410 results on '"Zhang, Jeffrey"'
Search Results
2. A general condition for bias attenuation by a nondifferentially mismeasured confounder
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Zhang, Jeffrey and Lee, Junu
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Statistics - Methodology - Abstract
In real-world studies, the collected confounders may suffer from measurement error. Although mismeasurement of confounders is typically unintentional -- originating from sources such as human oversight or imprecise machinery -- deliberate mismeasurement also occurs and is becoming increasingly more common. For example, in the 2020 U.S. Census, noise was added to measurements to assuage privacy concerns. Sensitive variables such as income or age are oftentimes partially censored and are only known up to a range of values. In such settings, obtaining valid estimates of the causal effect of a binary treatment can be impossible, as mismeasurement of confounders constitutes a violation of the no unmeasured confounding assumption. A natural question is whether the common practice of simply adjusting for the mismeasured confounder is justifiable. In this article, we answer this question in the affirmative and demonstrate that in many realistic scenarios not covered by previous literature, adjusting for the mismeasured confounders reduces bias compared to not adjusting.
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- 2024
3. Bridging the Gap Between Design and Analysis: Randomization Inference and Sensitivity Analysis for Matched Observational Studies with Treatment Doses
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Zhang, Jeffrey and Heng, Siyu
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Statistics - Methodology - Abstract
Matching is a commonly used causal inference study design in observational studies. Through matching on measured confounders between different treatment groups, valid randomization inferences can be conducted under the no unmeasured confounding assumption, and sensitivity analysis can be further performed to assess sensitivity of randomization inference results to potential unmeasured confounding. However, for many common matching designs, there is still a lack of valid downstream randomization inference and sensitivity analysis approaches. Specifically, in matched observational studies with treatment doses (e.g., continuous or ordinal treatments), with the exception of some special cases such as pair matching, there is no existing randomization inference or sensitivity analysis approach for studying analogs of the sample average treatment effect (Neyman-type weak nulls), and no existing valid sensitivity analysis approach for testing the sharp null of no effect for any subject (Fisher's sharp null) when the outcome is non-binary. To fill these gaps, we propose new methods for randomization inference and sensitivity analysis that can work for general matching designs with treatment doses, applicable to general types of outcome variables (e.g., binary, ordinal, or continuous), and cover both Fisher's sharp null and Neyman-type weak nulls. We illustrate our approaches via comprehensive simulation studies and a real-data application.
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- 2024
4. Doubly robust and computationally efficient high-dimensional variable selection
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Chakraborty, Abhinav, Zhang, Jeffrey, and Katsevich, Eugene
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Statistics - Methodology - Abstract
The variable selection problem is to discover which of a large set of predictors is associated with an outcome of interest, conditionally on the other predictors. This problem has been widely studied, but existing approaches lack either power against complex alternatives, robustness to model misspecification, computational efficiency, or quantification of evidence against individual hypotheses. We present tower PCM (tPCM), a statistically and computationally efficient solution to the variable selection problem that does not suffer from these shortcomings. tPCM adapts the best aspects of two existing procedures that are based on similar functionals: the holdout randomization test (HRT) and the projected covariance measure (PCM). The former is a model-X test that utilizes many resamples and few machine learning fits, while the latter is an asymptotic doubly-robust style test for a single hypothesis that requires no resamples and many machine learning fits. Theoretically, we demonstrate the validity of tPCM, and perhaps surprisingly, the asymptotic equivalence of HRT, PCM, and tPCM. In so doing, we clarify the relationship between two methods from two separate literatures. An extensive simulation study verifies that tPCM can have significant computational savings compared to HRT and PCM, while maintaining nearly identical power.
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- 2024
5. ACDG-VTON: Accurate and Contained Diffusion Generation for Virtual Try-On
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Zhang, Jeffrey, Li, Kedan, Chang, Shao-Yu, and Forsyth, David
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
Virtual Try-on (VTON) involves generating images of a person wearing selected garments. Diffusion-based methods, in particular, can create high-quality images, but they struggle to maintain the identities of the input garments. We identified this problem stems from the specifics in the training formulation for diffusion. To address this, we propose a unique training scheme that limits the scope in which diffusion is trained. We use a control image that perfectly aligns with the target image during training. In turn, this accurately preserves garment details during inference. We demonstrate our method not only effectively conserves garment details but also allows for layering, styling, and shoe try-on. Our method runs multi-garment try-on in a single inference cycle and can support high-quality zoomed-in generations without training in higher resolutions. Finally, we show our method surpasses prior methods in accuracy and quality.
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- 2024
6. On Identification of Dynamic Treatment Regimes with Proxies of Hidden Confounders
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Zhang, Jeffrey and Tchetgen, Eric Tchetgen
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Statistics - Methodology - Abstract
We consider identification of optimal dynamic treatment regimes in a setting where time-varying treatments are confounded by hidden time-varying confounders, but proxy variables of the unmeasured confounders are available. We show that, with two independent proxy variables at each time point that are sufficiently relevant for the hidden confounders, identification of the joint distribution of counterfactuals is possible, thereby facilitating identification of an optimal treatment regime.
