2,028 results on '"Maulik P."'
Search Results
52. Author Correction: Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.)
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Satasiya, Pratik, Patel, Sanyam, Patel, Ritesh, Raigar, Om Prakash, Modha, Kaushal, Parekh, Vipul, Joshi, Haimil, Patel, Vipul, Chaudhary, Ankit, Sharma, Deepak, and Prajapati, Maulik
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- 2024
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53. Meta-analysis of identified genomic regions and candidate genes underlying salinity tolerance in rice (Oryza sativa L.)
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Satasiya, Pratik, Patel, Sanyam, Patel, Ritesh, Raigar, Om Prakash, Modha, Kaushal, Parekh, Vipul, Joshi, Haimil, Patel, Vipul, Chaudhary, Ankit, Sharma, Deepak, and Prajapati, Maulik
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- 2024
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54. Using formative research to inform a mental health intervention for adolescents living in Indian slums: the ARTEMIS study
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Mukherjee, Ankita, Yatirajula, Sandhya Kanaka, Kallakuri, Sudha, Paslawar, Srilatha, Lempp, Heidi, Raman, Usha, Essue, Beverley M., Sagar, Rajesh, Singh, Renu, Peiris, David, Norton, Robyn, Thornicroft, Graham, and Maulik, Pallab K.
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- 2024
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55. Integrating field- and remote sensing data to perceive species heterogeneity across a climate gradient
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Chaurasia, Amrita N., Parmar, Reshma M., Dave, Maulik G., and Krishnayya, N. S. R.
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- 2024
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56. Logarithmic enumerative geometry for curves and sheaves
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Maulik, Davesh and Ranganathan, Dhruv
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Mathematics - Algebraic Geometry - Abstract
We propose a logarithmic enhancement of the Gromov-Witten/Donaldson-Thomas correspondence, with descendants, and study its behavior under simple normal crossings degenerations. The formulation of the logarithmic correspondence requires a matching of tangency conditions with relative insertions. This is achieved via a version of the Nakajima basis for the cohomology of the Hilbert schemes of points on a logarithmic surface. Next, we establish a strong form of the degeneration formula in logarithmic DT theory - the numerical DT invariants of the general fiber of a degeneration are determined by the numerical DT invariants attached to strata of the special fiber. The GW version of this result, which we prove in all target dimensions, strengthens currently known formulas. A key role is played by a certain exotic class of insertions, introduced here, that impose non-local incidence conditions coupled across multiple boundary strata of the target geometry. Finally, we prove compatibility of the new logarithmic GW/DT correspondence with degenerations. In particular, the logarithmic conjecture for all strata of the special fiber of a degeneration implies the traditional GW/DT conjecture on the general fiber. Compatibility is a strong constraint, and can be used to calculate logarithmic DT invariants. Several examples are included to illustrate the nature and utility of the formula., Comment: 90 pages. v2: Minor changes. Final version, to appear in Cambridge Journal of Mathematics
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- 2023
57. Interpretable A-posteriori Error Indication for Graph Neural Network Surrogate Models
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Barwey, Shivam, Kim, Hojin, and Maulik, Romit
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Computer Science - Machine Learning ,Physics - Computational Physics ,Physics - Fluid Dynamics - Abstract
Data-driven surrogate modeling has surged in capability in recent years with the emergence of graph neural networks (GNNs), which can operate directly on mesh-based representations of data. The goal of this work is to introduce an interpretability enhancement procedure for GNNs, with application to unstructured mesh-based fluid dynamics modeling. Given a black-box baseline GNN model, the end result is an interpretable GNN model that isolates regions in physical space, corresponding to sub-graphs, that are intrinsically linked to the forecasting task while retaining the predictive capability of the baseline. These structures identified by the interpretable GNNs are adaptively produced in the forward pass and serve as explainable links between the baseline model architecture, the optimization goal, and known problem-specific physics. Additionally, through a regularization procedure, the interpretable GNNs can also be used to identify, during inference, graph nodes that correspond to a majority of the anticipated forecasting error, adding a novel interpretable error-tagging capability to baseline models. Demonstrations are performed using unstructured flow field data sourced from flow over a backward-facing step at high Reynolds numbers, with geometry extrapolations demonstrated for ramp and wall-mounted cube configurations.
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- 2023
58. Influencing factors on false positive rates when classifying tumor cell line response to drug treatment
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Vasanthakumari, Priyanka, Brettin, Thomas, Zhu, Yitan, Yoo, Hyunseung, Shukla, Maulik, Partin, Alexander, Xia, Fangfang, Narykov, Oleksandr, and Stevens, Rick L.
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Quantitative Biology - Quantitative Methods - Abstract
Informed selection of drug candidates for laboratory experimentation provides an efficient means of identifying suitable anti-cancer treatments. The advancement of artificial intelligence has led to the development of computational models to predict cancer cell line response to drug treatment. It is important to analyze the false positive rate (FPR) of the models, to increase the number of effective treatments identified and to minimize unnecessary laboratory experimentation. Such analysis will also aid in identifying drugs or cancer types that require more data collection to improve model predictions. This work uses an attention based neural network classification model to identify responsive/non-responsive drug treatments across multiple types of cancer cell lines. Two data filtering techniques have been applied to generate 10 data subsets, including removing samples for which dose response curves are poorly fitted and removing samples whose area under the dose response curve (AUC) values are marginal around 0.5 from the training set. One hundred trials of 10-fold cross-validation analysis is performed to test the model prediction performance on all the data subsets and the subset with the best model prediction performance is selected for further analysis. Several error analysis metrics such as the false positive rate (FPR), and the prediction uncertainty are evaluated, and the results are summarized by cancer type and drug mechanism of action (MoA) category. The FPR of cancer type spans between 0.262 and 0.5189, while that of drug MoA category spans almost the full range of [0, 1]. This study identifies cancer types and drug MoAs with high FPRs. Additional drug screening data of these cancer and drug categories may improve response modeling. Our results also demonstrate that the two data filtering approaches help improve the drug response prediction performance.
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- 2023
59. Unlocking massively parallel spectral proper orthogonal decompositions in the PySPOD package
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Rogowski, Marcin, Yeung, Brandon C. Y., Schmidt, Oliver T., Maulik, Romit, Dalcin, Lisandro, Parsani, Matteo, and Mengaldo, Gianmarco
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Physics - Computational Physics ,Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Mathematical Software - Abstract
We propose a parallel (distributed) version of the spectral proper orthogonal decomposition (SPOD) technique. The parallel SPOD algorithm distributes the spatial dimension of the dataset preserving time. This approach is adopted to preserve the non-distributed fast Fourier transform of the data in time, thereby avoiding the associated bottlenecks. The parallel SPOD algorithm is implemented in the PySPOD (https://github.com/MathEXLab/PySPOD) library and makes use of the standard message passing interface (MPI) library, implemented in Python via mpi4py (https://mpi4py.readthedocs.io/en/stable/). An extensive performance evaluation of the parallel package is provided, including strong and weak scalability analyses. The open-source library allows the analysis of large datasets of interest across the scientific community. Here, we present applications in fluid dynamics and geophysics, that are extremely difficult (if not impossible) to achieve without a parallel algorithm. This work opens the path toward modal analyses of big quasi-stationary data, helping to uncover new unexplored spatio-temporal patterns.
