Emily Fox

All Publications

• Smart Start - Designing Powerful Clinical Trials Using Pilot Study Data. NEJM evidence Ferstad, J. O., Prahalad, P., Maahs, D. M., Zaharieva, D. P., Fox, E., Desai, M., Johari, R., Scheinker, D. 2024; 3 (2): EVIDoa2300164

  Abstract

  Using Pilot Study Data to Design Clinical TrialsDigital health interventions are often studied in a pilot trial before full evaluation in a randomized controlled trial. The authors introduce Smart Start, a framework for using pilot study data to optimize the intervention and design the subsequent randomized controlled trial to maximize the chance of success.

  View details for DOI 10.1056/EVIDoa2300164

  View details for PubMedID 38320487

• The evolving role of data & safety monitoring boards for real-world clinical trials. Journal of clinical and translational science Bunning, B. J., Hedlin, H., Chen, J. H., Ciolino, J. D., Ferstad, J. O., Fox, E., Garcia, A., Go, A., Johari, R., Lee, J., Maahs, D. M., Mahaffey, K. W., Opsahl-Ong, K., Perez, M., Rochford, K., Scheinker, D., Spratt, H., Turakhia, M. P., Desai, M. 2023; 7 (1): e179

  Abstract

  Clinical trials provide the "gold standard" evidence for advancing the practice of medicine, even as they evolve to integrate real-world data sources. Modern clinical trials are increasingly incorporating real-world data sources - data not intended for research and often collected in free-living contexts. We refer to trials that incorporate real-world data sources as real-world trials. Such trials may have the potential to enhance the generalizability of findings, facilitate pragmatic study designs, and evaluate real-world effectiveness. However, key differences in the design, conduct, and implementation of real-world vs traditional trials have ramifications in data management that can threaten their desired rigor.Three examples of real-world trials that leverage different types of data sources - wearables, medical devices, and electronic health records are described. Key insights applicable to all three trials in their relationship to Data and Safety Monitoring Boards (DSMBs) are derived.Insight and recommendations are given on four topic areas: A. Charge of the DSMB; B. Composition of the DSMB; C. Pre-launch Activities; and D. Post-launch Activities. We recommend stronger and additional focus on data integrity.Clinical trials can benefit from incorporating real-world data sources, potentially increasing the generalizability of findings and overall trial scale and efficiency. The data, however, present a level of informatic complexity that relies heavily on a robust data science infrastructure. The nature of monitoring the data and safety must evolve to adapt to new trial scenarios to protect the rigor of clinical trials.

  View details for DOI 10.1017/cts.2023.582

  View details for PubMedID 37745930

  View details for PubMedCentralID PMC10514684

• A pharmacokinetic model of anti-seizure medication load to guide care in the Epilepsy Monitoring Unit. Epilepsia Ghosn, N. J., Xie, K., Pattnaik, A. R., Gugger, J. J., Ellis, C. A., Sweeney, E., Fox, E., Bernabei, J. M., Johnson, J., Boccanfuso, J., Litt, B., Conrad, E. C. 2023

  Abstract

  OBJECTIVE: Evaluating patients with drug-resistant epilepsy often requires inducing seizures by tapering anti-seizure medications (ASMs) in the Epilepsy Monitoring Unit (EMU). The relationship between ASM taper strategy, seizure timing and severity remains unclear. In this study, we developed and validated a pharmacokinetic model of total ASM load and tested its association with seizure occurrence and severity in the EMU.METHODS: We studied 80 patients who underwent intracranial EEG recording for epilepsy surgery planning. We developed a first-order pharmacokinetic model of the ASMs administered in the EMU to generate a continuous metric of overall ASM load. We then related modeled ASM load to seizure likelihood and severity. We determined the association between the rate of ASM load reduction, the length of hospital stay and the probability of having a severe seizure. Finally, we used modeled ASM load to predict oncoming seizures.RESULTS: Seizures occurred in the bottom 50th -percentile of sampled ASM loads across the cohort (p <0.0001, Wilcoxon sign-rank test), and seizures requiring rescue therapy occurred at lower ASM loads than seizures that did not require rescue therapy (logistic regression mixed effects model, odds ratio=0.27, p =0.01). Greater ASM decrease early in the EMU was not associated with an increased likelihood of having a severe seizure, nor with a shorter length of stay.SIGNIFICANCE: A pharmacokinetic model can accurately estimate ASM levels for patients in the EMU. Lower modeled ASM levels are associated with increased seizure likelihood and seizure severity. We show that ASM load, rather than ASM taper speed, is associated with severe seizures. ASM modeling has the potential to help optimize taper strategy to minimize severe seizures while maximizing diagnostic yield.