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- 2024
7. Me LLaMA: Foundation Large Language Models for Medical Applications
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Xie, Qianqian, Chen, Qingyu, Chen, Aokun, Peng, Cheng, Hu, Yan, Lin, Fongci, Peng, Xueqing, Huang, Jimin, Zhang, Jeffrey, Keloth, Vipina, Zhou, Xinyu, Qian, Lingfei, He, Huan, Shung, Dennis, Ohno-Machado, Lucila, Wu, Yonghui, Xu, Hua, and Bian, Jiang
- Subjects
Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Recent advancements in large language models (LLMs) like ChatGPT and LLaMA show promise in medical applications, yet challenges remain in medical language comprehension. This study presents Me-LLaMA, a new medical LLM family based on open-source LLaMA models, optimized for medical text analysis and diagnosis by leveraging large-scale, domain-specific datasets. The Me-LLaMA family, including foundation models Me-LLaMA 13/70B and their chat-enhanced versions, was developed through continued pre-training and instruction tuning with 129B tokens and 214K samples from biomedical and clinical sources. Training the 70B models required over 100,000 A100 GPU hours. Me-LLaMA's performance was evaluated across six medical text analysis tasks using 12 benchmark datasets and complex clinical case diagnosis, with automatic and human evaluations. Results indicate Me-LLaMA outperforms LLaMA and other open-source medical LLMs in zero-shot and supervised settings. Task-specific tuning further boosts performance, surpassing ChatGPT on 7 of 8 datasets and GPT-4 on 5 of 8. For complex clinical cases, Me-LLaMA achieves performance comparable to ChatGPT and GPT-4. This work underscores the importance of domain-specific data in developing medical LLMs and addresses the high computational costs involved in training, highlighting a balance between pre-training and fine-tuning strategies. Me-LLaMA models are now accessible under user agreements, providing a valuable resource for advancing medical AI., Comment: 21 pages, 4 figures, 8 tables
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- 2024
8. Preserving Image Properties Through Initializations in Diffusion Models
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Zhang, Jeffrey, Chang, Shao-Yu, Li, Kedan, and Forsyth, David
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Retail photography imposes specific requirements on images. For instance, images may need uniform background colors, consistent model poses, centered products, and consistent lighting. Minor deviations from these standards impact a site's aesthetic appeal, making the images unsuitable for use. We show that Stable Diffusion methods, as currently applied, do not respect these requirements. The usual practice of training the denoiser with a very noisy image and starting inference with a sample of pure noise leads to inconsistent generated images during inference. This inconsistency occurs because it is easy to tell the difference between samples of the training and inference distributions. As a result, a network trained with centered retail product images with uniform backgrounds generates images with erratic backgrounds. The problem is easily fixed by initializing inference with samples from an approximation of noisy images. However, in using such an approximation, the joint distribution of text and noisy image at inference time still slightly differs from that at training time. This discrepancy is corrected by training the network with samples from the approximate noisy image distribution. Extensive experiments on real application data show significant qualitative and quantitative improvements in performance from adopting these procedures. Finally, our procedure can interact well with other control-based methods to further enhance the controllability of diffusion-based methods.
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- 2024
9. Higher-Order Newton Methods with Polynomial Work per Iteration
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Ahmadi, Amir Ali, Chaudhry, Abraar, and Zhang, Jeffrey
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Mathematics - Optimization and Control ,Computer Science - Machine Learning - Abstract
We present generalizations of Newton's method that incorporate derivatives of an arbitrary order $d$ but maintain a polynomial dependence on dimension in their cost per iteration. At each step, our $d^{\text{th}}$-order method uses semidefinite programming to construct and minimize a sum of squares-convex approximation to the $d^{\text{th}}$-order Taylor expansion of the function we wish to minimize. We prove that our $d^{\text{th}}$-order method has local convergence of order $d$. This results in lower oracle complexity compared to the classical Newton method. We show on numerical examples that basins of attraction around local minima can get larger as $d$ increases. Under additional assumptions, we present a modified algorithm, again with polynomial cost per iteration, which is globally convergent and has local convergence of order $d$.
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- 2023
10. Predicting a Protein's Stability under a Million Mutations
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Ouyang-Zhang, Jeffrey, Diaz, Daniel J., Klivans, Adam R., and Krähenbühl, Philipp
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Quantitative Biology - Biomolecules - Abstract
Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep learning has recently emerged as a powerful tool for identifying promising mutations. Existing approaches, however, are computationally expensive, as the number of model inferences scales with the number of mutations queried. Our main contribution is a simple, parallel decoding algorithm. Our Mutate Everything is capable of predicting the effect of all single and double mutations in one forward pass. It is even versatile enough to predict higher-order mutations with minimal computational overhead. We build Mutate Everything on top of ESM2 and AlphaFold, neither of which were trained to predict thermodynamic stability. We trained on the Mega-Scale cDNA proteolysis dataset and achieved state-of-the-art performance on single and higher-order mutations on S669, ProTherm, and ProteinGym datasets. Code is available at https://github.com/jozhang97/MutateEverything, Comment: NeurIPS 2023. Code available at https://github.com/jozhang97/MutateEverything
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- 2023
11. Randomization-Based Inference for Average Treatment Effect in Inexactly Matched Observational Studies
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Zhu, Jianan, Zhang, Jeffrey, Guo, Zijian, and Heng, Siyu
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Statistics - Methodology - Abstract
Matching is a widely used causal inference study design in observational studies. It seeks to mimic a randomized experiment by forming matched sets of treated and control units based on proximity in covariates. Ideally, treated units are exactly matched with controls for the covariates, and randomization-based inference for the treatment effect can then be conducted as in a randomized experiment under the ignorability assumption. However, matching is typically inexact when continuous covariates or many covariates exist. Previous studies have routinely ignored inexact matching in the downstream randomization-based inference as long as some covariate balance criteria are satisfied. Some recent studies found that this routine practice can cause severe bias. They proposed new inference methods for correcting for bias due to inexact matching. However, these inference methods focus on the constant treatment effect (i.e., Fisher's sharp null) and are not directly applicable to the average treatment effect (i.e., Neyman's weak null). To address this problem, we propose a new framework - inverse post-matching probability weighting (IPPW) - for randomization-based average treatment effect inference under inexact matching. Compared with the routinely used randomization-based inference framework based on the difference-in-means estimator, our proposed IPPW framework can substantially reduce bias due to inexact matching and improve the coverage rate. We have also developed an open-source R package RIIM (Randomization-Based Inference under Inexact Matching) for implementing our methods., Comment: This updated version focuses on the average treatment effect and adds the inference part for it. For the constant treatment effect estimation part, please see the previous versions
