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783 results on '"Smith, Zachary P."'

1. Efficient LLM Context Distillation

Author

Upadhayayaya, Rajesh, Smith, Zachary, Kottmyer, Chritopher, and Osti, Manish Raj

Subjects
Computer Science - Machine Learning
Abstract

This paper specifically investigates context distillation a method that extends the utility of task-specific examples by internalizing them, thus augmenting the example set accessible for model inference.

Published
2024

2. Low-Crosstalk, Silicon-Fabricated Optical Waveguides for Laser Delivery to Matter Qubits

Author

Craft, Clayton L., Barton, Nicholas J., Klug, Andrew C., Scalzi, Kenneth, Wildemann, Ian, Asagodu, Pramod, Broz, Joseph D., Porto, Nikola L., Macalik, Michael, Rizzo, Anthony, Percevault, Garrett, Tison, Christopher C., Smith, A. Matthew, Fanto, Michael L., Schneeloch, James, Sheridan, Erin, Heberle, Dylan, Brownell, Andrew, Sundaram, Vijay S. S., Deenadayalan, Venkatesh, van Niekerk, Matthew, Manfreda-Schulz, Evan, Howland, Gregory A., Preble, Stefan F., Coleman, Daniel, Leake, Gerald, Antohe, Alin, Vo, Tuan, Fahrenkopf, Nicholas M., Stievater, Todd H., Brickman-Soderberg, Kathy-Anne, Smith, Zachary S., and Hucul, David

Subjects
Quantum Physics
Abstract

Reliable control of quantum information in matter-based qubits requires precisely applied external fields, and unaccounted for spatial cross-talk of these fields between adjacent qubits leads to loss of fidelity. We report a CMOS foundry-produced, micro-fabricated silicon nitride (Si3N4) optical waveguide for addressing a chain of eight, unequally-spaced trapped barium ions with crosstalk compatible with scalable quantum information processing. The crosstalk mitigation techniques incorporated into the chip design result in a reduction of the measured optical field by at least 50.8(1.3) dB between adjacent waveguide outputs near 650 nm and similar behavior for devices designed for 493 nm and 585 nm. The waveguide outputs near 650 nm, along with a global laser near 493 nm were used to laser-cool a chain of eight barium-138 ions, and a camera imaged the resulting fluorescence at 493 nm., Comment: 9 pages, 7 figures

Published
2024

3. Representing Molecules as Random Walks Over Interpretable Grammars

Author

Sun, Michael, Guo, Minghao, Yuan, Weize, Thost, Veronika, Owens, Crystal Elaine, Grosz, Aristotle Franklin, Selvan, Sharvaa, Zhou, Katelyn, Mohiuddin, Hassan, Pedretti, Benjamin J, Smith, Zachary P, Chen, Jie, and Matusik, Wojciech

Subjects
Computer Science - Machine Learning, Quantitative Biology - Biomolecules
Abstract

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex molecular structures with fewer examples that are carefully designed using known substructures. We propose a data-efficient and interpretable model for representing and reasoning over such molecules in terms of graph grammars that explicitly describe the hierarchical design space featuring motifs to be the design basis. We present a novel representation in the form of random walks over the design space, which facilitates both molecule generation and property prediction. We demonstrate clear advantages over existing methods in terms of performance, efficiency, and synthesizability of predicted molecules, and we provide detailed insights into the method's chemical interpretability.

Published
2024

7. Curve attractors for marked rational maps

Author

Smith, Zachary

Subjects
Mathematics - Dynamical Systems, 37F20 (Primary) 37F10, 37F34 (Secondary)
Abstract

A Thurston map $f\colon (S^2, A) \to (S^2, A)$ with marking set $A$ induces a pullback relation on isotopy classes of Jordan curves in $(S^2, A)$. If every curve lands in a finite list of possible curve classes after iterating this pullback relation, then the pair $(f,A)$ is said to have a finite global curve attractor. It is conjectured by Pilgrim that all rational Thurston maps that are not flexible Latt\`{e}s maps have a finite global curve attractor. We present partial progress on this problem. Specifically, we prove that if $A$ has four points and the postcritical set (which is a subset of $A$) has two or three points, then $(f,A)$ has a finite global curve attractor. We also discuss extensions of the main result to certain special cases where $f$ has four postcritical points and $A=P_f$. Additionally, we speculate on how some of these ideas might be used in the more general case., Comment: 29 pages, 2 figures