  View details for DOI 10.1111/epi.17558

  View details for PubMedID 36815252

• A Platform for the Personalized Management of Diabetes and Cardiovascular Disease at Population Scale With Data From Multiple Sensors Senanayake, R., Ferstad, J. O., Thapa, I., Giammarino, F., Vasu, M., Zaharieva, D., Prahalad, P., Maahs, D. M., Rosenthal, D. N., Rodriguez, F., Bambos, N., Miller, D., Shin, A., Roth, S. J., Guestrin, C., Fox, E. B., Scheinker, D. LIPPINCOTT WILLIAMS & WILKINS. 2022

  View details for Web of Science ID 000890856905274

• Statistical Deconvolution for Inference of Infection Time Series EPIDEMIOLOGY Miller, A. C., Hannah, L. A., Futoma, J., Foti, N. J., Fox, E. B., D'Amour, A., Sandler, M., Saurous, R. A., Lewnard, J. A. 2022; 33 (4): 470-479

  Abstract

  Accurate measurement of daily infection incidence is crucial to epidemic response. However, delays in symptom onset, testing, and reporting obscure the dynamics of transmission, necessitating methods to remove the effects of stochastic delays from observed data. Existing estimators can be sensitive to model misspecification and censored observations; many analysts have instead used methods that exhibit strong bias. We develop an estimator with a regularization scheme to cope with stochastic delays, which we term the robust incidence deconvolution estimator. We compare the method to existing estimators in a simulation study, measuring accuracy in a variety of experimental conditions. We then use the method to study COVID-19 records in the United States, highlighting its stability in the face of misspecification and right censoring. To implement the robust incidence deconvolution estimator, we release incidental, a ready-to-use R implementation of our estimator that can aid ongoing efforts to monitor the COVID-19 pandemic.

  View details for DOI 10.1097/EDE.0000000000001495

  View details for Web of Science ID 000803310600009

  View details for PubMedID 35545230

  View details for PubMedCentralID PMC9148632

• The Association between Patient Characteristics and the Efficacy of Remote Patient Monitoring and Messaging Ferstad, J., Prahalad, P., Maahs, D. M., Fox, E., Johari, R., Scheinker, D. AMER DIABETES ASSOC. 2022

  View details for DOI 10.2337/db22-1009-P

  View details for Web of Science ID 000854899301502

• Granger Causality: A Review and Recent Advances. Annual review of statistics and its application Shojaie, A., Fox, E. B. 2022; 9 (1): 289-319

  Abstract

  Introduced more than a half-century ago, Granger causality has become a popular tool for analyzing time series data in many application domains, from economics and finance to genomics and neuroscience. Despite this popularity, the validity of this framework for inferring causal relationships among time series has remained the topic of continuous debate. Moreover, while the original definition was general, limitations in computational tools have constrained the applications of Granger causality to primarily simple bivariate vector autoregressive processes. Starting with a review of early developments and debates, this article discusses recent advances that address various shortcomings of the earlier approaches, from models for high-dimensional time series to more recent developments that account for nonlinear and non-Gaussian observations and allow for subsampled and mixed-frequency time series.