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- 2023
60. Robust experimental data assimilation for the Spalart-Allmaras turbulence model
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Aulakh, Deepinder Jot Singh, Yang, Xiang, and Maulik, Romit
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Physics - Fluid Dynamics ,Computer Science - Machine Learning ,Physics - Computational Physics ,Physics - Data Analysis, Statistics and Probability - Abstract
This study presents a methodology focusing on the use of computational model and experimental data fusion to improve the Spalart-Allmaras (SA) closure model for Reynolds-averaged Navier-Stokes solutions. In particular, our goal is to develop a technique that not only assimilates sparse experimental data to improve turbulence model performance, but also preserves generalization for unseen cases by recovering classical SA behavior. We achieve our goals using data assimilation, namely the Ensemble Kalman filtering approach (EnKF), to calibrate the coefficients of the SA model for separated flows. A holistic calibration strategy is implemented via the parameterization of the production, diffusion, and destruction terms. This calibration relies on the assimilation of experimental data collected in the form of velocity profiles, skin friction, and pressure coefficients. Despite using observational data from a single flow condition around a backward-facing step (BFS), the recalibrated SA model demonstrates generalization to other separated flows, including cases such as the 2D NASA wall mounted hump (2D-WMH) and modified BFS. Significant improvement is observed in the quantities of interest, i.e., skin friction coefficient ($C_f$) and pressure coefficient ($C_p$) for each flow tested. Finally, it is also demonstrated that the newly proposed model recovers SA proficiency for flows, such as a NACA-0012 airfoil and axisymmetric jet (ASJ), and that the individually calibrated terms in the SA model target specific flow-physics wherein the calibrated production term improves the re-circulation zone while destruction improves the recovery zone.
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- 2023
61. Detection of High‐Risk Paraneoplastic Antibodies against TRIM9 and TRIM67 Proteins
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Bartley, Christopher M, Ngo, Thomas T, Duy, Le, Zekeridou, Anastasia, Dandekar, Ravi, Muñiz‐Castrillo, Sergio, Alvarenga, Bonny D, Zorn, Kelsey C, Tubati, Asritha, Pinto, Anne‐Laurie, Browne, Weston D, Hullett, Patrick W, Terrelonge, Mark, Schubert, Ryan D, Piquet, Amanda L, Yang, Binxia, Montalvo, Mayra, Kung, Andrew F, Mann, Sabrina A, Shah, Maulik P, Geschwind, Michael D, Gelfand, Jeffrey M, DeRisi, Joseph L, Pittock, Sean J, Honnorat, Jérôme, Pleasure, Samuel J, and Wilson, Michael R
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Biomedical and Clinical Sciences ,Clinical Sciences ,Oncology and Carcinogenesis ,Biotechnology ,Rare Diseases ,Clinical Research ,Cancer ,4.1 Discovery and preclinical testing of markers and technologies ,Humans ,Retrospective Studies ,Nerve Tissue Proteins ,Paraneoplastic Cerebellar Degeneration ,Biomarkers ,Autoantibodies ,Immunoglobulin G ,Neurosciences ,Neurology & Neurosurgery ,Clinical sciences - Abstract
ObjectiveCo-occurring anti-tripartite motif-containing protein 9 and 67 autoantibodies (TRIM9/67-IgG) have been reported in only a very few cases of paraneoplastic cerebellar syndrome. The value of these biomarkers and the most sensitive methods of TRIM9/67-IgG detection are not known.MethodsWe performed a retrospective, multicenter study to evaluate the cerebrospinal fluid and serum of candidate TRIM9/67-IgG cases by tissue-based immunofluorescence, peptide phage display immunoprecipitation sequencing, overexpression cell-based assay (CBA), and immunoblot. Cases in which TRIM9/67-IgG was detected by at least 2 assays were considered TRIM9/67-IgG positive.ResultsAmong these cases (n = 13), CBA was the most sensitive (100%) and revealed that all cases had TRIM9 and TRIM67 autoantibodies. Of TRIM9/67-IgG cases with available clinical history, a subacute cerebellar syndrome was the most common presentation (n = 7/10), followed by encephalitis (n = 3/10). Of these 10 patients, 70% had comorbid cancer (7/10), 85% of whom (n = 6/7) had confirmed metastatic disease. All evaluable cancer biopsies expressed TRIM9 protein (n = 5/5), whose expression was elevated in the cancerous regions of the tissue in 4 of 5 cases.InterpretationTRIM9/67-IgG is a rare but likely high-risk paraneoplastic biomarker for which CBA appears to be the most sensitive diagnostic assay. ANN NEUROL 2023;94:1086-1101.
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- 2023
62. QSHO: Quantum spotted hyena optimizer for global optimization: QSHO: Quantum Spotted Hyena Optimizer for Global...
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Si, Tapas, Miranda, Péricles B. C., Nandi, Utpal, Jana, Nanda Dulal, Maulik, Ujjwal, Mallik, Saurav, and Shah, Mohd Asif
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- 2025
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63. Design and development of IoT enabled modular melting, pouring, and, stirring system for casting of non-ferrous alloys and sustainable aluminum matrix composites (AMCs)
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Ayar, Vivek S., Khandelwal, Himanshu, Parida, Sambit Kumar, Shah, Maulik J., Vyas, Akash V., Barot, Ravi P., and Sutaria, Mayurkumar P.
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- 2024
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64. Extracellular Proteomic Profiling from the Erythrocytes Infected with Plasmodium Falciparum 3D7 Holds Promise for the Detection of Biomarkers
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Joshi, Urja, Pandya, Maulik, Gupta, Sharad, George, Linz-Buoy, and Highland, Hyacinth
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- 2024
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65. Production of a Bacteriocin Like Protein PEG 446 from Clostridium tyrobutyricum NRRL B-67062
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Liu, Siqing, Lu, Shao-Yeh, Patel, Maulik, Qureshi, Nasib, Dunlap, Christopher, Hoecker, Eric, and Skory, Christopher D.