- Published
- 2023
12. Structure-based design of nanobodies that inhibit seeding of Alzheimers patient-extracted tau fibrils.
- Author
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Abskharon, Romany, Pan, Hope, Sawaya, Michael, Seidler, Paul, Olivares, Eileen, Chen, Yu, Murray, Kevin, Zhang, Jeffrey, Lantz, Carter, Bentzel, Megan, Boyer, David, Cascio, Duilio, Nguyen, Binh, Hou, Ke, Cheng, Xinyi, Pardon, Els, Williams, Christopher, Nana, Alissa, Spina, Salvatore, Seeley, William, Steyaert, Jan, Glabe, Charles, Ogorzalek Loo, Rachel, Grinberg, Lea, Loo, Joseph, Vinters, Harry, and Eisenberg, David
- Subjects
amyloid ,nanobody ,prion-like spreading ,synthetic antibody ,tau ,Humans ,Animals ,Mice ,Alzheimer Disease ,tau Proteins ,Single-Domain Antibodies ,Neurofibrillary Tangles ,Supranuclear Palsy ,Progressive ,Antibodies ,Brain - Abstract
Despite much effort, antibody therapies for Alzheimers disease (AD) have shown limited efficacy. Challenges to the rational design of effective antibodies include the difficulty of achieving specific affinity to critical targets, poor expression, and antibody aggregation caused by buried charges and unstructured loops. To overcome these challenges, we grafted previously determined sequences of fibril-capping amyloid inhibitors onto a camel heavy chain antibody scaffold. These sequences were designed to cap fibrils of tau, known to form the neurofibrillary tangles of AD, thereby preventing fibril elongation. The nanobodies grafted with capping inhibitors blocked tau aggregation in biosensor cells seeded with postmortem brain extracts from AD and progressive supranuclear palsy (PSP) patients. The tau capping nanobody inhibitors also blocked seeding by recombinant tau oligomers. Another challenge to the design of effective antibodies is their poor blood-brain barrier (BBB) penetration. In this study, we also designed a bispecific nanobody composed of a nanobody that targets a receptor on the BBB and a tau capping nanobody inhibitor, conjoined by a flexible linker. We provide evidence that the bispecific nanobody improved BBB penetration over the tau capping inhibitor alone after intravenous administration in mice. Our results suggest that the design of synthetic antibodies that target sequences that drive protein aggregation may be a promising approach to inhibit the prion-like seeding of tau and other proteins involved in AD and related proteinopathies.
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- 2023
13. Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations
- Author
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Diaz, Daniel J., Gong, Chengyue, Ouyang-Zhang, Jeffrey, Loy, James M., Wells, Jordan, Yang, David, Ellington, Andrew D., Dimakis, Alexandros G., and Klivans, Adam R.
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- 2024
- Full Text
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14. Proximal Causal Inference without Uniqueness Assumptions
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Zhang, Jeffrey, Li, Wei, Miao, Wang, and Tchetgen, Eric Tchetgen
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Statistics - Methodology - Abstract
We consider identification and inference about a counterfactual outcome mean when there is unmeasured confounding using tools from proximal causal inference (Miao et al. [2018], Tchetgen Tchetgen et al. [2020]). Proximal causal inference requires existence of solutions to at least one of two integral equations. We motivate the existence of solutions to the integral equations from proximal causal inference by demonstrating that, assuming the existence of a solution to one of the integral equations, $\sqrt{n}$-estimability of a linear functional (such as its mean) of that solution requires the existence of a solution to the other integral equation. Solutions to the integral equations may not be unique, which complicates estimation and inference. We construct a consistent estimator for the solution set for one of the integral equations and then adapt the theory of extremum estimators to find from the estimated set a consistent estimator for a uniquely defined solution. A debiased estimator for the counterfactual mean is shown to be root-$n$ consistent, regular, and asymptotically semiparametrically locally efficient under additional regularity conditions., Comment: Fixed some errors and added to acknowledgements
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- 2023
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15. NMS Strikes Back
- Author
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Ouyang-Zhang, Jeffrey, Cho, Jang Hyun, Zhou, Xingyi, and Krähenbühl, Philipp
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Detection Transformer (DETR) directly transforms queries to unique objects by using one-to-one bipartite matching during training and enables end-to-end object detection. Recently, these models have surpassed traditional detectors on COCO with undeniable elegance. However, they differ from traditional detectors in multiple designs, including model architecture and training schedules, and thus the effectiveness of one-to-one matching is not fully understood. In this work, we conduct a strict comparison between the one-to-one Hungarian matching in DETRs and the one-to-many label assignments in traditional detectors with non-maximum supervision (NMS). Surprisingly, we observe one-to-many assignments with NMS consistently outperform standard one-to-one matching under the same setting, with a significant gain of up to 2.5 mAP. Our detector that trains Deformable-DETR with traditional IoU-based label assignment achieved 50.2 COCO mAP within 12 epochs (1x schedule) with ResNet50 backbone, outperforming all existing traditional or transformer-based detectors in this setting. On multiple datasets, schedules, and architectures, we consistently show bipartite matching is unnecessary for performant detection transformers. Furthermore, we attribute the success of detection transformers to their expressive transformer architecture. Code is available at https://github.com/jozhang97/DETA., Comment: Code is available at https://github.com/jozhang97/DETA
- Published
- 2022
16. Wearing the Same Outfit in Different Ways -- A Controllable Virtual Try-on Method
- Author
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Li, Kedan, Zhang, Jeffrey, Chang, Shao-Yu, and Forsyth, David
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Computer Science - Graphics ,Computer Science - Computer Vision and Pattern Recognition - Abstract
An outfit visualization method generates an image of a person wearing real garments from images of those garments. Current methods can produce images that look realistic and preserve garment identity, captured in details such as collar, cuffs, texture, hem, and sleeve length. However, no current method can both control how the garment is worn -- including tuck or untuck, opened or closed, high or low on the waist, etc.. -- and generate realistic images that accurately preserve the properties of the original garment. We describe an outfit visualization method that controls drape while preserving garment identity. Our system allows instance independent editing of garment drape, which means a user can construct an edit (e.g. tucking a shirt in a specific way) that can be applied to all shirts in a garment collection. Garment detail is preserved by relying on a warping procedure to place the garment on the body and a generator then supplies fine shading detail. To achieve instance independent control, we use control points with garment category-level semantics to guide the warp. The method produces state-of-the-art quality images, while allowing creative ways to style garments, including allowing tops to be tucked or untucked; jackets to be worn open or closed; skirts to be worn higher or lower on the waist; and so on. The method allows interactive control to correct errors in individual renderings too. Because the edits are instance independent, they can be applied to large pools of garments automatically and can be conditioned on garment metadata (e.g. all cropped jackets are worn closed or all bomber jackets are worn closed).
- Published
- 2022
17. An Unregularized Third Order Newton Method
- Author
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Silina, Olha and Zhang, Jeffrey
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Mathematics - Optimization and Control ,49M15, 65K05, 90C25, 90C22 - Abstract
In this paper, we propose a third-order Newton's method which in each iteration solves a semidefinite program as a subproblem. Our approach is based on moving to the local minimum of the third-order Taylor expansion at each iteration, rather than that of the second order. We show that this scheme has local cubic convergence. We then provide numerical experiments comparing this scheme to some standard algorithms., Comment: 22 pages, 15 figures
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- 2022
18. Sensitivity Analysis for Observational Studies with Recurrent Events
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Zhang, Jeffrey and Small, Dylan S.