  View details for DOI 10.1146/annurev-statistics-040120-010930

  View details for PubMedID 37840549

  View details for PubMedCentralID PMC10571505

• Granger Causality: A Review and Recent Advances ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION Shojaie, A., Fox, E. B. 2022; 9: 289-319

  View details for DOI 10.1146/annurev-statistics-040120-010930

  View details for Web of Science ID 000797038500013

• Adding glycemic and physical activity metrics to a multimodal algorithm-enabled decision-support tool for type 1 diabetes care: Keys to implementation and opportunities. Frontiers in endocrinology Zaharieva, D. P., Senanayake, R., Brown, C., Watkins, B., Loving, G., Prahalad, P., Ferstad, J. O., Guestrin, C., Fox, E. B., Maahs, D. M., Scheinker, D. 2022; 13: 1096325

  Abstract

  Algorithm-enabled patient prioritization and remote patient monitoring (RPM) have been used to improve clinical workflows at Stanford and have been associated with improved glucose time-in-range in newly diagnosed youth with type 1 diabetes (T1D). This novel algorithm-enabled care model currently integrates continuous glucose monitoring (CGM) data to prioritize patients for weekly reviews by the clinical diabetes team. The use of additional data may help clinical teams make more informed decisions around T1D management. Regular exercise and physical activity are essential to increasing cardiovascular fitness, increasing insulin sensitivity, and improving overall well-being of youth and adults with T1D. However, exercise can lead to fluctuations in glycemia during and after the activity. Future iterations of the care model will integrate physical activity metrics (e.g., heart rate and step count) and physical activity flags to help identify patients whose needs are not fully captured by CGM data. Our aim is to help healthcare professionals improve patient care with a better integration of CGM and physical activity data. We hypothesize that incorporating exercise data into the current CGM-based care model will produce specific, clinically relevant information such as identifying whether patients are meeting exercise guidelines. This work provides an overview of the essential steps of integrating exercise data into an RPM program and the most promising opportunities for the use of these data.

  View details for DOI 10.3389/fendo.2022.1096325

  View details for PubMedID 36714600

• Neural Granger Causality IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE Tank, A., Covert, I., Foti, N., Shojaie, A., Fox, E. B. 2021; 44 (8): 4267-4279

  Abstract

  While most classical approaches to Granger causality detection assume linear dynamics, many interactions in real-world applications, like neuroscience and genomics, are inherently nonlinear. In these cases, using linear models may lead to inconsistent estimation of Granger causal interactions. We propose a class of nonlinear methods by applying structured multilayer perceptrons (MLPs) or recurrent neural networks (RNNs) combined with sparsity-inducing penalties on the weights. By encouraging specific sets of weights to be zero-in particular, through the use of convex group-lasso penalties-we can extract the Granger causal structure. To further contrast with traditional approaches, our framework naturally enables us to efficiently capture long-range dependencies between series either via our RNNs or through an automatic lag selection in the MLP. We show that our neural Granger causality methods outperform state-of-the-art nonlinear Granger causality methods on the DREAM3 challenge data. This data consists of nonlinear gene expression and regulation time courses with only a limited number of time points. The successes we show in this challenging dataset provide a powerful example of how deep learning can be useful in cases that go beyond prediction on large datasets. We likewise illustrate our methods in detecting nonlinear interactions in a human motion capture dataset.

  View details for DOI 10.1109/TPAMI.2021.3065601

  View details for Web of Science ID 000820522700002

  View details for PubMedID 33705309

• Improving Reproducibility in Machine Learning Research (A Report from the NeurIPS 2019 Reproducibility Program) JOURNAL OF MACHINE LEARNING RESEARCH Pineau, J., Vincent-Lamarre, P., Sinha, K., Lariviere, V., Beygelzimer, A., d'Alche-Buc, F., Fox, E., Larochelle, H. 2021; 22

  View details for Web of Science ID 000687303300001

• The Convex Mixture Distribution: Granger Causality for Categorical Time Series. SIAM journal on mathematics of data science Tank, A., Li, X., Fox, E. B., Shojaie, A. 2021; 3 (1): 83-112

