrete Mathematics ,Computer Science - Performance ,Computer Science - Software Engineering ,Mathematics - Combinatorics - Abstract
The MIT/IEEE/Amazon GraphChallenge encourages community approaches to developing new solutions for analyzing graphs and sparse data derived from social media, sensor feeds, and scientific data to discover relationships between events as they unfold in the field. The anonymized network sensing Graph Challenge seeks to enable large, open, community-based approaches to protecting networks. Many large-scale networking problems can only be solved with community access to very broad data sets with the highest regard for privacy and strong community buy-in. Such approaches often require community-based data sharing. In the broader networking community (commercial, federal, and academia) anonymized source-to-destination traffic matrices with standard data sharing agreements have emerged as a data product that can meet many of these requirements. This challenge provides an opportunity to highlight novel approaches for optimizing the construction and analysis of anonymized traffic matrices using over 100 billion network packets derived from the largest Internet telescope in the world (CAIDA). This challenge specifies the anonymization, construction, and analysis of these traffic matrices. A GraphBLAS reference implementation is provided, but the use of GraphBLAS is not required in this Graph Challenge. As with prior Graph Challenges the goal is to provide a well-defined context for demonstrating innovation. Graph Challenge participants are free to select (with accompanying explanation) the Graph Challenge elements that are appropriate for highlighting their innovations., Comment: Accepted to IEEE HPEC 2024
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- 2024
34. Towards Agentic AI on Particle Accelerators
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Sulc, Antonin, Hellert, Thorsten, Kammering, Raimund, Houscher, Hayden, and John, Jason St.
- Subjects
Physics - Accelerator Physics ,Computer Science - Artificial Intelligence - Abstract
As particle accelerators grow in complexity, traditional control methods face increasing challenges in achieving optimal performance. This paper envisions a paradigm shift: a decentralized multi-agent framework for accelerator control, powered by Large Language Models (LLMs) and distributed among autonomous agents. We present a proposition of a self-improving decentralized system where intelligent agents handle high-level tasks and communication and each agent is specialized control individual accelerator components. This approach raises some questions: What are the future applications of AI in particle accelerators? How can we implement an autonomous complex system such as a particle accelerator where agents gradually improve through experience and human feedback? What are the implications of integrating a human-in-the-loop component for labeling operational data and providing expert guidance? We show two examples, where we demonstrate viability of such architecture., Comment: 4 pages, 3 figures, Machine Learning and the Physical Sciences at Workshop at the 38th conference on Neural Information Processing Systems (NeurIPS)
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- 2024
35. What is Normal? A Big Data Observational Science Model of Anonymized Internet Traffic
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Kepner, Jeremy, Jananthan, Hayden, Jones, Michael, Arcand, William, Bestor, David, Bergeron, William, Burrill, Daniel, Buluc, Aydin, Byun, Chansup, Davis, Timothy, Gadepally, Vijay, Grant, Daniel, Houle, Michael, Hubbell, Matthew, Luszczek, Piotr, Milechin, Lauren, Milner, Chasen, Morales, Guillermo, Morris, Andrew, Mullen, Julie, Patel, Ritesh, Pentland, Alex, Pisharody, Sandeep, Prout, Andrew, Reuther, Albert, Rosa, Antonio, Wachman, Gabriel, Yee, Charles, and Michaleas, Peter
- Subjects
Computer Science - Networking and Internet Architecture ,Computer Science - Cryptography and Security ,Computer Science - Computers and Society ,Computer Science - Social and Information Networks - Abstract
Understanding what is normal is a key aspect of protecting a domain. Other domains invest heavily in observational science to develop models of normal behavior to better detect anomalies. Recent advances in high performance graph libraries, such as the GraphBLAS, coupled with supercomputers enables processing of the trillions of observations required. We leverage this approach to synthesize low-parameter observational models of anonymized Internet traffic with a high regard for privacy., Comment: Accepted to IEEE HPEC, 7 pages, 6 figures, 1 table, 41 references
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- 2024
36. Virtual Reality in Criminal Justice: Exploring the Role of Emotion in Student Learning
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Hayden P. Smith, Bobbie Ticknor, and Alicia H. Sitren
- Abstract
The role of emotion in the context of virtual reality learning environments (VRLEs) has lately received increased attention, though there is a gap in the research on VRLEs in criminal justice. The current study examines the impact of a virtual reality experience that focuses on mental illness occurring in those within the criminal justice system. A qualitative methodology was employed to examine student responses from 242 students in five criminal justice classes taught in two states between 2019 and 2020. Three themes emerged from the students' responses, including personal connections, empathy for others, and emotional responses to situational factors. Students experienced considerable presence and immersion during the virtual reality experience, and this generated emotional responses in them to the material. While the use of virtual reality in the pedagogy of social science is still emerging, the current study indicates that student can be provided a high degree of control and value in learning from the experience while simultaneously minimizing student exposure to risk.