Published
2024

13. Enhanced Sampling with Machine Learning: A Review

Author

Mehdi, Shams, Smith, Zachary, Herron, Lukas, Zou, Ziyue, and Tiwary, Pratyush

Subjects
Condensed Matter - Statistical Mechanics, Computer Science - Machine Learning, Physics - Chemical Physics, Physics - Computational Physics
Abstract

Molecular dynamics (MD) enables the study of physical systems with excellent spatiotemporal resolution but suffers from severe time-scale limitations. To address this, enhanced sampling methods have been developed to improve exploration of configurational space. However, implementing these is challenging and requires domain expertise. In recent years, integration of machine learning (ML) techniques in different domains has shown promise, prompting their adoption in enhanced sampling as well. Although ML is often employed in various fields primarily due to its data-driven nature, its integration with enhanced sampling is more natural with many common underlying synergies. This review explores the merging of ML and enhanced MD by presenting different shared viewpoints. It offers a comprehensive overview of this rapidly evolving field, which can be difficult to stay updated on. We highlight successful strategies like dimensionality reduction, reinforcement learning, and flow-based methods. Finally, we discuss open problems at the exciting ML-enhanced MD interface., Comment: Submitted as invited article to Annual Review of Physical Chemistry vol 75; updated formatting issues

Published
2023

14. Evaluating the implementation of the Pediatric Acute Care Education (PACE) program in northwestern Tanzania: a mixed-methods study guided by normalization process theory

Author

Mwanga, Joseph R., Hokororo, Adolfine, Ndosi, Hanston, Masenge, Theopista, Kalabamu, Florence S., Tawfik, Daniel, Mediratta, Rishi P., Rozenfeld, Boris, Berg, Marc, Smith, Zachary H., Chami, Neema, Mkopi, Namala P., Mwanga, Castory, Diocles, Enock, Agweyu, Ambrose, and Meaney, Peter A.

Published
2024
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16. Glutathione synthesis in the mouse liver supports lipid abundance through NRF2 repression

Author

Asantewaa, Gloria, Tuttle, Emily T., Ward, Nathan P., Kang, Yun Pyo, Kim, Yumi, Kavanagh, Madeline E., Girnius, Nomeda, Chen, Ying, Rodriguez, Katherine, Hecht, Fabio, Zocchi, Marco, Smorodintsev-Schiller, Leonid, Scales, TashJaé Q., Taylor, Kira, Alimohammadi, Fatemeh, Duncan, Renae P., Sechrist, Zachary R., Agostini-Vulaj, Diana, Schafer, Xenia L., Chang, Hayley, Smith, Zachary R., O’Connor, Thomas N., Whelan, Sarah, Selfors, Laura M., Crowdis, Jett, Gray, G. Kenneth, Bronson, Roderick T., Brenner, Dirk, Rufini, Alessandro, Dirksen, Robert T., Hezel, Aram F., Huber, Aaron R., Munger, Joshua, Cravatt, Benjamin F., Vasiliou, Vasilis, Cole, Calvin L., DeNicola, Gina M., and Harris, Isaac S.

Published
2024
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17. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue

Author

Dhavale, Dhruva D., Barclay, Alexander M., Borcik, Collin G., Basore, Katherine, Berthold, Deborah A., Gordon, Isabelle R., Liu, Jialu, Milchberg, Moses H., O’Shea, Jennifer Y., Rau, Michael J., Smith, Zachary, Sen, Soumyo, Summers, Brock, Smith, John, Warmuth, Owen A., Perrin, Richard J., Perlmutter, Joel S., Chen, Qian, Fitzpatrick, James A. J., Schwieters, Charles D., Tajkhorshid, Emad, Rienstra, Chad M., and Kotzbauer, Paul T.