  Abstract

  We present a framework for learning Granger causality networks for multivariate categorical time series based on the mixture transition distribution (MTD) model. Traditionally, MTD is plagued by a nonconvex objective, non-identifiability, and presence of local optima. To circumvent these problems, we recast inference in the MTD as a convex problem. The new formulation facilitates the application of MTD to high-dimensional multivariate time series. As a baseline, we also formulate a multi-output logistic autoregressive model (mLTD), which while a straightforward extension of autoregressive Bernoulli generalized linear models, has not been previously applied to the analysis of multivariate categorial time series. We establish identifiability conditions of the MTD model and compare them to those for mLTD. We further devise novel and efficient optimization algorithms for MTD based on our proposed convex formulation, and compare the MTD and mLTD in both simulated and real data experiments. Finally, we establish consistency of the convex MTD in high dimensions. Our approach simultaneously provides a comparison of methods for network inference in categorical time series and opens the door to modern, regularized inference with the MTD model.

  View details for DOI 10.1137/20m133097x

  View details for PubMedID 37859797

  View details for PubMedCentralID PMC10586348

• The Convex Mixture Distribution: Granger Causality for Categorical Time Series SIAM JOURNAL ON MATHEMATICS OF DATA SCIENCE Tank, A., Li, X., Fox, E. B., Shojaie, A. 2021; 3 (1): 83-112

  View details for DOI 10.1137/20M133097X

  View details for Web of Science ID 000646591200004

• Adaptively Truncating Backpropagation Through Time to Control Gradient Bias Aicher, C., Foti, N. J., Fox, E. B., Adams, R. P., Gogate JMLR-JOURNAL MACHINE LEARNING RESEARCH. 2020: 799-808

  View details for Web of Science ID 000722423500073

• sgmcmc: An R Package for Stochastic Gradient Markov Chain Monte Carlo JOURNAL OF STATISTICAL SOFTWARE Baker, J., Fearnhead, P., Fox, E. B., Nemeth, C. 2019; 91 (3): 1-27

  View details for DOI 10.18637/jss.v091.i03

  View details for Web of Science ID 000494429900001

• Control variates for stochastic gradient MCMC STATISTICS AND COMPUTING Baker, J., Fearnhead, P., Fox, E. B., Nemeth, C. 2019; 29 (3): 599-615

  View details for DOI 10.1007/s11222-018-9826-2

  View details for Web of Science ID 000464741100012

• Statistical model-based approaches for functional connectivity analysis of neuroimaging data CURRENT OPINION IN NEUROBIOLOGY Foti, N. J., Fox, E. B. 2019; 55: 48-54

  Abstract

  We present recent literature on model-based approaches to estimating functional connectivity from neuroimaging data. In contrast to the typical focus on a particular scientific question, we reframe a wider literature in terms of the underlying statistical model used. We distinguish between directed versus undirected and static versus time-varying connectivity. There are numerous advantages to a model-based approach, including easily specified inductive bias, handling limited data scenarios, and building complex models from simpler building blocks.

  View details for DOI 10.1016/j.conb.2019.01.009

  View details for Web of Science ID 000472127600008

  View details for PubMedID 30739880

• DYNAMICS OF HOMELESSNESS IN URBAN AMERICA ANNALS OF APPLIED STATISTICS Glynn, C., Fox, E. B. 2019; 13 (1): 573-605

  View details for DOI 10.1214/18-AOAS1200

  View details for Web of Science ID 000464000700023

• Stochastic Gradient MCMC for State Space Models SIAM JOURNAL ON MATHEMATICS OF DATA SCIENCE Aicher, C., Ma, Y., Foti, N. J., Fox, E. B. 2019; 1 (3): 555-587

  View details for DOI 10.1137/18M1214780

  View details for Web of Science ID 000646580300008

• Irreversible samplers from jump and continuous Markov processes STATISTICS AND COMPUTING Ma, Y., Fox, E. B., Chen, T., Wu, L. 2019; 29 (1): 177-202