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- 2024
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66. Perverse filtrations and Fourier transforms
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Maulik, Davesh, Shen, Junliang, and Yin, Qizheng
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Mathematics - Algebraic Geometry ,Mathematics - Representation Theory - Abstract
We study the interaction between Fourier-Mukai transforms and perverse filtrations for a certain class of dualizable abelian fibrations. Multiplicativity of the perverse filtration and the "Perverse $\supset$ Chern" phenomenon for these abelian fibrations are immediate consequences of our theory. We also show that our class of fibrations include families of compactified Jacobians of integral locally planar curves. Applications include the following: (a) we prove the motivic decomposition conjecture for this class (including compactified Jacobian fibrations), which generalizes Deninger-Murre's theorem for abelian schemes; (b) we provide a new proof of the P=W conjecture for $\mathrm{GL}_r$; (c) we prove half of the P=C conjecture concerning refined BPS invariants for the local $\mathbb{P}^2$; (d) we show that the perverse filtration for the compactified Jacobian associated with an integral locally planar curve is multiplicative, which generalizes a result of Oblomkov-Yun for homogeneous singularities. Our techniques combine Arinkin's autoduality for coherent categories, Ng\^o's support theorem for the decomposition theorem, Adams operations in operational K-theory, and Corti-Hanamura's theory of relative Chow motives., Comment: 55 pages; comments are welcome
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- 2023
67. Strategic Decision-Making in Multi-Agent Domains: A Weighted Potential Dynamic Game Approach
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Bhatt, Maulik and Mehr, Negar
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Computer Science - Robotics - Abstract
In interactive multi-agent settings, decision-making complexity arises from agents' interconnected objectives. Dynamic game theory offers a formal framework for analyzing such intricacies. Yet, solving dynamic games and determining Nash equilibria pose computational challenges due to the need of solving coupled optimal control problems. To address this, our key idea is to leverage potential games, which are games with a potential function that allows for the computation of Nash equilibria by optimizing the potential function. We argue that dynamic potential games, can effectively facilitate interactive decision-making in many multi-agent interactions. We will identify structures in realistic multi-agent interactive scenarios that can be transformed into weighted potential dynamic games. We will show that the open-loop Nash equilibria of the resulting weighted potential dynamic game can be obtained by solving a single optimal control problem. We will demonstrate the effectiveness of the proposed method through various simulation studies, showing close proximity to feedback Nash equilibria and significant improvements in solve time compared to state-of-the-art game solvers.
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- 2023
68. Generalizable data-driven turbulence closure modeling on unstructured grids with differentiable physics
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Kim, Hojin, Shankar, Varun, Viswanathan, Venkatasubramanian, and Maulik, Romit
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Physics - Fluid Dynamics ,Computer Science - Machine Learning - Abstract
Differentiable physical simulators are proving to be valuable tools for developing data-driven models in computational fluid dynamics (CFD). These simulators enable end-to-end training of machine learning (ML) models embedded within CFD solvers. This paradigm enables novel algorithms which combine the generalization power and low cost of physics-based simulations with the flexibility and automation of deep learning methods. In this study, we introduce a framework for embedding deep learning models within a generic finite element solver to solve the Navier-Stokes equations, specifically applying this approach to learn a subgrid scale closure with a graph neural network (GNN). We validate our method for flow over a backwards-facing step and test its performance on novel geometries, demonstrating the ability to generalize to novel geometries without sacrificing stability. Additionally, we show that our GNN-based closure model may be learned in a data-limited scenario by interpreting closure modeling as a solver-constrained optimization. Our end-to-end learning paradigm demonstrates a viable pathway for physically consistent and generalizable data-driven closure modeling across complex geometries.
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- 2023
69. Privacy-Utility Trade-offs in Neural Networks for Medical Population Graphs: Insights from Differential Privacy and Graph Structure
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Mueller, Tamara T., Chevli, Maulik, Daigavane, Ameya, Rueckert, Daniel, and Kaissis, Georgios
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Computer Science - Machine Learning ,Computer Science - Cryptography and Security - Abstract
We initiate an empirical investigation into differentially private graph neural networks on population graphs from the medical domain by examining privacy-utility trade-offs at different privacy levels on both real-world and synthetic datasets and performing auditing through membership inference attacks. Our findings highlight the potential and the challenges of this specific DP application area. Moreover, we find evidence that the underlying graph structure constitutes a potential factor for larger performance gaps by showing a correlation between the degree of graph homophily and the accuracy of the trained model.
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- 2023
70. One-Loop Quantum Effects in Carroll Scalars
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Banerjee, Kinjal, Basu, Rudranil, Krishnan, Bhagya, Maulik, Sabyasachi, Mehra, Aditya, and Ray, Augniva
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High Energy Physics - Theory - Abstract
Carrollian field theories at the classical level possess an infinite number of space-time symmetries, namely the supertranslations. In this article, we inquire whether these symmetries for interacting Carrollian scalar field theory survive in the presence of quantum effects. For interactions polynomial in the field, the answer is in the affirmative. We also study a renormalization group flow particularly tailored to respect the manifest Carroll invariance and analyze the consequences of introducing Carroll-breaking deformations. The renormalization group flow, with perturbative loop-level effects taken into account, indicates a new fixed point apart from the Gaussian ones., Comment: 20 pages, 6 figures. Version accepted for publication in Phys. Rev. D
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- 2023
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71. Differentiable Turbulence: Closure as a partial differential equation constrained optimization
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Shankar, Varun, Chakraborty, Dibyajyoti, Viswanathan, Venkatasubramanian, and Maulik, Romit
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Physics - Fluid Dynamics ,Computer Science - Machine Learning - Abstract
Deep learning is increasingly becoming a promising pathway to improving the accuracy of sub-grid scale (SGS) turbulence closure models for large eddy simulations (LES). We leverage the concept of differentiable turbulence, whereby an end-to-end differentiable solver is used in combination with physics-inspired choices of deep learning architectures to learn highly effective and versatile SGS models for two-dimensional turbulent flow. We perform an in-depth analysis of the inductive biases in the chosen architectures, finding that the inclusion of small-scale non-local features is most critical to effective SGS modeling, while large-scale features can improve pointwise accuracy of the \textit{a-posteriori} solution field. The velocity gradient tensor on the LES grid can be mapped directly to the SGS stress via decomposition of the inputs and outputs into isotropic, deviatoric, and anti-symmetric components. We see that the model can generalize to a variety of flow configurations, including higher and lower Reynolds numbers and different forcing conditions. We show that the differentiable physics paradigm is more successful than offline, \textit{a-priori} learning, and that hybrid solver-in-the-loop approaches to deep learning offer an ideal balance between computational efficiency, accuracy, and generalization. Our experiments provide physics-based recommendations for deep-learning based SGS modeling for generalizable closure modeling of turbulence.