Published
2024
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31. Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients

Author

Chauhan, Pradeep S., Shiang, Alexander, Alahi, Irfan, Sundby, R. Taylor, Feng, Wenjia, Gungoren, Bilge, Nawaf, Cayce, Chen, Kevin, Babbra, Ramandeep K., Harris, Peter K., Qaium, Faridi, Hatscher, Casey, Antiporda, Anna, Brunt, Lindsey, Mayer, Lindsey R., Shern, Jack F., Baumann, Brian C., Kim, Eric H., Reimers, Melissa A., Smith, Zachary L., and Chaudhuri, Aadel A.

Published
2023
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36. SGOOP-d: Estimating kinetic distances and reaction coordinate dimensionality for rare event systems from biased/unbiased simulations

Author

Tsai, Sun-Ting, Smith, Zachary, and Tiwary, Pratyush

Subjects
Physics - Computational Physics, Condensed Matter - Statistical Mechanics
Abstract

Understanding kinetics including reaction pathways and associated transition rates is an important yet difficult problem in numerous chemical and biological systems especially in situations with multiple competing pathways. When these high-dimensional systems are projected on low-dimensional coordinates, which are often needed for enhanced sampling or for interpretation of simulations and experiments, one can end up losing the kinetic connectivity of the underlying high-dimensional landscape. Thus in the low-dimensional projection metastable states might appear closer or further than they actually are. To deal with this issue, in this work we develop a formalism that learns a multi-dimensional yet minimally complex reaction coordinate (RC) for generic high-dimensional systems. When projected along this RC, all possible kinetically relevant pathways can be demarcated and the true high-dimensional connectivity is maintained. One of the defining attributes of our method lies in that it can work on long unbiased simulations as well as biased simulations often needed for rare event systems. We demonstrate the utility of the method by studying a range of model systems including conformational transitions in a small peptide Ace-Ala$_3$-Nme, where we show how two-dimensional and three-dimensional reaction coordinate found by our previously published spectral gap optimization method "SGOOP" [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. 113, 2839 (2016)] can capture the kinetics for 23 and all 28 out of the 28 dominant state-to-state transitions respectively., Comment: 10 pages, 4 figures, 2 tables

Published
2021

43. Digestive Manifestations in Patients Hospitalized With Coronavirus Disease 2019.

Author

Elmunzer, B, Spitzer, Rebecca, Foster, Lydia, Merchant, Ambreen, Howard, Eric, Patel, Vaishali, West, Mary, Qayed, Emad, Nustas, Rosemary, Zakaria, Ali, Piper, Marc, Taylor, Jason, Jaza, Lujain, Forbes, Nauzer, Chau, Millie, Lara, Luis, Papachristou, Georgios, Volk, Michael, Hilson, Liam, Zhou, Selena, Kushnir, Vladimir, Lenyo, Alexandria, McLeod, Caroline, Amin, Sunil, Kuftinec, Gabriela, Yadav, Dhiraj, Fox, Charlie, Kolb, Jennifer, Pawa, Swati, Pawa, Rishi, Canakis, Andrew, Huang, Christopher, Jamil, Laith, Aneese, Andrew, Glamour, Benita, Smith, Zachary, Hanley, Katherine, Wood, Jordan, Patel, Harsh, Shah, Janak, Agarunov, Emil, Sethi, Amrita, Fogel, Evan, McNulty, Gail, Haseeb, Abdul, Trieu, Judy, Dixon, Rebekah, Yang, Jeong, Mendelsohn, Robin, Calo, Delia, Aroniadis, Olga, LaComb, Joseph, Scheiman, James, Sauer, Bryan, Dang, Duyen, Piraka, Cyrus, Shah, Eric, Pohl, Heiko, Tierney, William, Mitchell, Stephanie, Condon, Ashwinee, Lenhart, Adrienne, Dua, Kulwinder, Kanagala, Vikram, Kamal, Ayesha, Singh, Vikesh, Pinto-Sanchez, Maria, Hutchinson, Joy, Kwon, Richard, Korsnes, Sheryl, Singh, Harminder, Solati, Zahra, Willingham, Field, Yachimski, Patrick, Conwell, Darwin, Mosier, Evan, Azab, Mohamed, Patel, Anish, Buxbaum, James, Wani, Sachin, Chak, Amitabh, Hosmer, Amy, Keswani, Rajesh, DiMaio, Christopher, Bronze, Michael, Muthusamy, Raman, Canto, Marcia, Gjeorgjievski, V, Imam, Zaid, Odish, Fadi, Edhi, Ahmed, Orosey, Molly, Tiwari, Abhinav, Patwardhan, Soumil, Brown, Nicholas, Ordiah, Collins, Sloan, Ian, Cruz, Lilian, and Koza, Casey