  View details for DOI 10.1007/s11222-018-9802-x

  View details for Web of Science ID 000457464800012

• A Simple Adaptive Tracker with Reminiscences Xie, C., Fox, E., Harchaoui, Z., IEEE, Howard, A., Althoefer, K., Arai, F., Arrichiello, F., Caputo, B., Castellanos, J., Hauser, K., Isler, Kim, J., Liu, H., Oh, P., Santos, Scaramuzza, D., Ude, A., Voyles, R., Yamane, K., Okamura, A. IEEE. 2019: 6596-6603

  View details for Web of Science ID 000494942304121

• oi-VAE: Output Interpretable VAEs for Nonlinear Group Factor Analysis Ainsworth, S. K., Foti, N. J., Lee, A. C., Fox, E. B., Dy, J., Krause, A. JMLR-JOURNAL MACHINE LEARNING RESEARCH. 2018

  View details for Web of Science ID 000683379200013

• Large-Scale Stochastic Sampling from the Probability Simplex Baker, J., Fearnhead, P., Fox, E. B., Nemeth, C., Bengio, S., Wallach, H., Larochelle, H., Grauman, K., CesaBianchi, N., Garnett, R. NEURAL INFORMATION PROCESSING SYSTEMS (NIPS). 2018

  View details for Web of Science ID 000461852001028

• Sparse graphs using exchangeable random measures JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY Caron, F., Fox, E. B. 2017; 79 (5): 1295-1366

  Abstract

  Statistical network modelling has focused on representing the graph as a discrete structure, namely the adjacency matrix. When assuming exchangeability of this array-which can aid in modelling, computations and theoretical analysis-the Aldous-Hoover theorem informs us that the graph is necessarily either dense or empty. We instead consider representing the graph as an exchangeable random measure and appeal to the Kallenberg representation theorem for this object. We explore using completely random measures (CRMs) to define the exchangeable random measure, and we show how our CRM construction enables us to achieve sparse graphs while maintaining the attractive properties of exchangeability. We relate the sparsity of the graph to the Lévy measure defining the CRM. For a specific choice of CRM, our graphs can be tuned from dense to sparse on the basis of a single parameter. We present a scalable Hamiltonian Monte Carlo algorithm for posterior inference, which we use to analyse network properties in a range of real data sets, including networks with hundreds of thousands of nodes and millions of edges.

  View details for DOI 10.1111/rssb.12233

  View details for Web of Science ID 000413946300001

  View details for PubMedID 29200934

  View details for PubMedCentralID PMC5699441

• CLUSTERING CORRELATED, SPARSE DATA STREAMS TO ESTIMATE A LOCALIZED HOUSING PRICE INDEX ANNALS OF APPLIED STATISTICS Ren, Y., Fox, E. B., Bruce, A. 2017; 11 (2): 808-839

  View details for DOI 10.1214/17-AOAS1019

  View details for Web of Science ID 000408732000014

• Stochastic Gradient MCMC Methods for Hidden Markov Models Ma, Y., Foti, N. J., Fox, E. B., Precup, D., Teh, Y. W. JMLR-JOURNAL MACHINE LEARNING RESEARCH. 2017

  View details for Web of Science ID 000683309502037

• Comment: Nonparametric Bayes Modeling of Populations of Networks JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION Foti, N. J., Fox, E. B. 2017; 112 (520): 1539-1543

  View details for DOI 10.1080/01621459.2017.1388245

  View details for Web of Science ID 000423299400016

• Temporal behavior of seizures and interictal bursts in prolonged intracranial recordings from epileptic canines EPILEPSIA Ung, H., Davis, K. A., Wulsin, D., Wagenaar, J., Fox, E., McDonnell, J. J., Patterson, N., Vite, C. H., Worrell, G., Litt, B. 2016; 57 (12): 1949-1957