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- 2024
- Full Text
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19. Efficacy of Radicava® IV (intravenous edaravone) in subjects with differing trajectories of disease progression in amyotrophic lateral sclerosis: Use of a novel statistical approach for post hoc analysis of a pivotal phase 3 clinical trial
- Author
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Pioro, Erik P., Brooks, Benjamin Rix, Liu, Ying, Zhang, Jeffrey, and Apple, Stephen
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- 2024
- Full Text
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20. Real Robot Challenge: A Robotics Competition in the Cloud
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Bauer, Stefan, Widmaier, Felix, Wüthrich, Manuel, Buchholz, Annika, Stark, Sebastian, Goyal, Anirudh, Steinbrenner, Thomas, Akpo, Joel, Joshi, Shruti, Berenz, Vincent, Agrawal, Vaibhav, Funk, Niklas, De Jesus, Julen Urain, Peters, Jan, Watson, Joe, Chen, Claire, Srinivasan, Krishnan, Zhang, Junwu, Zhang, Jeffrey, Walter, Matthew R., Madan, Rishabh, Schaff, Charles, Maeda, Takahiro, Yoneda, Takuma, Yarats, Denis, Allshire, Arthur, Gordon, Ethan K., Bhattacharjee, Tapomayukh, Srinivasa, Siddhartha S., Garg, Animesh, Sikchi, Harshit, Wang, Jilong, Yao, Qingfeng, Yang, Shuyu, McCarthy, Robert, Sanchez, Francisco Roldan, Wang, Qiang, Bulens, David Cordova, McGuinness, Kevin, O'Connor, Noel, Redmond, Stephen J., and Schölkopf, Bernhard
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Computer Science - Robotics ,Statistics - Applications - Abstract
Dexterous manipulation remains an open problem in robotics. To coordinate efforts of the research community towards tackling this problem, we propose a shared benchmark. We designed and built robotic platforms that are hosted at MPI for Intelligent Systems and can be accessed remotely. Each platform consists of three robotic fingers that are capable of dexterous object manipulation. Users are able to control the platforms remotely by submitting code that is executed automatically, akin to a computational cluster. Using this setup, i) we host robotics competitions, where teams from anywhere in the world access our platforms to tackle challenging tasks ii) we publish the datasets collected during these competitions (consisting of hundreds of robot hours), and iii) we give researchers access to these platforms for their own projects.
- Published
- 2021
21. Higher-order Newton methods with polynomial work per iteration
- Author
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Ahmadi, Amir Ali, Chaudhry, Abraar, and Zhang, Jeffrey
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- 2024
- Full Text
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22. Auxora vs. placebo for the treatment of patients with severe COVID-19 pneumonia: a randomized-controlled clinical trial.
- Author
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Bruen, Charles, Al-Saadi, Mukhtar, Michelson, Edward, Tanios, Maged, Mendoza-Ayala, Raul, Miller, Joseph, Zhang, Jeffrey, Stauderman, Kenneth, Hebbar, Sudarshan, and Hou, Peter
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Adult ,Benzamides ,Calcium Release Activated Calcium Channels ,Humans ,Pyrazines ,Respiration ,Artificial ,Respiratory Distress Syndrome ,SARS-CoV-2 ,Treatment Outcome ,COVID-19 Drug Treatment - Abstract
BACKGROUND: Calcium release-activated calcium (CRAC) channel inhibitors block proinflammatory cytokine release, preserve endothelial integrity and may effectively treat patients with severe COVID-19 pneumonia. METHODS: CARDEA was a phase 2, randomized, double-blind, placebo-controlled trial evaluating the addition of Auxora, a CRAC channel inhibitor, to corticosteroids and standard of care in adults with severe COVID-19 pneumonia. Eligible patients were adults with ≥ 1 symptom consistent with COVID-19 infection, a diagnosis of COVID-19 confirmed by laboratory testing using polymerase chain reaction or other assay, and pneumonia documented by chest imaging. Patients were also required to be receiving oxygen therapy using either a high flow or low flow nasal cannula at the time of enrolment and have at the time of enrollment a baseline imputed PaO2/FiO2 ratio > 75 and ≤ 300. The PaO2/FiO2 was imputed from a SpO2/FiO2 determine by pulse oximetry using a non-linear equation. Patients could not be receiving either non-invasive or invasive mechanical ventilation at the time of enrolment. The primary endpoint was time to recovery through Day 60, with secondary endpoints of all-cause mortality at Day 60 and Day 30. Due to declining rates of COVID-19 hospitalizations and utilization of standard of care medications prohibited by regulatory guidance, the trial was stopped early. RESULTS: The pre-specified efficacy set consisted of the 261 patients with a baseline imputed PaO2/FiO2≤ 200 with 130 and 131 in the Auxora and placebo groups, respectively. Time to recovery was 7 vs. 10 days (P = 0.0979) for patients who received Auxora vs. placebo, respectively. The all-cause mortality rate at Day 60 was 13.8% with Auxora vs. 20.6% with placebo (P = 0.1449); Day 30 all-cause mortality was 7.7% and 17.6%, respectively (P = 0.0165). Similar trends were noted in all randomized patients, patients on high flow nasal cannula at baseline or those with a baseline imputed PaO2/FiO2 ≤ 100. Serious adverse events (SAEs) were less frequent in patients treated with Auxora vs. placebo and occurred in 34 patients (24.1%) receiving Auxora and 49 (35.0%) receiving placebo (P = 0.0616). The most common SAEs were respiratory failure, acute respiratory distress syndrome, and pneumonia. CONCLUSIONS: Auxora was safe and well tolerated with strong signals in both time to recovery and all-cause mortality through Day 60 in patients with severe COVID-19 pneumonia. Further studies of Auxora in patients with severe COVID-19 pneumonia are warranted. Trial registration NCT04345614.