Subjects
COVID-19, Digestive Manifestations, Gastrointestinal Symptoms, Hepatic Manifestations, SARS-CoV-2, Adolescent, Adult, Aged, Aged, 80 and over, COVID-19, Female, Gastrointestinal Diseases, Humans, Male, Middle Aged, North America, Young Adult
Abstract

BACKGROUND & AIMS: The prevalence and significance of digestive manifestations in coronavirus disease 2019 (COVID-19) remain uncertain. We aimed to assess the prevalence, spectrum, severity, and significance of digestive manifestations in patients hospitalized with COVID-19. METHODS: Consecutive patients hospitalized with COVID-19 were identified across a geographically diverse alliance of medical centers in North America. Data pertaining to baseline characteristics, symptomatology, laboratory assessment, imaging, and endoscopic findings from the time of symptom onset until discharge or death were abstracted manually from electronic health records to characterize the prevalence, spectrum, and severity of digestive manifestations. Regression analyses were performed to evaluate the association between digestive manifestations and severe outcomes related to COVID-19. RESULTS: A total of 1992 patients across 36 centers met eligibility criteria and were included. Overall, 53% of patients experienced at least 1 gastrointestinal symptom at any time during their illness, most commonly diarrhea (34%), nausea (27%), vomiting (16%), and abdominal pain (11%). In 74% of cases, gastrointestinal symptoms were judged to be mild. In total, 35% of patients developed an abnormal alanine aminotransferase or total bilirubin level; these were increased to less than 5 times the upper limit of normal in 77% of cases. After adjusting for potential confounders, the presence of gastrointestinal symptoms at any time (odds ratio, 0.93; 95% CI, 0.76-1.15) or liver test abnormalities on admission (odds ratio, 1.31; 95% CI, 0.80-2.12) were not associated independently with mechanical ventilation or death. CONCLUSIONS: Among patients hospitalized with COVID-19, gastrointestinal symptoms and liver test abnormalities were common, but the majority were mild and their presence was not associated with a more severe clinical course.

Published
2021

44. Thurston theory and polymorphic maps

Author

Smith, Zachary Bruce

Subjects
Mathematics, curve attractor, polymorphic map, pullback map, Thurston maps
Abstract

Let A⊆S^2 be a finite set of points on the 2-sphere. A Thurston map f: (S^2,A) to (S^2,A) induces an associated holomorphic pullback map σ_f: T_A to T_A, where T_A is the Teichmüller space of the marked sphere (S^2,A). By [KPS16] this pullback map is known to satisfy a family of functional identities of the form σ_f ○ g = g̃ ○ σ_f where g, g̃ in Aut(T_A). In the case of four marked points we have T_A=H, and such maps are known as polymorphic maps. In this dissertation we develop a general framework for studying the cusp dynamics of polymorphic maps of the upper half-plane H. Applying this framework to the Thurston pullback map, we obtain a new proof of Thurston’s characterization theorem in the special case of four marked points. We also obtain new progress on the finite curve attractor conjecture of [Pil22]. Specifically, we prove that if a Thurston map f: (S^2,A) to (S^2,A) is totally unobstructed in the sense that all of its Thurston multipliers are strictly less than one, then (f,A) has a finite curve attractor.