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- 2024
37. Early expression of CD94 and loss of CD96 on CD8+ T cells after allogeneic stem cell tranplantation is predictive of subsequent relapse and survival
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Kriti Verma, Wayne Croft, Hayden Pearce, Jianmin Zuo, Christine Stephens, Jane Nunnick, Francesca AM Kinsella, Ram Malladi, and Paul Moss
- Subjects
Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
Allogeneic stem cell transplantation is used widely in the treatment of hematopoietic malignancy. However, relapse of malignant disease is the primary cause of treatment failure and reflects loss of immunological graft-versus-leukemia effect. We studied the transcriptional and phenotypic profile of CD8+ T cells in the first month following transplantation and related this to risk of subsequent relapse. Single cell transcriptional profiling identified five discrete CD8+ T-cell clusters. High levels of T-cell activation and acquisition of a regulatory transcriptome were apparent in patients who went on to suffer disease relapse. A relapse-associated gene signature of 47 genes was then assessed in a confirmation cohort of 34 patients. High expression of the inhibitory receptor CD94/NKG2A on CD8+ T cells within the first month was associated with 4.8 fold increased risk of relapse and 2.7 fold reduction in survival. Furthermore, reduced expression of the activatory molecule CD96 was associated with 2.2 fold increased risk of relapse and 1.9 fold reduction in survival. This work identifies CD94 and CD96 as potential targets for CD8-directed immunotherapy in the very early phase following allogeneic transplantation with the potential to reduce long term relapse rates and improve patient survival.
- Published
- 2022
- Full Text
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38. Diabetic Kidney Disease Is Associated With Increased Complications Following Operative Management of Ankle Fractures
- Author
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William S. Polachek MD, Hayden P. Baker MD, James S. Dahm MD, Jason A. Strelzow MD, and Kelly K. Hynes MD
- Subjects
Orthopedic surgery ,RD701-811 - Abstract
Background: Diabetes mellitus and peripheral neuropathy are established risk factors for complications in operatively treated ankle fractures. Generally, the presence of peripheral neuropathy and diabetic nephropathy have been used as independent variables in studies of diabetic ankle fracture cohorts but are typically treated as binary risk factors. Our purpose was to quantify the effects of risk factors on complication rate specific to diabetic patients undergoing ankle fracture fixation. Methods: We identified 617 rotational ankle fractures treated operatively at a single academic medical center from 2010 to 2019, of which 160 were identified as diabetic. Of these, 91 ankle fractures in 90 diabetic patients met criteria for retrospective review of clinical and radiographic data. Criteria included perioperative laboratory studies, including glycated hemoglobin (HbA 1c ) and estimated glomerular filtration rate (eGFR), as well as follow-up radiographs in the electronic record. We defined complications in this surgical cohort as deep surgical site infection, unplanned return to the operating room, and failure of fixation. Logistic regression was performed and odds ratios (ORs) calculated. Results: The overall complication rate was 28.6% (26/91) in this cohort. Median follow-up was 29 weeks (range: 5-520 weeks). Mean perioperative HbA 1c in patients who experienced postoperative complications was 7.6% (range: 5.1%-14.2%) compared with 7.8% (range: 5.6%-13.5%) who did not ( P = .69). Diabetic patients with chronic kidney disease (eGFR