- Published
- 2022
23. Toward Accurate and Realistic Outfits Visualization with Attention to Details
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Li, Kedan, Chong, Min jin, Zhang, Jeffrey, and Liu, Jingen
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Graphics ,Computer Science - Machine Learning - Abstract
Virtual try-on methods aim to generate images of fashion models wearing arbitrary combinations of garments. This is a challenging task because the generated image must appear realistic and accurately display the interaction between garments. Prior works produce images that are filled with artifacts and fail to capture important visual details necessary for commercial applications. We propose Outfit Visualization Net (OVNet) to capture these important details (e.g. buttons, shading, textures, realistic hemlines, and interactions between garments) and produce high quality multiple-garment virtual try-on images. OVNet consists of 1) a semantic layout generator and 2) an image generation pipeline using multiple coordinated warps. We train the warper to output multiple warps using a cascade loss, which refines each successive warp to focus on poorly generated regions of a previous warp and yields consistent improvements in detail. In addition, we introduce a method for matching outfits with the most suitable model and produce significant improvements for both our and other previous try-on methods. Through quantitative and qualitative analysis, we demonstrate our method generates substantially higher-quality studio images compared to prior works for multi-garment outfits. An interactive interface powered by this method has been deployed on fashion e-commerce websites and received overwhelmingly positive feedback., Comment: Accepted to CVPR2021. Live demo here https://revery.ai/demo.html
- Published
- 2021
24. Dexterous Manipulation Primitives for the Real Robot Challenge
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Chen, Claire, Srinivasan, Krishnan, Zhang, Jeffrey, Zhang, Junwu, Shao, Lin, Yuan, Shenli, Culbertson, Preston, Dai, Hongkai, Schwager, Mac, and Bohg, Jeannette
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Computer Science - Robotics - Abstract
This report describes our approach for Phase 3 of the Real Robot Challenge. To solve cuboid manipulation tasks of varying difficulty, we decompose each task into the following primitives: moving the fingers to the cuboid to grasp it, turning it on the table to minimize orientation error, and re-positioning it to the goal position. We use model-based trajectory optimization and control to plan and execute these primitives. These grasping, turning, and re-positioning primitives are sequenced with a state-machine that determines which primitive to execute given the current object state and goal. Our method shows robust performance over multiple runs with randomized initial and goal positions. With this approach, our team placed second in the challenge, under the anonymous name "sombertortoise" on the leaderboard. Example runs of our method solving each of the four levels can be seen in this video (https://www.youtube.com/watch?v=I65Kwu9PGmg&list=PLt9QxrtaftrHGXcp4Oh8-s_OnQnBnLtei&index=1)., Comment: For a video of our method, see https://www.youtube.com/watch?v=I65Kwu9PGmg&list=PLt9QxrtaftrHGXcp4Oh8-s_OnQnBnLtei&index=1 . For our code, visit https://github.com/stanford-iprl-lab/rrc_package
- Published
- 2021
25. Complexity Aspects of Fundamental Questions in Polynomial Optimization
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Zhang, Jeffrey
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Mathematics - Optimization and Control ,Computer Science - Computational Complexity ,Computer Science - Machine Learning ,90C23 (Primary) 90C20, 90C22, 90C26, 90C30, 90C46, 90C60, 68Q17, 68Q25, 91A05 (Secondary) - Abstract
In this thesis, we settle the computational complexity of some fundamental questions in polynomial optimization. These include the questions of (i) finding a local minimum, (ii) testing local minimality of a point, and (iii) deciding attainment of the optimal value. Our results characterize the complexity of these three questions for all degrees of the defining polynomials left open by prior literature. Regarding (i) and (ii), we show that unless P=NP, there cannot be a polynomial-time algorithm that finds a point within Euclidean distance $c^n$ (for any constant $c$) of a local minimum of an $n$-variate quadratic program. By contrast, we show that a local minimum of a cubic polynomial can be found efficiently by semidefinite programming (SDP). We prove that second-order points of cubic polynomials admit an efficient semidefinite representation, even though their critical points are NP-hard to find. We also give an efficiently-checkable necessary and sufficient condition for local minimality of a point for a cubic polynomial. Regarding (iii), we prove that testing whether a quadratically constrained quadratic program with a finite optimal value has an optimal solution is NP-hard. We also show that testing coercivity of the objective function, compactness of the feasible set, and the Archimedean property associated with the description of the feasible set are all NP-hard. We also give a new characterization of coercive polynomials that lends itself to a hierarchy of SDPs. In our final chapter, we present an SDP relaxation for finding approximate Nash equilibria in bimatrix games. We show that for a symmetric game, a $1/3$-Nash equilibrium can be efficiently recovered from any rank-2 solution to this relaxation. We also propose SDP relaxations for NP-hard problems related to Nash equilibria, such as that of finding the highest achievable welfare under any Nash equilibrium., Comment: 196 pages, 11 figures, PhD Thesis
- Published
- 2020
26. Complexity aspects of local minima and related notions
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Ahmadi, Amir Ali and Zhang, Jeffrey
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Mathematics - Optimization and Control ,Computer Science - Computational Complexity ,Computer Science - Machine Learning ,90C60 (Primary), 90C22, 90C30, 90C46 (Secondary) - Abstract
We consider the notions of (i) critical points, (ii) second-order points, (iii) local minima, and (iv) strict local minima for multivariate polynomials. For each type of point, and as a function of the degree of the polynomial, we study the complexity of deciding (1) if a given point is of that type, and (2) if a polynomial has a point of that type. Our results characterize the complexity of these two questions for all degrees left open by prior literature. Our main contributions reveal that many of these questions turn out to be tractable for cubic polynomials. In particular, we present an efficiently-checkable necessary and sufficient condition for local minimality of a point for a cubic polynomial. We also show that a local minimum of a cubic polynomial can be efficiently found by solving semidefinite programs of size linear in the number of variables. By contrast, we show that it is strongly NP-hard to decide if a cubic polynomial has a critical point. We also prove that the set of second-order points of any cubic polynomial is a spectrahedron, and conversely that any spectrahedron is the projection of the set of second-order points of a cubic polynomial. In our final section, we briefly present a potential application of finding local minima of cubic polynomials to the design of a third-order Newton method., Comment: 41 pages, 10 figures
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- 2020
27. On the complexity of finding a local minimizer of a quadratic function over a polytope
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Ahmadi, Amir Ali and Zhang, Jeffrey
- Subjects
Mathematics - Optimization and Control ,Computer Science - Computational Complexity ,Computer Science - Machine Learning ,90C20 (Primary), 90C30, 90C60 (Secondary) - Abstract
We show that unless P=NP, there cannot be a polynomial-time algorithm that finds a point within Euclidean distance $c^n$ (for any constant $c \ge 0$) of a local minimizer of an $n$-variate quadratic function over a polytope. This result (even with $c=0$) answers a question of Pardalos and Vavasis that appeared in 1992 on a list of seven open problems in complexity theory for numerical optimization. Our proof technique also implies that the problem of deciding whether a quadratic function has a local minimizer over an (unbounded) polyhedron, and that of deciding if a quartic polynomial has a local minimizer are NP-hard., Comment: 9 pages
- Published
- 2020
- Full Text
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28. Memory-Efficient Incremental Learning Through Feature Adaptation
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Iscen, Ahmet, Zhang, Jeffrey, Lazebnik, Svetlana, and Schmid, Cordelia
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Computer Science - Computer Vision and Pattern Recognition - Abstract
We introduce an approach for incremental learning that preserves feature descriptors of training images from previously learned classes, instead of the images themselves, unlike most existing work. Keeping the much lower-dimensional feature embeddings of images reduces the memory footprint significantly. We assume that the model is updated incrementally for new classes as new data becomes available sequentially.This requires adapting the previously stored feature vectors to the updated feature space without having access to the corresponding original training images. Feature adaptation is learned with a multi-layer perceptron, which is trained on feature pairs corresponding to the outputs of the original and updated network on a training image. We validate experimentally that such a transformation generalizes well to the features of the previous set of classes, and maps features to a discriminative subspace in the feature space. As a result, the classifier is optimized jointly over new and old classes without requiring old class images. Experimental results show that our method achieves state-of-the-art classification accuracy in incremental learning benchmarks, while having at least an order of magnitude lower memory footprint compared to image-preserving strategies.