Published
2024

46. Grade Inflation: Undergraduate Students' Perspective

Author

Baglione, Stephen L. and Smith, Zachary

Abstract

Purpose: The purpose of this paper is to determine whether students perceive grade inflation as a problem. It questions whether differences exist in perceptions based upon gender and grade point average (GPA). Design/methodology/approach: Previously validated scales were used to assess perceptions. The sample included 108 full-time traditional-aged undergraduate students from a private university. Findings: Students do not believe A grades are given more than deserved; however, they believe some receive higher grades than deserved. Grades are seen as an accurate reflection of achievement. Neither gender nor GPA differences were found on grade inflation perceptions, although women believe faculty give higher grades to receive better student evaluations. Originality/value: This paper combines student perceptions about grade inflation and analysis by gender and GPA.

Published
2022
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47. Reaction coordinates and rate constants for liquid droplet nucleation: quantifying the interplay between driving force and memory

Author

Tsai, Sun-Ting, Smith, Zachary, and Tiwary, Pratyush

Subjects
Physics - Computational Physics
Abstract

In this work we revisit the classic problem of homogeneous nucleation of a liquid droplet in a supersaturated vapor phase. We consider this at different extents of the driving force, which here is the extent of supersaturation, and calculate a reaction coordinate (RC) for nucleation as the driving force is varied. The RC is constructed as a linear combination of three order parameters, where one accounts for the number of liquid-like atoms, and the other two for local density fluctuations. The RC is calculated from all-atom biased and unbiased molecular dynamics (MD) simulations using the spectral gap optimization approach "SGOOP" [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)]. Our key finding is that as the supersaturation decreases, the RC ceases to simply be the number of liquid-like atoms, and instead it becomes important to explicitly consider local density fluctuations that correlate with shape and density variations in the nucleus. All three order parameters are found to have similar barriers in their respective potentials of mean force, however, as the supersaturation decreases the density fluctuations decorrelate slower and thus carry longer memory. Thus at lower supersaturations density fluctuations are non-Markovian and can not be simply ignored from the RC by virtue of being noise. Finally, we use this optimized RC to calculate nucleation rates in the infrequent metadynamics framework, and show it leads to more accurate estimate of the nucleation rate with four orders of magnitude acceleration relative to unbiased MD., Comment: 10 pages, 5 figures

Published
2019
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49. Acute Transverse Myelitis Secondary to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): A Case Report

Author

Durrani, Muhammad, Kucharski, Kevin, Smith, Zachary, and Fien, Stephanie

Subjects
Acute Transverse Myelitis, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Para-infectious Acute Transverse Myelitis, Post-infectious Acute Transverse Myelitis
Abstract

Introduction: Respiratory viral illnesses are associated with diverse neurological complications, including acute transverse myelitis (ATM). Among the respiratory viral pathogens, the Coronaviridae family and its genera coronaviruses have been implicated as having neurotropic and neuroinvasive capabilities in human hosts. Despite previous strains of coronaviruses exhibiting neurotropic and neuroinvasive capabilities, little is known about the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its involvement with the central nervous system (CNS). The current pandemic has highlighted the diverse clinical presentation of SARS-CoV-2 including a possible link to CNS manifestation with disease processes such as Guillain-Barré syndrome and cerebrovascular disease. It is critical to shed light on the varied neurological manifestation of SARS-CoV-2 to ensure clinicians do not overlook at-risk patient populations and are able to provide targeted therapies appropriately.Case Report: While there are currently no published reports on post-infectious ATM secondary to SARS-CoV-2, there is one report of parainfectious ATM attributed to SARS-CoV-2 in pre-print. Here, we present a case of infectious ATM attributed to SARS-CoV-2 in a 24-year-old male who presented with bilateral lower-extremity weakness and overflow urinary incontinence after confirmed SARS-CoV-2 infection. Magnetic resonance imaging revealed non-enhancing T2-weighted hyperintense signal abnormalities spanning from the seventh through the twelfth thoracic level consistent with acute myelitis.Conclusion: The patient underwent further workup and treatment with intravenous corticosteroids with improvement of symptoms and a discharge diagnosis of ATM secondary to SARS-CoV-2.

Published
2020

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