  Abstract

  Epilepsy is a chronic disorder, but seizure recordings are usually obtained in the acute setting. The chronic behavior of seizures and the interictal bursts that sometimes initiate them is unknown. We investigate the variability of these electrographic patterns over an extended period of time using chronic intracranial recordings in canine epilepsy.Continuous, yearlong intracranial electroencephalography (iEEG) recordings from four dogs with naturally occurring epilepsy were analyzed for seizures and interictal bursts. Following automated detection and clinician verification of interictal bursts and seizures, temporal trends of seizures, burst count, and burst-burst similarities were determined. One dog developed status epilepticus, the recordings of which were also investigated.Multiple seizure types, determined by onset channels, were observed in each dog, with significant temporal variation between types. The first 14 days of invasive recording, analogous to the average duration of clinical invasive recordings in humans, did not capture the entirety of seizure types. Seizures typically occurred in clusters, and isolated seizures were rare. The count and dynamics of interictal bursts form distinct groups and do not stabilize until several weeks after implantation.There is significant temporal variability in seizures and interictal bursts after electrode implantation that requires several weeks to reach steady state. These findings, comparable to those reported in humans implanted with the NeuroPace Responsive Neurostimulator System (RNS) device, suggest that transient network changes following electrode implantation may need to be taken into account when interpreting or analyzing iEEG during evaluation for epilepsy surgery. Chronic, ambulatory iEEG may be better suited to accurately map epileptic networks in appropriate individuals.

  View details for DOI 10.1111/epi.13591

  View details for Web of Science ID 000390353100002

  View details for PubMedID 27807850

  View details for PubMedCentralID PMC5241889

• SPATIO-TEMPORAL LOW COUNT PROCESSES WITH APPLICATION TO VIOLENT CRIME EVENTS Aldor-Noiman, S., Brown, L. D., Fox, E. B., Stine, R. A. STATISTICA SINICA. 2016: 1587-1610

  View details for DOI 10.5705/ss.2014.217t

  View details for Web of Science ID 000387199200014

• A novel seizure detection algorithm informed by hidden Markov model event states JOURNAL OF NEURAL ENGINEERING Baldassano, S., Wulsin, D., Ung, H., Blevins, T., Brown, M., Fox, E., Litt, B. 2016; 13 (3): 036011

  Abstract

  Recently the FDA approved the first responsive, closed-loop intracranial device to treat epilepsy. Because these devices must respond within seconds of seizure onset and not miss events, they are tuned to have high sensitivity, leading to frequent false positive stimulations and decreased battery life. In this work, we propose a more robust seizure detection model.We use a Bayesian nonparametric Markov switching process to parse intracranial EEG (iEEG) data into distinct dynamic event states. Each event state is then modeled as a multidimensional Gaussian distribution to allow for predictive state assignment. By detecting event states highly specific for seizure onset zones, the method can identify precise regions of iEEG data associated with the transition to seizure activity, reducing false positive detections associated with interictal bursts. The seizure detection algorithm was translated to a real-time application and validated in a small pilot study using 391 days of continuous iEEG data from two dogs with naturally occurring, multifocal epilepsy. A feature-based seizure detector modeled after the NeuroPace RNS System was developed as a control.Our novel seizure detection method demonstrated an improvement in false negative rate (0/55 seizures missed versus 2/55 seizures missed) as well as a significantly reduced false positive rate (0.0012 h versus 0.058 h(-1)). All seizures were detected an average of 12.1 ± 6.9 s before the onset of unequivocal epileptic activity (unequivocal epileptic onset (UEO)).This algorithm represents a computationally inexpensive, individualized, real-time detection method suitable for implantable antiepileptic devices that may considerably reduce false positive rate relative to current industry standards.