- Published
- 2022
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39. Revised Alcohol Protective Behavioral Strategies Scale--20 (PBSS-20) Sub-Types: An Analysis of Direct/Controlled Consumption and Indirect/Harm Reduction PBS
- Author
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Roselyn Peterson, Robert D. Dvorak, Emily K. Burr, Ardhys N. De Leon, Samantha J. Klaver, Madison H. Maynard, Emma R. Hayden, and Bradley Aguilar
- Abstract
Alcohol protective behavioral strategies (PBS) are commonly conceptualized with a three-factor model, as used in the Protective Behavioral Strategies Scale--20 (PBSS-20). However, inconsistencies exist between factors and drinking outcomes. The current study used factor analysis to test a two-factor structure directly via controlled consumption (Direct/CC) and indirectly via harm reduction (Indirect/HR) using the PBSS-20 among a combined sample of n = 4,883 drinkers. Both the two- and three-factor structures evince similar model fit. A two-factor model yielded more concise PBS measurement. Negative associations were observed with consumption (Direct/CC PBS) and problems (Indirect/HR). A condensed, eight-item, two-factor model accounted for less variance in alcohol consumption, however more variance in alcohol-related problems. A more consistent framework for understanding the impact of PBS on alcohol-related outcomes is provided.
- Published
- 2024
- Full Text
- View/download PDF
40. LeMON: Learning to Learn Multi-Operator Networks
- Author
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Sun, Jingmin, Zhang, Zecheng, and Schaeffer, Hayden
- Subjects
Computer Science - Machine Learning - Abstract
Single-operator learning involves training a deep neural network to learn a specific operator, whereas recent work in multi-operator learning uses an operator embedding structure to train a single neural network on data from multiple operators. Thus, multi-operator learning is capable of predicting a range of operators within one model. In this work, we propose pretraining and fine-tuning strategies for solving PDEs using multi-operator learning. One key aspect is that by increasing the number of families of operators used in pretraining, a PDE foundation model can be fine-tuned to downstream tasks involving new PDEs with a limited number of samples, thus outperforming single operator neural networks. Specifically, a multi-operator learning model pre-trained with data from diverse PDE families can predict unseen operators after fine-tuning with only a limited number of operators from the new family, enabling them to serve as a data-free PDE solver. We also show that the proposed training and fine-tuning method is able to predict new operators in zero-shot prediction without samples. Additionally, we introduce a PDE-agnostic meta-learning algorithm to improve the adaptability of the model to various PDEs by providing a better parameter initialization process. To address the needs of applications with limited computing resources, we explore low-rank adaptation methods that reduce computational costs while enhancing solver accuracy. Lastly, by examining the scaling law with respect to the number of operator families, we establish and highlight its potential for broad adaptation in PDE-solving tasks.