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- 2023
72. Reduced-order Modeling on a Near-term Quantum Computer
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Asztalos, Katherine, Steijl, René, and Maulik, Romit
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Physics - Computational Physics ,Mathematics - Dynamical Systems ,Physics - Fluid Dynamics - Abstract
Quantum computing is an advancing area of research in which computer hardware and algorithms are developed to take advantage of quantum mechanical phenomena. In recent studies, quantum algorithms have shown promise in solving linear systems of equations as well as systems of linear ordinary differential equations (ODEs) and partial differential equations (PDEs). Reduced-order modeling (ROM) algorithms for studying fluid dynamics have shown success in identifying linear operators that can describe flowfields, where dynamic mode decomposition (DMD) is a particularly useful method in which a linear operator is identified from data. In this work, DMD is reformulated as an optimization problem to propagate the state of the linearized dynamical system on a quantum computer. Quadratic unconstrained binary optimization (QUBO), a technique for optimizing quadratic polynomials in binary variables, allows for quantum annealing algorithms to be applied. A quantum circuit model (quantum approximation optimization algorithm, QAOA) is utilized to obtain predictions of the state trajectories. Results are shown for the quantum-ROM predictions for flow over a 2D cylinder at Re = 220 and flow over a NACA0009 airfoil at Re = 500 and $\alpha = 15^\circ{}$. The quantum-ROM predictions are found to depend on the number of bits utilized for a fixed point representation and the truncation level of the DMD model. Comparisons with DMD predictions from a classical computer algorithm are made, as well as an analysis of the computational complexity and prospects for future, more fault-tolerant quantum computers.
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- 2023
73. Elevating Mentees Leads to Organizational Success
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Maulik Singh
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Youth mentoring organizations miss the opportunity to re-engage the people they serve to help others within their organization. As such, they may perpetuate the marginalization of the youth served. Through the Clark and Estes (2008) gap analytical framework, this study sought to understand the gaps in knowledge, motivation, and organizational influences affecting the re-engagement of alumni mentees. Further, using the lens of Bourdieu's (1986) social capital theory, this study first sought to investigate if the organization understood the personal gains of mentors in the relationship. Second, this study sought to understand if executive leaders understand the social capital gains for a mentee to advance to a mentor. This study employed semi-structured qualitative interviews, supplemented by a document analysis for triangulation of collected data. The validated gaps from this study were in motivation, organizational influences, and social capital understanding. The key findings from this study were in knowledge, motivation, and organizational influences, as well as in social capital. Most notably the participants indicated the social capital finding of mentors feeling like they receive more out of the match than the mentees. Certainly, if the organization encouraged alumni mentees to elevate to mentees, they too could receive this social capital gain. Further, encouraging alumni mentees could help the organization sustain itself with a cyclical mentor pool. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]
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- 2024
74. Clinical Reasoning: A Young Adult With New Seizures and Chapeau de Gendarme.
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Valdrighi, Alexandria, Douglas, Anne, Knowlton, Robert, Shah, Maulik, and Kleen, Jonathan
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Humans ,Young Adult ,Adult ,Electroencephalography ,Seizures ,Clinical Reasoning - Abstract
The evaluation of new seizures is a common clinical query for neurologists. It can be challenging to delineate between the numerous etiologies of new focal or generalized seizures and, if focal, to localize their onset. In this case report, we present a 26-year-old patient with a new onset of stereotyped events concerning for seizures featuring facial grimacing, dystonic left-hand posturing, and convulsions with immediate return to baseline. Throughout the case, we highlight a stepwise diagnostic approach to the evaluation of new-onset seizures, discuss clues that seizure semiology can provide for localization of ictal onset, and review a novel and atypical presentation of a disease entity frequently encountered by neurologists.
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- 2023
75. A Survey on Multi-Objective based Parameter Optimization for Deep Learning
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Chakraborty, Mrittika, Pal, Wreetbhas, Bandyopadhyay, Sanghamitra, and Maulik, Ujjwal
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Computer Science - Machine Learning ,Mathematics - Optimization and Control - Abstract
Deep learning models form one of the most powerful machine learning models for the extraction of important features. Most of the designs of deep neural models, i.e., the initialization of parameters, are still manually tuned. Hence, obtaining a model with high performance is exceedingly time-consuming and occasionally impossible. Optimizing the parameters of the deep networks, therefore, requires improved optimization algorithms with high convergence rates. The single objective-based optimization methods generally used are mostly time-consuming and do not guarantee optimum performance in all cases. Mathematical optimization problems containing multiple objective functions that must be optimized simultaneously fall under the category of multi-objective optimization sometimes referred to as Pareto optimization. Multi-objective optimization problems form one of the alternatives yet useful options for parameter optimization. However, this domain is a bit less explored. In this survey, we focus on exploring the effectiveness of multi-objective optimization strategies for parameter optimization in conjunction with deep neural networks. The case studies used in this study focus on how the two methods are combined to provide valuable insights into the generation of predictions and analysis in multiple applications., Comment: The paper has been accepted for publication in Computer Science journal: http://journals.agh.edu.pl/csci
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- 2023
76. Online data-driven changepoint detection for high-dimensional dynamical systems
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Lin, Sen, Mengaldo, Gianmarco, and Maulik, Romit
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Mathematics - Dynamical Systems ,Physics - Computational Physics ,Physics - Fluid Dynamics - Abstract
The detection of anomalies or transitions in complex dynamical systems is of critical importance to various applications. In this study, we propose the use of machine learning to detect changepoints for high-dimensional dynamical systems. Here, changepoints indicate instances in time when the underlying dynamical system has a fundamentally different characteristic - which may be due to a change in the model parameters or due to intermittent phenomena arising from the same model. We propose two complementary approaches to achieve this, with the first devised using arguments from probabilistic unsupervised learning and the latter devised using supervised deep learning. Our emphasis is also on detection for high-dimensional dynamical systems, for which we introduce the use of dimensionality reduction techniques to accelerate the deployment of transition detection algorithms. Our experiments demonstrate that transitions can be detected efficiently, in real-time, for the two-dimensional forced Kolmogorov flow, which is characterized by anomalous regimes in phase space where dynamics are perturbed off the attractor at uneven intervals.
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- 2023
77. Importance of equivariant and invariant symmetries for fluid flow modeling
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Shankar, Varun, Barwey, Shivam, Kolter, Zico, Maulik, Romit, and Viswanathan, Venkatasubramanian
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Physics - Fluid Dynamics ,Computer Science - Machine Learning - Abstract
Graph neural networks (GNNs) have shown promise in learning unstructured mesh-based simulations of physical systems, including fluid dynamics. In tandem, geometric deep learning principles have informed the development of equivariant architectures respecting underlying physical symmetries. However, the effect of rotational equivariance in modeling fluids remains unclear. We build a multi-scale equivariant GNN to forecast fluid flow and study the effect of modeling invariant and non-invariant representations of the flow state. We evaluate the model performance of several equivariant and non-equivariant architectures on predicting the evolution of two fluid flows, flow around a cylinder and buoyancy-driven shear flow, to understand the effect of equivariance and invariance on data-driven modeling approaches. Our results show that modeling invariant quantities produces more accurate long-term predictions and that these invariant quantities may be learned from the velocity field using a data-driven encoder.