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- 2020
29. Exploring Extended Reality with ILLIXR: A New Playground for Architecture Research
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Huzaifa, Muhammad, Desai, Rishi, Grayson, Samuel, Jiang, Xutao, Jing, Ying, Lee, Jae, Lu, Fang, Pang, Yihan, Ravichandran, Joseph, Sinclair, Finn, Tian, Boyuan, Yuan, Hengzhi, Zhang, Jeffrey, and Adve, Sarita V.
- Subjects
Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Emerging Technologies - Abstract
As we enter the era of domain-specific architectures, systems researchers must understand the requirements of emerging application domains. Augmented and virtual reality (AR/VR) or extended reality (XR) is one such important domain. This paper presents ILLIXR, the first open source end-to-end XR system (1) with state-of-the-art components, (2) integrated with a modular and extensible multithreaded runtime, (3) providing an OpenXR compliant interface to XR applications (e.g., game engines), and (4) with the ability to report (and trade off) several quality of experience (QoE) metrics. We analyze performance, power, and QoE metrics for the complete ILLIXR system and for its individual components. Our analysis reveals several properties with implications for architecture and systems research. These include demanding performance, power, and QoE requirements, a large diversity of critical tasks, inter-dependent execution pipelines with challenges in scheduling and resource management, and a large tradeoff space between performance/power and human perception related QoE metrics. ILLIXR and our analysis have the potential to propel new directions in architecture and systems research in general, and impact XR in particular. ILLIXR is open-source and available at https://illixr.github.io
- Published
- 2020
30. Side-Tuning: A Baseline for Network Adaptation via Additive Side Networks
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Zhang, Jeffrey O, Sax, Alexander, Zamir, Amir, Guibas, Leonidas, and Malik, Jitendra
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Computer Science - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Neural and Evolutionary Computing ,Computer Science - Robotics - Abstract
When training a neural network for a desired task, one may prefer to adapt a pre-trained network rather than starting from randomly initialized weights. Adaptation can be useful in cases when training data is scarce, when a single learner needs to perform multiple tasks, or when one wishes to encode priors in the network. The most commonly employed approaches for network adaptation are fine-tuning and using the pre-trained network as a fixed feature extractor, among others. In this paper, we propose a straightforward alternative: side-tuning. Side-tuning adapts a pre-trained network by training a lightweight "side" network that is fused with the (unchanged) pre-trained network via summation. This simple method works as well as or better than existing solutions and it resolves some of the basic issues with fine-tuning, fixed features, and other common approaches. In particular, side-tuning is less prone to overfitting, is asymptotically consistent, and does not suffer from catastrophic forgetting in incremental learning. We demonstrate the performance of side-tuning under a diverse set of scenarios, including incremental learning (iCIFAR, iTaskonomy), reinforcement learning, imitation learning (visual navigation in Habitat), NLP question-answering (SQuAD v2), and single-task transfer learning (Taskonomy), with consistently promising results., Comment: In ECCV 2020 (Spotlight). For more, see project website and code at http://sidetuning.berkeley.edu
- Published
- 2019
31. Learning to Navigate Using Mid-Level Visual Priors
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Sax, Alexander, Zhang, Jeffrey O., Emi, Bradley, Zamir, Amir, Savarese, Silvio, Guibas, Leonidas, and Malik, Jitendra
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning ,Computer Science - Neural and Evolutionary Computing ,Computer Science - Robotics - Abstract
How much does having visual priors about the world (e.g. the fact that the world is 3D) assist in learning to perform downstream motor tasks (e.g. navigating a complex environment)? What are the consequences of not utilizing such visual priors in learning? We study these questions by integrating a generic perceptual skill set (a distance estimator, an edge detector, etc.) within a reinforcement learning framework (see Fig. 1). This skill set ("mid-level vision") provides the policy with a more processed state of the world compared to raw images. Our large-scale study demonstrates that using mid-level vision results in policies that learn faster, generalize better, and achieve higher final performance, when compared to learning from scratch and/or using state-of-the-art visual and non-visual representation learning methods. We show that conventional computer vision objectives are particularly effective in this regard and can be conveniently integrated into reinforcement learning frameworks. Finally, we found that no single visual representation was universally useful for all downstream tasks, hence we computationally derive a task-agnostic set of representations optimized to support arbitrary downstream tasks., Comment: In Conference on Robot Learning, 2019. See project website and demos at http://perceptual.actor/
- Published
- 2019
32. Sex, but not juvenile stress, affects reversal learning and DRL performance following cocaine administration
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Paine, Tracie A., Pierotti, Caroline, Swanson, Evan S., Martin del Campo, Zoë, Kulkarni, Sydney, and Zhang, Jeffrey
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- 2023
- Full Text
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33. On the complexity of finding a local minimizer of a quadratic function over a polytope
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Ahmadi, Amir Ali and Zhang, Jeffrey
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- 2022
- Full Text
- View/download PDF
34. Modular Architecture for StarCraft II with Deep Reinforcement Learning
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Lee, Dennis, Tang, Haoran, Zhang, Jeffrey O, Xu, Huazhe, Darrell, Trevor, and Abbeel, Pieter
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Computer Science - Artificial Intelligence - Abstract
We present a novel modular architecture for StarCraft II AI. The architecture splits responsibilities between multiple modules that each control one aspect of the game, such as build-order selection or tactics. A centralized scheduler reviews macros suggested by all modules and decides their order of execution. An updater keeps track of environment changes and instantiates macros into series of executable actions. Modules in this framework can be optimized independently or jointly via human design, planning, or reinforcement learning. We apply deep reinforcement learning techniques to training two out of six modules of a modular agent with self-play, achieving 94% or 87% win rates against the "Harder" (level 5) built-in Blizzard bot in Zerg vs. Zerg matches, with or without fog-of-war., Comment: Accepted to The 14th AAAI Conference on Artificial Intelligence and Interactive Digital Entertainment (AIIDE'18)
- Published
- 2018
35. Generalized Latent Variable Recovery for Generative Adversarial Networks
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Egan, Nicholas, Zhang, Jeffrey, and Shen, Kevin
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
The Generator of a Generative Adversarial Network (GAN) is trained to transform latent vectors drawn from a prior distribution into realistic looking photos. These latent vectors have been shown to encode information about the content of their corresponding images. Projecting input images onto the latent space of a GAN is non-trivial, but previous work has successfully performed this task for latent spaces with a uniform prior. We extend these techniques to latent spaces with a Gaussian prior, and demonstrate our technique's effectiveness.