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- 2024
41. Segue 2 Recently Collided with the Cetus-Palca Stream: New Opportunities to Constrain Dark Matter in an Ultra-Faint Dwarf
- Author
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Foote, Hayden R., Besla, Gurtina, Garavito-Camargo, Nicolás, Patel, Ekta, Thomas, Guillaume F., Bonaca, Ana, Price-Whelan, Adrian M., Peter, Annika H. G., Zaritsky, Dennis, and Conroy, Charlie
- Subjects
Astrophysics - Astrophysics of Galaxies - Abstract
Stellar streams in the Milky Way are promising detectors of low-mass dark matter (DM) subhalos predicted by $\Lambda$CDM. Passing subhalos induce perturbations in streams that indicate the presence of the subhalos. Understanding how known DM-dominated satellites impact streams is a crucial step towards using stream perturbations to constrain the properties of dark perturbers. Here, we cross-match a $\textit{Gaia}$ EDR3 and SEGUE member catalog of the Cetus-Palca stream (CPS) with H3 for additional radial velocity measurements and fit the orbit of the CPS using this 6-D data. We demonstrate for the first time that the ultra-faint dwarf Segue 2 had a recent (77$\pm$5 Myr ago) close flyby (within the stream's 2$\sigma$ width) with the CPS. This interaction enables constraints on Segue 2's mass and density profile at larger radii ($\mathcal{O}(1)$ kpc) than are probed by its stars ($\mathcal{O}(10)$ pc). While Segue 2 is not expected to strongly affect the portion of the stream covered by our 6-D data, we predict that if Segue 2's mass within $\sim 6$ kpc is $5\times 10^9\,M_\odot$, the CPS's velocity dispersion will be $\sim 40$ km/s larger ahead of the impact site than behind it. If no such heating is detected, Segue 2's mass cannot exceed $10^9\,M_\odot$ within $\sim 6$ kpc. The proper motion distribution of the CPS near the impact site is mildly sensitive to the shape of Segue 2's density profile. This study presents a critical test for frameworks designed to constrain properties of dark subhalos from stream perturbations., Comment: 33 pages, 14 figures, 6 tables. Submitted to ApJ, comments welcome
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- 2024
42. Knowledge AI: Fine-tuning NLP Models for Facilitating Scientific Knowledge Extraction and Understanding
- Author
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Muralidharan, Balaji, Beadles, Hayden, Marzban, Reza, and Mupparaju, Kalyan Sashank
- Subjects
Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
This project investigates the efficacy of Large Language Models (LLMs) in understanding and extracting scientific knowledge across specific domains and to create a deep learning framework: Knowledge AI. As a part of this framework, we employ pre-trained models and fine-tune them on datasets in the scientific domain. The models are adapted for four key Natural Language Processing (NLP) tasks: summarization, text generation, question answering, and named entity recognition. Our results indicate that domain-specific fine-tuning significantly enhances model performance in each of these tasks, thereby improving their applicability for scientific contexts. This adaptation enables non-experts to efficiently query and extract information within targeted scientific fields, demonstrating the potential of fine-tuned LLMs as a tool for knowledge discovery in the sciences., Comment: 11 pages
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- 2024
43. Air-blood interface engineered microfluidic device to mimic shear rate gradient induced human bleeding model
- Author
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Das, Shobhit, Pandey, Shilpi, and Hayden, Oliver
- Subjects
Physics - Biological Physics ,Quantitative Biology - Cell Behavior ,Quantitative Biology - Tissues and Organs - Abstract
Microfluidic technology has emerged as a powerful tool for studying complex biological processes with enhanced precision and control. A microfluidic chip was designed to emulate human-like microvascular networks with precise control over channel geometry and flow conditions. By simulating blood flow dynamics during bleeding events, we successfully observed the real-time interactions of platelets and their aggregation induced by shear rate gradient at the wound site. Platelet dynamics is primarily influenced by physico-mechanical condition of blood vessels with pathophysiological condition of blood at close proximity of vascular injury site. This microfluidic platform facilitated the