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- 2023
78. RAPID: Autonomous Multi-Agent Racing using Constrained Potential Dynamic Games
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Jia, Yixuan, Bhatt, Maulik, and Mehr, Negar
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Electrical Engineering and Systems Science - Systems and Control - Abstract
In this work, we consider the problem of autonomous racing with multiple agents where agents must interact closely and influence each other to compete. We model interactions among agents through a game-theoretical framework and propose an efficient algorithm for tractably solving the resulting game in real time. More specifically, we capture interactions among multiple agents through a constrained dynamic game. We show that the resulting dynamic game is an instance of a simple-to-analyze class of games. Namely, we show that our racing game is an instance of a constrained dynamic potential game. An important and appealing property of dynamic potential games is that a generalized Nash equilibrium of the underlying game can be computed by solving a single constrained optimal control problem instead of multiple coupled constrained optimal control problems. Leveraging this property, we show that the problem of autonomous racing is greatly simplified and develop RAPID (autonomous multi-agent RAcing using constrained PotentIal Dynamic games), a racing algorithm that can be solved tractably in real-time. Through simulation studies, we demonstrate that our algorithm outperforms the state-of-the-art approach. We further show the real-time capabilities of our algorithm in hardware experiments., Comment: 8 pages
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- 2023
79. Generative modeling of time-dependent densities via optimal transport and projection pursuit
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Botvinick-Greenhouse, Jonah, Yang, Yunan, and Maulik, Romit
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
Motivated by the computational difficulties incurred by popular deep learning algorithms for the generative modeling of temporal densities, we propose a cheap alternative which requires minimal hyperparameter tuning and scales favorably to high dimensional problems. In particular, we use a projection-based optimal transport solver [Meng et al., 2019] to join successive samples and subsequently use transport splines [Chewi et al., 2020] to interpolate the evolving density. When the sampling frequency is sufficiently high, the optimal maps are close to the identity and are thus computationally efficient to compute. Moreover, the training process is highly parallelizable as all optimal maps are independent and can thus be learned simultaneously. Finally, the approach is based solely on numerical linear algebra rather than minimizing a nonconvex objective function, allowing us to easily analyze and control the algorithm. We present several numerical experiments on both synthetic and real-world datasets to demonstrate the efficiency of our method. In particular, these experiments show that the proposed approach is highly competitive compared with state-of-the-art normalizing flows conditioned on time across a wide range of dimensionalities., Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Chaos: An Interdisciplinary Journal of Nonlinear Science, Volume 33, Issue 10, October 2023 and may be found at https://doi.org/10.1063/5.0155783
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- 2023
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80. Vanishing of Brauer classes on K3 surfaces under reduction
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Maulik, Davesh and Tayou, Salim
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Mathematics - Algebraic Geometry ,Mathematics - Number Theory ,14J28, 14F22, 14G35, 11G18 - Abstract
Given a Brauer class on a K3 surface defined over a number field, we prove that there exists infinitely many reductions where the Brauer class vanishes, under certain technical hypotheses, answering a question of Frei--Hassett--V\'arilly-Alvarado., Comment: Fixed an erroneous Lemma and some other minor typos. Main result unchanged. Added a corollary about applications to elliptic fibrations on K3 surfaces. To appear in the Journal of the London Mathematical Society
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- 2023
81. Quantifying uncertainty for deep learning based forecasting and flow-reconstruction using neural architecture search ensembles
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Maulik, Romit, Egele, Romain, Raghavan, Krishnan, and Balaprakash, Prasanna
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Computer Science - Machine Learning ,Mathematics - Dynamical Systems - Abstract
Classical problems in computational physics such as data-driven forecasting and signal reconstruction from sparse sensors have recently seen an explosion in deep neural network (DNN) based algorithmic approaches. However, most DNN models do not provide uncertainty estimates, which are crucial for establishing the trustworthiness of these techniques in downstream decision making tasks and scenarios. In recent years, ensemble-based methods have achieved significant success for the uncertainty quantification in DNNs on a number of benchmark problems. However, their performance on real-world applications remains under-explored. In this work, we present an automated approach to DNN discovery and demonstrate how this may also be utilized for ensemble-based uncertainty quantification. Specifically, we propose the use of a scalable neural and hyperparameter architecture search for discovering an ensemble of DNN models for complex dynamical systems. We highlight how the proposed method not only discovers high-performing neural network ensembles for our tasks, but also quantifies uncertainty seamlessly. This is achieved by using genetic algorithms and Bayesian optimization for sampling the search space of neural network architectures and hyperparameters. Subsequently, a model selection approach is used to identify candidate models for an ensemble set construction. Afterwards, a variance decomposition approach is used to estimate the uncertainty of the predictions from the ensemble. We demonstrate the feasibility of this framework for two tasks - forecasting from historical data and flow reconstruction from sparse sensors for the sea-surface temperature. We demonstrate superior performance from the ensemble in contrast with individual high-performing models and other benchmarks.
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- 2023
82. Multiscale Graph Neural Network Autoencoders for Interpretable Scientific Machine Learning
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Barwey, Shivam, Shankar, Varun, Viswanathan, Venkatasubramanian, and Maulik, Romit
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Computer Science - Machine Learning ,Physics - Fluid Dynamics - Abstract
The goal of this work is to address two limitations in autoencoder-based models: latent space interpretability and compatibility with unstructured meshes. This is accomplished here with the development of a novel graph neural network (GNN) autoencoding architecture with demonstrations on complex fluid flow applications. To address the first goal of interpretability, the GNN autoencoder achieves reduction in the number nodes in the encoding stage through an adaptive graph reduction procedure. This reduction procedure essentially amounts to flowfield-conditioned node sampling and sensor identification, and produces interpretable latent graph representations tailored to the flowfield reconstruction task in the form of so-called masked fields. These masked fields allow the user to (a) visualize where in physical space a given latent graph is active, and (b) interpret the time-evolution of the latent graph connectivity in accordance with the time-evolution of unsteady flow features (e.g. recirculation zones, shear layers) in the domain. To address the goal of unstructured mesh compatibility, the autoencoding architecture utilizes a series of multi-scale message passing (MMP) layers, each of which models information exchange among node neighborhoods at various lengthscales. The MMP layer, which augments standard single-scale message passing with learnable coarsening operations, allows the decoder to more efficiently reconstruct the flowfield from the identified regions in the masked fields. Analysis of latent graphs produced by the autoencoder for various model settings are conducted using using unstructured snapshot data sourced from large-eddy simulations in a backward-facing step (BFS) flow configuration with an OpenFOAM-based flow solver at high Reynolds numbers., Comment: 30 pages, 17 figures. Correction: Fixed authorship
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- 2023
83. Fourier-Mukai transforms and the decomposition theorem for integrable systems
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Maulik, Davesh, Shen, Junliang, and Yin, Qizheng
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Mathematics - Algebraic Geometry ,Mathematics - Representation Theory ,Mathematics - Symplectic Geometry - Abstract
We study the interplay between the Fourier-Mukai transform and the decomposition theorem for an integrable system $\pi: M \rightarrow B$. Our main conjecture is that the Fourier-Mukai transform of sheaves of K\"ahler differentials, after restriction to the formal neighborhood of the zero section, are quantized by the Hodge modules arising in the decomposition theorem for $\pi$. For an integrable system, our formulation unifies the Fourier-Mukai calculation of the structure sheaf by Arinkin-Fedorov, the theorem of the higher direct images by Matsushita, and the "perverse = Hodge" identity by the second and the third authors. As evidence, we show that these Fourier-Mukai images are Cohen-Macaulay sheaves with middle-dimensional support on the relative Picard space, with support governed by the higher discriminants of the integrable system. We also prove the conjecture for smooth integrable systems and certain 2-dimensional families with nodal singular fibers. Finally, we sketch the proof when cuspidal fibers appear., Comment: 46 pages. Comments are welcome!