  View details for DOI 10.1088/1741-2560/13/3/036011

  View details for Web of Science ID 000375701200015

  View details for PubMedID 27098152

  View details for PubMedCentralID PMC4888894

• Mining continuous intracranial EEG in focal canine epilepsy: Relating interictal bursts to seizure onsets EPILEPSIA Davis, K. A., Ung, H., Wulsin, D., Wagenaar, J., Fox, E., Patterson, N., Vite, C., Worrell, G., Litt, B. 2016; 57 (1): 89-98

  Abstract

  Brain regions are localized for resection during epilepsy surgery based on rare seizures observed during a short period of intracranial electroencephalography (iEEG) monitoring. Interictal epileptiform bursts, which are more prevalent than seizures, may provide complementary information to aid in epilepsy evaluation. In this study, we leverage a long-term iEEG dataset from canines with naturally occurring epilepsy to investigate interictal bursts and their electrographic relationship to seizures.Four dogs were included in this study, each monitored previously with continuous iEEG for periods of 475.7, 329.9, 45.8, and 451.8 days, respectively, for a total of >11,000 h. Seizures and bursts were detected and validated by two board-certified epileptologists. A published Bayesian model was applied to analyze the dynamics of interictal epileptic bursts on EEG and compare them to seizures.In three dogs, bursts were stereotyped and found to be statistically similar to periods before or near seizure onsets. Seizures from one dog during status epilepticus were markedly different from other seizures in terms of burst similarity.Shorter epileptic bursts explored in this work have the potential to yield significant information about the distribution of epileptic events. In our data, bursts are at least an order of magnitude more prevalent than seizures and occur much more regularly. Our finding that bursts often display pronounced similarity to seizure onsets suggests that they contain relevant information about the epileptic networks from which they arise and may aide in the clinical evaluation of epilepsy in patients.

  View details for DOI 10.1111/epi.13249

  View details for Web of Science ID 000368132100016

  View details for PubMedID 26608448

  View details for PubMedCentralID PMC4770560

• Bayesian Nonparametric Covariance Regression JOURNAL OF MACHINE LEARNING RESEARCH Fox, E. B., Dunson, D. B. 2015; 16: 2501-2542

  View details for Web of Science ID 000369888000006

• Guest Editors' Introduction to the Special Issue on Bayesian Nonparametrics IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE Adams, R. P., Fox, E. B., Sudderth, E. B., Teh, Y. 2015; 37 (2): 209-211

  View details for DOI 10.1109/TPAMI.2014.2380478

  View details for Web of Science ID 000349625500001

  View details for PubMedID 26598765

• A Complete Recipe for Stochastic Gradient MCMC Ma, Y., Chen, T., Fox, E. B., Cortes, C., Lawrence, N. D., Lee, D. D., Sugiyama, M., Garnett, R. NEURAL INFORMATION PROCESSING SYSTEMS (NIPS). 2015

  View details for Web of Science ID 000450913102040

• Streaming Variational Inference for Bayesian Nonparametric Mixture Models Tank, A., Foti, N. J., Fox, E. B., Lebanon, G., Vishwanathan, S. V. MICROTOME PUBLISHING. 2015: 968-976

  View details for Web of Science ID 000508399700106

• Bayesian Structure Learning for Stationary Time Series Tank, A., Foti, N. J., Fox, E. B., Meila, M., Heskes, T. AUAI PRESS. 2015: 872-881

  View details for Web of Science ID 000493121100089

• Modeling the complex dynamics and changing correlations of epileptic events ARTIFICIAL INTELLIGENCE Wulsin, D. F., Fox, E. B., Litt, B. 2014; 216: 55-75

  Abstract

  Patients with epilepsy can manifest short, sub-clinical epileptic "bursts" in addition to full-blown clinical seizures. We believe the relationship between these two classes of events-something not previously studied quantitatively-could yield important insights into the nature and intrinsic dynamics of seizures. A goal of our work is to parse these complex epileptic events into distinct dynamic regimes. A challenge posed by the intracranial EEG (iEEG) data we study is the fact that the number and placement of electrodes can vary between patients. We develop a Bayesian nonparametric Markov switching process that allows for (i) shared dynamic regimes between a variable number of channels, (ii) asynchronous regime-switching, and (iii) an unknown dictionary of dynamic regimes. We encode a sparse and changing set of dependencies between the channels using a Markov-switching Gaussian graphical model for the innovations process driving the channel dynamics and demonstrate the importance of this model in parsing and out-of-sample predictions of iEEG data. We show that our model produces intuitive state assignments that can help automate clinical analysis of seizures and enable the comparison of sub-clinical bursts and full clinical seizures.