investigation of platelet adhesion, activation, and clot formation, providing a unique opportunity to study the spatiotemporal dynamics of platelet aggregation and blood clot. Our findings shed light on the intricate mechanisms underlying thrombus formation and platelet-mediated aggregation, offering a more accurate and dynamic representation of human haemostasis compared to traditional animal models. In the conventional approach, the human bleeding model is tried on mouse due to anatomy and pathological similarities between mouse and humans. This study will simplify and standardize the blood and vasculature conditions. The microfluidic-based replication of the bleeding model holds significant promise in advancing our understanding of clotting disorders and wound healing processes. Furthermore, it paves the way for targeted therapeutic interventions in managing bleeding disorders and enhancing clinical strategies for promoting efficient wound closure. Ultimately, this study demonstrates the potential of microfluidics to revolutionize haemostasis research and opens up new avenues for the development of personalized medicine approaches in the field of clotting disorders., Comment: 11 pages, 8 figures
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- 2024
44. Candidate Distant Trans-Neptunian Objects Detected by the New Horizons Subaru TNO Survey
- Author
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Fraser, Wesley C., Porter, Simon B., Peltier, Lowell, Kavelaars, JJ, Verbiscer, Anne J., Buie, Marc W., Stern, S. Alan, Spencer, John R., Benecchi, Susan D., Terai, Tsuyoshi, Ito, Takashi, Yoshida, Fumi, Gerdes, David W., Napier, Kevin J., Lin, Hsing Wen, Gwyn, Stephen D. J., Smotherman, Hayden, Fabbro, Sebastien, Singer, Kelsi N., Alexander, Amanda M., Arimatsu, Ko, Banks, Maria E., Bray, Veronica J., El-Maarry, Mohamed Ramy, Ferrell, Chelsea L., Fuse, Tetsuharu, Glass, Florian, Holt, Timothy R., Hong, Peng, Ishimaru, Ryo, Johnson, Perianne E., Lauer, Tod R., Leiva, Rodrigo, Lykawka, Patryk S., Marschall, Raphael, Núñez, Jorge I., Postman, Marc, Quirico, Eric, Rhoden, Alyssa R., Simpson, Anna M., Schenk, Paul, Skrutskie, Michael F., Steffl, Andrew J., and Throop, Henry
- Subjects
Astrophysics - Earth and Planetary Astrophysics - Abstract
We report the detection of 239 trans-Neptunian Objects discovered through the on-going New Horizons survey for distant minor bodies being performed with the Hyper Suprime-Cam mosaic imager on the Subaru Telescope. These objects were discovered in images acquired with either the r2 or the recently commissioned EB-gri filter using shift and stack routines. Due to the extremely high stellar density of the search region down stream of the spacecraft, new machine learning techniques had to be developed to manage the extremely high false positive rate of bogus candidates produced from the shift and stack routines. We report discoveries as faint as r2$\sim26.5$. We highlight an overabundance of objects found at heliocentric distances $R\gtrsim70$~au compared to expectations from modelling of the known outer Solar System. If confirmed, these objects betray the presence of a heretofore unrecognized abundance of distant objects that can help explain a number of other observations that otherwise remain at odds with the known Kuiper Belt, including detections of serendipitous stellar occultations, and recent results from the Student Dust Counter on-board the New Horizons spacecraft., Comment: Accepted for publication in the Planetary Science Journal, 28 pages, 7 figures, 3 tables
- Published
- 2024
45. Impact of electron correlations on two-particle charge response in electron- and hole-doped cuprates
- Author
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Nag, Abhishek, Zinni, Luciano, Choi, Jaewon, Li, J., Tu, Sijia, Walters, A. C., Agrestini, S., Hayden, S. M., Bejas, Matías, Lin, Zefeng, Yamase, H., Jin, Kui, García-Fernández, M., Fink, J., Greco, Andrés, and Zhou, Ke-Jin
- Subjects
Condensed Matter - Strongly Correlated Electrons - Abstract