- Published
- 2023
84. Physics-Informed Neural Networks for Mesh Deformation with Exact Boundary Enforcement
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Aygun, Atakan, Maulik, Romit, and Karakus, Ali
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Physics - Fluid Dynamics - Abstract
In this work, we have applied physics-informed neural networks (PINN) for solving mesh deformation problems. We used the collocation PINN method to capture the new positions of the vertex nodes while preserving the connectivity information. We use linear elasticity equations for mesh deformation. To prevent vertex collisions or edge overlap, the mesh movement in this work is conducted in steps with relatively small movements. For moving boundary problems, the exact position of the boundary is essential for having an accurate solution. However, PINNs are frequently unable to satisfy Dirichlet boundary conditions exactly. To overcome this issue, we have used hard boundary condition enforcement to automatically satisfy Dirichlet boundary conditions. Specifically, we first trained a PINN with soft boundary conditions to obtain a particular solution. Then, this solution was tuned with exact boundary positions and a proper distance function by using a new PINN considering only the equation residual. To assess the accuracy of our approach, we used the classical translation and rotation tests and compared them with a proper mesh quality metric considering the change in the element area and shape. The results show the accuracy of this approach is comparable with that of finite element solutions. We also solved different moving boundary problems, resembling commonly used fluid-structure interaction problems. This work provides insight into using PINN for mesh-deformation problems without needing a discretization scheme with reasonable accuracy.
- Published
- 2023
85. Quantum Gravity Fluctuations in the Timelike Raychaudhuri Equation
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Bak, Sang-Eon, Parikh, Maulik, Sarkar, Sudipta, and Setti, Francesco
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General Relativity and Quantum Cosmology ,High Energy Physics - Theory - Abstract
We consider a timelike geodesic congruence in the presence of perturbative quantum fluctuations of the spacetime metric. We calculate the change in the volume of a bundle of geodesics due to such fluctuations and thereby obtain a quantum-gravitationally modified timelike Raychaudhuri equation. Quantum gravity generically increases the convergence of congruences and the production of caustics., Comment: 12 pages, 2 figures; v2. published version
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- 2022
- Full Text
- View/download PDF
86. Structural transformation and environmental externalities
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Garg, Teevrat, Jagnani, Maulik, and Pullabhotla, Hemant K.
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Economics - General Economics - Abstract
Even as policymakers seek to encourage economic development by addressing misallocation due to frictions in labor markets, the associated production externalities - such as air pollution - remain unexplored. Using a regression discontinuity design, we show access to rural roads increases agricultural fires and particulate emissions. Farm labor exits are a likely mechanism responsible for the increase in agricultural fires: rural roads cause movement of workers out of agriculture and induce farmers to use fire - a labor-saving but polluting technology - to clear agricultural residue or to make harvesting less labor-intensive. Overall, the adoption of fires due to rural roads increases infant mortality rate by 5.5% in downwind locations.
- Published
- 2022
87. Modeling Wind Turbine Performance and Wake Interactions with Machine Learning
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Moss, C., Maulik, R., and Iungo, G. V.
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Physics - Fluid Dynamics ,Computer Science - Machine Learning - Abstract
Different machine learning (ML) models are trained on SCADA and meteorological data collected at an onshore wind farm and then assessed in terms of fidelity and accuracy for predictions of wind speed, turbulence intensity, and power capture at the turbine and wind farm levels for different wind and atmospheric conditions. ML methods for data quality control and pre-processing are applied to the data set under investigation and found to outperform standard statistical methods. A hybrid model, comprised of a linear interpolation model, Gaussian process, deep neural network (DNN), and support vector machine, paired with a DNN filter, is found to achieve high accuracy for modeling wind turbine power capture. Modifications of the incoming freestream wind speed and turbulence intensity, $TI$, due to the evolution of the wind field over the wind farm and effects associated with operating turbines are also captured using DNN models. Thus, turbine-level modeling is achieved using models for predicting power capture while farm-level modeling is achieved by combining models predicting wind speed and $TI$ at each turbine location from freestream conditions with models predicting power capture. Combining these models provides results consistent with expected power capture performance and holds promise for future endeavors in wind farm modeling and diagnostics. Though training ML models is computationally expensive, using the trained models to simulate the entire wind farm takes only a few seconds on a typical modern laptop computer, and the total computational cost is still lower than other available mid-fidelity simulation approaches.
- Published
- 2022
88. Efficacy, Safety and Immunogenicity of Sun’s Ranibizumab Biosimilar in Neovascular Age-Related Macular Degeneration: A Phase 3, Double-Blind Comparative Study
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Ghosh, Asim K., Nikumbh, Usha S., Shukla, Chaitanya K., Laul, Rohit S., Dixit, Abhishek, Mahapatra, Santosh K., Nayak, Sameera, Shah, Urmil M., Parwal, Sandeep, Venkatapathy, Narendran, Radhakrishnan, Natasha, Kelgaonkar, Anup, Saxena, Sandeep, Mishra, Divyansh, Dave, Vivek Pravin, Khan, Perwez, Saswade, Manojkumar R., Shantilal, Malli S., Ramasamy, Kim, Sreekanta, Smitha, Rajurkar, Mandodari, Doshi, Maulik, Behera, Sapan, Patel, Piyush, Dhawan, Shilpi, and Lakhwani, Lalit
- Published
- 2024
- Full Text
- View/download PDF
89. Feedback Interacting Urn Models
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Maulik, Krishanu and Paul, Manit
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Mathematics - Probability - Abstract
We introduce and discuss a special type of feedback interacting urn model with deterministic interaction. This is a generalisation of the very well known Eggenberger and Polya (1923) urn model. In our model, balls are added to a particular urn depending on the replacement matrix of that urn and the color of ball chosen from some other urn. This urn model can help in studying how various interacting models might behave in real life in the long run. We have also introduced a special type of interacting urn model with non-deterministic interaction and studied its behaviour. Furthermore, we have provided some nice examples to illustrate the various consequences of these interacting urn models.