  View details for DOI 10.1016/j.artint.2014.05.006

  View details for Web of Science ID 000342253000003

  View details for PubMedID 25284825

  View details for PubMedCentralID PMC4180222

• A BAYESIAN APPROACH FOR PREDICTING THE POPULARITY OF TWEETS ANNALS OF APPLIED STATISTICS Zaman, T., Fox, E. B., Bradlow, E. T. 2014; 8 (3): 1583-1611

  View details for DOI 10.1214/14-AOAS741

  View details for Web of Science ID 000347529300013

• JOINT MODELING OF MULTIPLE TIME SERIES VIA THE BETA PROCESS WITH APPLICATION TO MOTION CAPTURE SEGMENTATION ANNALS OF APPLIED STATISTICS Fox, E. B., Hughes, M. C., Sudderth, E. B., Jordan, M. I. 2014; 8 (3): 1281-1313

  View details for DOI 10.1214/14-AOAS742

  View details for Web of Science ID 000347529300001

• Expectation-Maximization for Learning Determinantal Point Processes Gillenwater, J., Kulesza, A., Fox, E., Taskar, B., Ghahramani, Z., Welling, M., Cortes, C., Lawrence, N. D., Weinberger, K. Q. NEURAL INFORMATION PROCESSING SYSTEMS (NIPS). 2014

  View details for Web of Science ID 000452647103015

• Stochastic Variational Inference for Hidden Markov Models Foti, N. J., Xu, J., Laird, D., Fox, E. B., Ghahramani, Z., Welling, M., Cortes, C., Lawrence, N. D., Weinberger, K. Q. NEURAL INFORMATION PROCESSING SYSTEMS (NIPS). 2014

  View details for Web of Science ID 000452647103011

• Learning the Parameters of Determinantal Point Process Kernels Affandi, R., Fox, E. B., Adams, R. P., Taskar, B., Xing, E. P., Jebara, T. JMLR-JOURNAL MACHINE LEARNING RESEARCH. 2014: 1224-1232

  View details for Web of Science ID 000724795400137

• Stochastic Gradient Hamiltonian Monte Carlo Chen, T., Fox, E. B., Guestrin, C., Xing, E. P., Jebara, T. JMLR-JOURNAL MACHINE LEARNING RESEARCH. 2014: 1683-1691

  View details for Web of Science ID 000724795400188

• Representing Documents Through Their Readers El-Arini, K., Xu, M., Fox, E. B., Guestrin, C., ACM ASSOC COMPUTING MACHINERY. 2013: 14-22

  View details for Web of Science ID 000502730600006

• A STICKY HDP-HMM WITH APPLICATION TO SPEAKER DIARIZATION ANNALS OF APPLIED STATISTICS Fox, E. B., Sudderth, E. B., Jordan, M. I., Willsky, A. S. 2011; 5 (2A): 1020-1056

  View details for DOI 10.1214/10-AOAS395

  View details for Web of Science ID 000295453300019

• Bayesian Nonparametric Inference of Switching Dynamic Linear Models IEEE TRANSACTIONS ON SIGNAL PROCESSING Fox, E., Sudderth, E. B., Jordan, M. I., Willsky, A. S. 2011; 59 (4): 1569-1585

  View details for DOI 10.1109/TSP.2010.2102756

  View details for Web of Science ID 000290810100019

• Bayesian Nonparametric Methods for Learning Markov Switching Processes IEEE SIGNAL PROCESSING MAGAZINE Fox, E. B., Sudderth, E. B., Jordan, M. I., Willsky, A. S. 2010; 27 (6): 43-54

  View details for DOI 10.1109/MSP.2010.937999

  View details for Web of Science ID 000283453800008