- Published
- 2018
36. Automated and Interpretable Patient ECG Profiles for Disease Detection, Tracking, and Discovery
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Tison, Geoffrey H., Zhang, Jeffrey, Delling, Francesca N., and Deo, Rahul C.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
The electrocardiogram or ECG has been in use for over 100 years and remains the most widely performed diagnostic test to characterize cardiac structure and electrical activity. We hypothesized that parallel advances in computing power, innovations in machine learning algorithms, and availability of large-scale digitized ECG data would enable extending the utility of the ECG beyond its current limitations, while at the same time preserving interpretability, which is fundamental to medical decision-making. We identified 36,186 ECGs from the UCSF database that were 1) in normal sinus rhythm and 2) would enable training of specific models for estimation of cardiac structure or function or detection of disease. We derived a novel model for ECG segmentation using convolutional neural networks (CNN) and Hidden Markov Models (HMM) and evaluated its output by comparing electrical interval estimates to 141,864 measurements from the clinical workflow. We built a 725-element patient-level ECG profile using downsampled segmentation data and trained machine learning models to estimate left ventricular mass, left atrial volume, mitral annulus e' and to detect and track four diseases: pulmonary arterial hypertension (PAH), hypertrophic cardiomyopathy (HCM), cardiac amyloid (CA), and mitral valve prolapse (MVP). CNN-HMM derived ECG segmentation agreed with clinical estimates, with median absolute deviations (MAD) as a fraction of observed value of 0.6% for heart rate and 4% for QT interval. Patient-level ECG profiles enabled quantitative estimates of left ventricular and mitral annulus e' velocity with good discrimination in binary classification models of left ventricular hypertrophy and diastolic function. Models for disease detection ranged from AUROC of 0.94 to 0.77 for MVP. Top-ranked variables for all models included known ECG characteristics along with novel predictors of these traits/diseases., Comment: 13 pages, 6 figures, 1 Table + Supplement
- Published
- 2018
37. On the Complexity of Testing Attainment of the Optimal Value in Nonlinear Optimization
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Ahmadi, Amir Ali and Zhang, Jeffrey
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Mathematics - Optimization and Control ,Computer Science - Computational Complexity ,Mathematics - Algebraic Geometry ,Mathematics - Numerical Analysis ,90C60 (Primary), 90C30 (Secondary) ,G.1.6 - Abstract
We prove that unless P=NP, there exists no polynomial time (or even pseudo-polynomial time) algorithm that can test whether the optimal value of a nonlinear optimization problem where the objective and constraints are given by low-degree polynomials is attained. If the degrees of these polynomials are fixed, our results along with previously-known "Frank-Wolfe type" theorems imply that exactly one of two cases can occur: either the optimal value is attained on every instance, or it is strongly NP-hard to distinguish attainment from non-attainment. We also show that testing for some well-known sufficient conditions for attainment of the optimal value, such as coercivity of the objective function and closedness and boundedness of the feasible set, is strongly NP-hard. As a byproduct, our proofs imply that testing the Archimedean property of a quadratic module is strongly NP-hard, a property that is of independent interest to the convergence of the Lasserre hierarchy. Finally, we give semidefinite programming (SDP)-based sufficient conditions for attainment of the optimal value, in particular a new characterization of coercive polynomials that lends itself to an SDP hierarchy., Comment: 18 pages
- Published
- 2018
38. Development of a Staphylococcus aureus reporter strain with click beetle red luciferase for enhanced in vivo imaging of experimental bacteremia and mixed infections.
- Author
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Miller, Robert J, Crosby, Heidi A, Schilcher, Katrin, Wang, Yu, Ortines, Roger V, Mazhar, Momina, Dikeman, Dustin A, Pinsker, Bret L, Brown, Isabelle D, Joyce, Daniel P, Zhang, Jeffrey, Archer, Nathan K, Liu, Haiyun, Alphonse, Martin P, Czupryna, Julie, Anderson, William R, Bernthal, Nicholas M, Fortuno-Miranda, Lea, Bulte, Jeff WM, Francis, Kevin P, Horswill, Alexander R, and Miller, Lloyd S
- Subjects
Animals ,Mice ,Inbred C57BL ,Rabbits ,Mice ,Pseudomonas aeruginosa ,Staphylococcus aureus ,Bacteremia ,Pseudomonas Infections ,Staphylococcal Infections ,Wound Infection ,Luciferases ,Diagnostic Imaging ,Luminescent Measurements ,Genes ,Reporter ,Female ,Male ,Coinfection ,Coleoptera - Abstract
In vivo bioluminescence imaging has been used to monitor Staphylococcus aureus infections in preclinical models by employing bacterial reporter strains possessing a modified lux operon from Photorhabdus luminescens. However, the relatively short emission wavelength of lux (peak 490 nm) has limited tissue penetration. To overcome this limitation, the gene for the click beetle (Pyrophorus plagiophtalamus) red luciferase (luc) (with a longer >600 emission wavelength), was introduced singly and in combination with the lux operon into a methicillin-resistant S. aureus strain. After administration of the substrate D-luciferin, the luc bioluminescent signal was substantially greater than the lux signal in vitro. The luc signal had enhanced tissue penetration and improved anatomical co-registration with infected internal organs compared with the lux signal in a mouse model of S. aureus bacteremia with a sensitivity of approximately 3 × 104 CFU from the kidneys. Finally, in an in vivo mixed bacterial wound infection mouse model, S. aureus luc signals could be spectrally unmixed from Pseudomonas aeruginosa lux signals to noninvasively monitor the bacterial burden of both strains. Therefore, the S. aureus luc reporter may provide a technological advance for monitoring invasive organ dissemination during S. aureus bacteremia and for studying bacterial dynamics during mixed infections.