Estimating many-body effects that deviate from an independent particle approach, has long been a key research interest in condensed matter physics. Layered cuprates are prototypical systems, where electron-electron interactions are found to strongly affect the dynamics of single-particle excitations. It is however, still unclear how the electron correlations influence charge excitations, such as plasmons, which have been variously treated with either weak or strong correlation models. In this work, we demonstrate the hybridised nature of collective valence charge fluctuations leading to dispersing acoustic-like plasmons in hole-doped La$_{1.84}$Sr$_{0.16}$CuO$_{4}$ and electron-doped La$_{1.84}$Ce$_{0.16}$CuO$_{4}$ using the two-particle probe, resonant inelastic x-ray scattering. We then describe the plasmon dispersions in both systems, within both the weak mean-field Random Phase Approximation (RPA) and strong coupling $t$-$J$-$V$ models. The $t$-$J$-$V$ model, which includes the correlation effects implicitly, accurately describes the plasmon dispersions as resonant excitations outside the single-particle intra-band continuum. In comparison, a quantitative description of the plasmon dispersion in the RPA approach is obtained only upon explicit consideration of re-normalized electronic band parameters. Our comparative analysis shows that electron correlations significantly impact the low-energy plasmon excitations across the cuprate doping phase diagram, even at long wavelengths. Thus, complementary information on the evolution of electron correlations, influenced by the rich electronic phases in condensed matter systems, can be extracted through the study of two-particle charge response., Comment: 6 Figures
- Published
- 2024
46. Nanoscale ferroelectric programming of van der Waals heterostructures
- Author
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Yang, Dengyu, Cao, Qingrui, Akyuz, Erin, Hayden, John, Nordlander, Josh, Yu, Muqing, Ramachandran, Ranjani, Irvin, Patrick, Maria, Jon-Paul, Hunt, Benjamin M., and Levy, Jeremy
- Subjects
Condensed Matter - Materials Science ,Condensed Matter - Mesoscale and Nanoscale Physics ,Physics - Applied Physics - Abstract
The ability to create superlattices in van der Waals (vdW) heterostructures via moir\'e interference heralded a new era in the science and technology of two-dimensional materials. Through precise control of the twist angle, flat bands and strongly correlated phases have been engineered. The precise twisting of vdW layers is in some sense a bottom-up approach--a single parameter can dial in a wide range of periodic structures. Here, we describe a top-down approach to engineering nanoscale potentials in vdW layers using a buried programmable ferroelectric layer. Ultra-low-voltage electron beam lithography (ULV-EBL) is used to program ferroelectric domains in a ferroelectric Al_{1-x}B_{x}N thin film through a graphene/hexagonal boron nitride (hBN) heterostructure that is transferred on top. We demonstrate ferroelectric field effects by creating a lateral p-n junction, and demonstrate spatial resolution down to 35 nm, limited by the resolution of our scanned probe characterization methods. This innovative, resist-free patterning method is predicted to achieve 10 nm resolution and enable arbitrary programming of vdW layers, opening a pathway to create new phases that are inaccessible by moir\'e techniques. The ability to "paint" different phases of matter on a single vdW "canvas" provides a wealth of new electronic and photonic functionalities., Comment: 9 pages, 4 figures and supplemental material
- Published
- 2024
47. Physics of 1 keV line in X-ray binaries
- Author
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Chakraborty, Priyanka, Ferland, Gary, Fabian, Andrew, Sarkar, Arnab, Ludlam, Renee, Bianchi, Stefano, Hall, Hayden, and Kosec, Peter
- Subjects
Astrophysics - High Energy Astrophysical Phenomena - Abstract
X-ray binaries (XRBs) often exhibit spectral residuals in the 0.5 to 2 keV range, known as the "1 keV residual/1 keV feature", with variable centroid and intensity across different systems. Yet a comprehensive scientific explanation of the variability of the 1 keV feature has remained largely elusive. In this paper, we explain for the first time the origin and variability of the 1 keV feature in XRBs using the spectral synthesis code \textsc{Cloudy}. We constructed line blends for the emission and absorption lines and study the variability of these blends with ionization parameters, temperature, and column density. We conducted a sample study involving five XRBs including two ultraluminous X-ray sources (ULXs): NGC 247 ULX-1, NGC 1313 X-1, a binary X-ray pulsar: Hercules X-1, and two typical low-mass X-ray binaries (LMXBs): Cygnus X-2, and Serpens X-1, providing a comprehensive explanation of the 1 keV feature observed across these targets., Comment: 22 pages, 12 figures, Submitted to MNRAS
- Published