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- 2022
90. Differentiable physics-enabled closure modeling for Burgers' turbulence
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Shankar, Varun, Puri, Vedant, Balakrishnan, Ramesh, Maulik, Romit, and Viswanathan, Venkatasubramanian
- Subjects
Physics - Fluid Dynamics ,Computer Science - Machine Learning - Abstract
Data-driven turbulence modeling is experiencing a surge in interest following algorithmic and hardware developments in the data sciences. We discuss an approach using the differentiable physics paradigm that combines known physics with machine learning to develop closure models for Burgers' turbulence. We consider the 1D Burgers system as a prototypical test problem for modeling the unresolved terms in advection-dominated turbulence problems. We train a series of models that incorporate varying degrees of physical assumptions on an a posteriori loss function to test the efficacy of models across a range of system parameters, including viscosity, time, and grid resolution. We find that constraining models with inductive biases in the form of partial differential equations that contain known physics or existing closure approaches produces highly data-efficient, accurate, and generalizable models, outperforming state-of-the-art baselines. Addition of structure in the form of physics information also brings a level of interpretability to the models, potentially offering a stepping stone to the future of closure modeling.
- Published
- 2022
91. More on entanglement properties of $Lif_4^{(2)}\times {S}^1\times S^5$ spacetime with string excitations
- Author
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Maulik, Sabyasachi
- Subjects
High Energy Physics - Theory - Abstract
The $Lif_{4}^{(2)} \times S^1 \times S^5$ spacetime is an exact solution of $F1-D2-D8$ configuration in type IIA supergravity and can accommodate charged excitations of the fundamental string. By gauge/gravity duality, it is related to an excited state of a non-relativistic QFT with anisotropic Lifshitz scaling symmetry. We study mutual and tripartite information and entanglement wedge cross-section in bulk gravity for boundary subsystems that are disjoint strips of very narrow width. Our work helps understand the nature of entanglement in the QFT excited state, which is in general a mixed one., Comment: Comments and references added. Published version
- Published
- 2022
- Full Text
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92. The $P=W$ conjecture for $\mathrm{GL}_n$
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Maulik, Davesh and Shen, Junliang
- Subjects
Mathematics - Algebraic Geometry ,Mathematics - Representation Theory - Abstract
We prove the $P=W$ conjecture for $\mathrm{GL}_n$ for all ranks $n$ and curves of arbitrary genus $g\geq 2$. The proof combines a strong perversity result on tautological classes with the curious Hard Lefschetz theorem of Mellit. For the perversity statement, we apply the vanishing cycles constructions in our earlier work to global Springer theory in the sense of Yun, and prove a parabolic support theorem., Comment: 25 pages. Final version; to appear at Annals of Math
- Published
- 2022
93. Quantum-gravitational null Raychaudhuri equation
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Bak, Sang-Eon, Parikh, Maulik, Sarkar, Sudipta, and Setti, Francesco
- Published
- 2024
- Full Text
- View/download PDF
94. Pseudo complexity of purification for free scalar field theories
- Author
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Bhattacharya, Aranya, Bhattacharyya, Arpan, and Maulik, Sabyasachi
- Subjects
High Energy Physics - Theory - Abstract
We compute the pseudo complexity of purification corresponding to the reduced transition matrices for free scalar field theories with an arbitrary dynamical exponent. We plot the behaviour of complexity with various parameters of the theory under study and compare it with the complexity of purification of the reduced density matrices of the two states $|\psi_1\rangle$ and $|\psi_2\rangle$ that constitute the transition matrix. We first find the transition matrix by reducing to a small number ($1$ and $2$) of degrees of freedom in lattice from a lattice system with many lattice points and then purify it by doubling the degrees of freedom ($2$ and $4$ respectively) for this reduced system. This is a primary step towards the natural extension to the idea of the complexity of purification for reduced density matrices relevant for the studies related to post-selection., Comment: 18 pages, 7 figures; version accepted for publication in Phys. Rev. D
- Published
- 2022
- Full Text
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95. Efficient Constrained Multi-Agent Trajectory Optimization using Dynamic Potential Games
- Author
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Bhatt, Maulik, Jia, Yixuan, and Mehr, Negar
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Computer Science - Robotics - Abstract
Although dynamic games provide a rich paradigm for modeling agents' interactions, solving these games for real-world applications is often challenging. Many real-world interactive settings involve general nonlinear state and input constraints that couple agents' decisions with one another. In this work, we develop an efficient and fast planner for interactive trajectory optimization in constrained setups using a constrained game-theoretical framework. Our key insight is to leverage the special structure of agents' objective and constraint functions that are common in multi-agent interactions for fast and reliable planning. More precisely, we identify the structure of agents' cost and constraint functions under which the resulting dynamic game is an instance of a constrained dynamic potential game. Constrained dynamic potential games are a class of games for which instead of solving a set of coupled constrained optimal control problems, a constrained Nash equilibrium, i.e. a Generalized Nash equilibrium, can be found by solving a single constrained optimal control problem. This simplifies constrained interactive trajectory optimization significantly. We compare the performance of our method in a navigation setup involving four planar agents and show that our method is on average 20 times faster than the state-of-the-art. We further provide experimental validation of our proposed method in a navigation setup involving two quadrotors carrying a rigid object while avoiding collisions with two humans.
- Published
- 2022
96. Discrete-time Rigid Body Pose Estimation based on Lagrange-d'Alembert principle
- Author
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Bhatt, Maulik, Sukumar, Srikant, and Sanyal, Amit K
- Subjects
Mathematics - Optimization and Control - Abstract
The problem of rigid body pose estimation is treated in discrete-time via discrete Lagrange-d'Alembert principle and discrete Lyapunov methods. The position and attitude of the rigid body are to be estimated simultaneously with the help of vision and inertial sensors. For the discrete-time estimation of pose, the continuous-time rigid body kinematics equations are discretized appropriately. We approach the pose estimation problem as minimising the energies stored in the errors of estimated quantities. With the help of measurements obtained through optical sensors, artificial rotational and translation potential energy-like terms have been designed. Similarly, artificial rotational and translation kinetic energy-like terms have been devised using inertial sensor measurements. This allows us to construct a discrete-time Lagrangian as the difference of the kinetic and potential energy like terms, to which a Lagrange-d'Alembert principle is applied to obtain an optimal pose estimation filter. The dissipation terms in the optimal filter are designed through discrete-Lyapunov analysis on a suitably constructed Morse-Lyapunov function and the overall scheme is proven to be almost globally asymptotically stable. The filtering scheme is simulated using noisy sensor data to verify the theoretical properties.