- 2024
48. LLload: Simplifying Real-Time Job Monitoring for HPC Users
- Author
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Byun, Chansup, Mullen, Julia, Reuther, Albert, Arcand, William, Bergeron, William, Bestor, David, Burrill, Daniel, Gadepally, Vijay, Houle, Michael, Hubbell, Matthew, Jananthan, Hayden, Jones, Michael, Michaleas, Peter, Morales, Guillermo, Prout, Andrew, Rosa, Antonio, Yee, Charles, Kepner, Jeremy, and Milechin, Lauren
- Subjects
Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Performance - Abstract
One of the more complex tasks for researchers using HPC systems is performance monitoring and tuning of their applications. Developing a practice of continuous performance improvement, both for speed-up and efficient use of resources is essential to the long term success of both the HPC practitioner and the research project. Profiling tools provide a nice view of the performance of an application but often have a steep learning curve and rarely provide an easy to interpret view of resource utilization. Lower level tools such as top and htop provide a view of resource utilization for those familiar and comfortable with Linux but a barrier for newer HPC practitioners. To expand the existing profiling and job monitoring options, the MIT Lincoln Laboratory Supercomputing Center created LLoad, a tool that captures a snapshot of the resources being used by a job on a per user basis. LLload is a tool built from standard HPC tools that provides an easy way for a researcher to track resource usage of active jobs. We explain how the tool was designed and implemented and provide insight into how it is used to aid new researchers in developing their performance monitoring skills as well as guide researchers in their resource requests.
- Published
- 2024
49. Coupled heat and fluid transport in pulled extrusion of cylinders
- Author
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Yuwono, Eunice B., Stokes, Yvonne M., Tronnolone, Hayden, and Wylie, Jonathan J.
- Subjects
Physics - Fluid Dynamics ,76D08, 80A19, 80-10 - Abstract
In the fabrication of optical fibres, the viscosity of the glass varies dramatically with temperature so that heat transfer plays an important role in the deformation of the fibre geometry. Surprisingly, for quasi-steady drawing, with measurement of pulling tension, the applied heat can be adjusted to control the tension and temperature modelling is not needed. However, when pulling tension is not measured, a coupled heat and fluid flow model is needed to determine the inputs required for a desired output. In the fast process of drawing a preform to a fibre, heat advection dominates conduction so that heat conduction may be neglected. By contrast, in the slow process of extruding a preform, heat conduction is important. This means that solving the coupled flow and temperature modelling is essential for prediction of preform geometry. In this paper we derive such a model that incorporates heat conduction for the extensional flow of fibres. The dramatic variations in viscosity with temperature means that this problem is extremely challenging to solve via standard numerical techniques and we therefore develop a novel finite-difference numerical solution method that proves to be highly robust. We use this method to show that conduction significantly affects the size of internal holes at the exit of the device., Comment: 32 pages, 6 figures, 1 table
- Published
- 2024
50. Tracking the perspectives of interacting language models
- Author
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Helm, Hayden, Duderstadt, Brandon, Park, Youngser, and Priebe, Carey E.
- Subjects
Computer Science - Artificial Intelligence ,Computer Science - Multiagent Systems - Abstract
Large language models (LLMs) are capable of producing high quality information at unprecedented rates. As these models continue to entrench themselves in society, the content they produce will become increasingly pervasive in databases that are, in turn, incorporated into the pre-training data, fine-tuning data, retrieval data, etc. of other language models. In this paper we formalize the idea of a communication network of LLMs and introduce a method for representing the perspective of individual models within a collection of LLMs. Given these tools we systematically study information diffusion in the communication network of LLMs in various simulated settings.
- Published
- 2024
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