- Published
- 2022
- Full Text
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97. Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.
- Author
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Olson, Robert D, Assaf, Rida, Brettin, Thomas, Conrad, Neal, Cucinell, Clark, Davis, James J, Dempsey, Donald M, Dickerman, Allan, Dietrich, Emily M, Kenyon, Ronald W, Kuscuoglu, Mehmet, Lefkowitz, Elliot J, Lu, Jian, Machi, Dustin, Macken, Catherine, Mao, Chunhong, Niewiadomska, Anna, Nguyen, Marcus, Olsen, Gary J, Overbeek, Jamie C, Parrello, Bruce, Parrello, Victoria, Porter, Jacob S, Pusch, Gordon D, Shukla, Maulik, Singh, Indresh, Stewart, Lucy, Tan, Gene, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Wallace, Zachary S, Warren, Andrew S, Wattam, Alice R, Xia, Fangfang, Yoo, Hyunseung, Zhang, Yun, Zmasek, Christian M, Scheuermann, Richard H, and Stevens, Rick L
- Subjects
Influenza ,Pneumonia & Influenza ,Prevention ,Infectious Diseases ,Infection ,Good Health and Well Being ,Humans ,Bacteria ,Computational Biology ,Databases ,Genetic ,Genomics ,Influenza ,Human ,Viruses ,Software ,Environmental Sciences ,Biological Sciences ,Information and Computing Sciences ,Developmental Biology - Abstract
The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.
- Published
- 2023
98. Successful Treatment of Balamuthia mandrillaris Granulomatous Amebic Encephalitis with Nitroxoline - Volume 29, Number 1—January 2023 - Emerging Infectious Diseases journal - CDC
- Author
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Spottiswoode, Natasha, Pet, Douglas, Kim, Annie, Gruenberg, Katherine, Shah, Maulik, Ramachandran, Amrutha, Laurie, Matthew T, Zia, Maham, Fouassier, Camille, Boutros, Christine L, Lu, Rufei, Zhang, Yueyuan, Servellita, Venice, Bollen, Andrew, Chiu, Charles Y, Wilson, Michael R, Valdivia, Liza, and DeRisi, Joseph L
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Clinical Sciences ,Urologic Diseases ,Orphan Drug ,Emerging Infectious Diseases ,Infectious Diseases ,Rare Diseases ,Biodefense ,5.1 Pharmaceuticals ,Infection ,Good Health and Well Being ,Humans ,Balamuthia mandrillaris ,Amebiasis ,Infectious Encephalitis ,Granuloma ,Brain ,Infectious encephalitis ,ameba ,ameba drug effects ,granulomatous amebic encephalitis ,meningitis/encephalitis ,nitroxoline ,parasites ,Public Health and Health Services ,Microbiology ,Clinical sciences ,Epidemiology ,Health services and systems - Abstract
A patient in California, USA, with rare and usually fatal Balamuthia mandrillaris granulomatous amebic encephalitis survived after receiving treatment with a regimen that included the repurposed drug nitroxoline. Nitroxoline, which is a quinolone typically used to treat urinary tract infections, was identified in a screen for drugs with amebicidal activity against Balamuthia.
- Published
- 2023
99. Amyloid-β related angiitis presenting as eosinophilic meningitis: a case report
- Author
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Tanner, Jeremy A, Richie, Megan B, Cadwell, Cathryn R, Eliaz, Amity, Kim, Shannen, Haq, Zeeshan, Rasool, Nailyn, Shah, Maulik P, and Guterman, Elan L
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Brain Disorders ,Clinical Research ,Neurosciences ,Rare Diseases ,Good Health and Well Being ,Aged ,Amyloid beta-Peptides ,Biopsy ,Humans ,Magnetic Resonance Imaging ,Male ,Meningitis ,Vasculitis ,Amyloid-beta related angiitis ,Eosinophilic meningitis ,Cerebral amyloid angiopathy-related inflammation ,Primary angiitis of the central nervous system ,Amyloid-β related angiitis ,Cognitive Sciences ,Neurology & Neurosurgery ,Clinical sciences - Abstract
BackgroundEosinophilic meningitis is uncommon and often attributed to infectious causes.Case presentationWe describe a case of a 72-year-old man who presented with subacute onset eosinophilic meningitis, vasculitis, and intracranial hypertension with progressive and severe neurologic symptoms. Brain MRI demonstrated multifocal strokes and co-localized right temporo-parieto-occipital vasogenic edema, cortical superficial siderosis, and diffuse leptomeningeal enhancement. He ultimately underwent brain biopsy with immunohistochemical stains for amyloid-β and Congo red that were extensively positive in the blood vessel walls and in numerous diffuse and neuritic parenchymal confirming a diagnosis of amyloid-β related angiitis. He was treated with immunosuppression with clinical stabilization.ConclusionsAmyloid-β related angiitis is an underrecognized cause of eosinophilic meningitis that can present fulminantly and is typically responsive to immunosuppression. The presence of eosinophils may provide additional clues to the underlying pathophysiology of amyloid-β related angiitis.
- Published
- 2022
100. Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images
- Author
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Partin, Alexander, Brettin, Thomas, Zhu, Yitan, Dolezal, James M., Kochanny, Sara, Pearson, Alexander T., Shukla, Maulik, Evrard, Yvonne A., Doroshow, James H., and Stevens, Rick L.
- Subjects
Quantitative Biology - Quantitative Methods - Abstract
Patient-derived xenografts (PDXs) are an appealing platform for preclinical drug studies because the in vivo environment of PDXs helps preserve tumor heterogeneity and usually better mimics drug response of patients with cancer compared to CCLs. We investigate multimodal neural network (MM-Net) and data augmentation for drug response prediction in PDXs. The MM-Net learns to predict response using drug descriptors, gene expressions (GE), and histology whole-slide images (WSIs) where the multi-modality refers to the tumor features. We explore whether the integration of WSIs with GE improves predictions as compared with models that use GE alone. We use two methods to address the limited number of response values: 1) homogenize drug representations which allows to combine single-drug and drug-pairs treatments into a single dataset, 2) augment drug-pair samples by switching the order of drug features which doubles the sample size of all drug-pair samples. These methods enable us to combine single-drug and drug-pair treatments, allowing us to train multimodal and unimodal neural networks (NNs) without changing architectures or the dataset. Prediction performance of three unimodal NNs which use GE are compared to assess the contribution of data augmentation methods. NN that uses the full dataset which includes the original and the augmented drug-pair treatments as well as single-drug treatments significantly outperforms NNs that ignore either the augmented drug-pairs or the single-drug treatments. In assessing the contribution of multimodal learning based on the MCC metric, MM-Net statistically significantly outperforms all the baselines. Our results show that data augmentation and integration of histology images with GE can improve prediction performance of drug response in PDXs.
- Published
- 2022
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