- Published
- 2019
39. Automated and Interpretable Patient ECG Profiles for Disease Detection, Tracking, and Discovery.
- Author
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Tison, Geoffrey H, Zhang, Jeffrey, Delling, Francesca N, and Deo, Rahul C
- Subjects
Humans ,Cardiovascular Diseases ,Diagnosis ,Computer-Assisted ,Electrocardiography ,Prognosis ,Markov Chains ,Reproducibility of Results ,Predictive Value of Tests ,Action Potentials ,Heart Rate ,Time Factors ,Signal Processing ,Computer-Assisted ,Databases ,Factual ,Pattern Recognition ,Automated ,Workflow ,Machine Learning ,Neural Networks ,Computer ,heart rate ,hypertension ,machine learning ,mitral valve prolapse ,work flow ,Diagnosis ,Computer-Assisted ,Signal Processing ,Databases ,Factual ,Pattern Recognition ,Automated ,Neural Networks ,Computer ,Cardiovascular System & Hematology ,Cardiorespiratory Medicine and Haematology ,Public Health and Health Services - Abstract
BackgroundThe ECG remains the most widely used diagnostic test for characterization of cardiac structure and electrical activity. We hypothesized that parallel advances in computing power, machine learning algorithms, and availability of large-scale data could substantially expand the clinical inferences derived from the ECG while at the same time preserving interpretability for medical decision-making.Methods and resultsWe identified 36 186 ECGs from the University of California, San Francisco database that would enable training of models for estimation of cardiac structure or function or detection of disease. We segmented the ECG into standard component waveforms and intervals using a novel combination of convolutional neural networks and hidden Markov models and evaluated this segmentation by comparing resulting electrical intervals against 141 864 measurements produced during the clinical workflow. We then built a patient-level ECG profile, a 725-element feature vector and used this profile to train and interpret machine learning models for examples of cardiac structure (left ventricular mass, left atrial volume, and mitral annulus e-prime) and disease (pulmonary arterial hypertension, hypertrophic cardiomyopathy, cardiac amyloid, and mitral valve prolapse). ECG measurements derived from the convolutional neural network-hidden Markov model segmentation agreed with clinical estimates, with median absolute deviations as a fraction of observed value of 0.6% for heart rate and 4% for QT interval. Models trained using patient-level ECG profiles enabled surprising quantitative estimates of left ventricular mass and mitral annulus e' velocity (median absolute deviation of 16% and 19%, respectively) with good discrimination for left ventricular hypertrophy and diastolic dysfunction as binary traits. Model performance using our approach for disease detection demonstrated areas under the receiver operating characteristic curve of 0.94 for pulmonary arterial hypertension, 0.91 for hypertrophic cardiomyopathy, 0.86 for cardiac amyloid, and 0.77 for mitral valve prolapse.ConclusionsModern machine learning methods can extend the 12-lead ECG to quantitative applications well beyond its current uses while preserving the transparency that is so fundamental to clinical care.
- Published
- 2019
40. Intravenous edaravone treatment in ALS and survival: An exploratory, retrospective, administrative claims analysis
- Author
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Brooks, Benjamin Rix, Berry, James D., Ciepielewska, Malgorzata, Liu, Ying, Zambrano, Gustavo Suarez, Zhang, Jeffrey, and Hagan, Melissa
- Published
- 2022
- Full Text
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41. Complexity aspects of local minima and related notions
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Ahmadi, Amir Ali and Zhang, Jeffrey
- Published
- 2022
- Full Text
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42. Semidefinite Programming and Nash Equilibria in Bimatrix Games
- Author
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Ahmadi, Amir Ali and Zhang, Jeffrey
- Subjects
Mathematics - Optimization and Control ,Computer Science - Data Structures and Algorithms ,Computer Science - Computer Science and Game Theory ,90C90 (Primary) 90C22, 91A5, 91A10 (Secondary) ,G.1.6 - Abstract
We explore the power of semidefinite programming (SDP) for finding additive $epsilon$-approximate Nash equilibria in bimatrix games. We introduce an SDP relaxation for a quadratic programming formulation of the Nash equilibrium (NE) problem and provide a number of valid inequalities to improve the quality of the relaxation. If a rank-1 solution to this SDP is found, then an exact NE can be recovered. We show that for a strictly competitive game, our SDP is guaranteed to return a rank-1 solution. We propose two algorithms based on iterative linearization of smooth nonconvex objective functions whose global minima by design coincide with rank-1 solutions. Empirically, we demonstrate that these algorithms often recover solutions of rank at most two and $epsilon$ close to zero. Furthermore, we prove that if a rank-2 solution to our SDP is found, then a 5/11-NE can be recovered for any game, or a 1/3-NE for a symmetric game. We then show how our SDP approach can address two (NP-hard) problems of economic interest: finding the maximum welfare achievable under any NE, and testing whether there exists a NE where a particular set of strategies is not played. Finally, we show the connection between our SDP and the first level of the Lasserre/sum of squares hierarchy., Comment: 38 pages
- Published
- 2017
43. A Computer Vision Pipeline for Automated Determination of Cardiac Structure and Function and Detection of Disease by Two-Dimensional Echocardiography
- Author
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Zhang, Jeffrey, Gajjala, Sravani, Agrawal, Pulkit, Tison, Geoffrey H., Hallock, Laura A., Beussink-Nelson, Lauren, Fan, Eugene, Aras, Mandar A., Jordan, ChaRandle, Fleischmann, Kirsten E., Melisko, Michelle, Qasim, Atif, Efros, Alexei, Shah, Sanjiv J., Bajcsy, Ruzena, and Deo, Rahul C.
- Subjects
Computer Science - Computer Vision and Pattern Recognition - Abstract
Automated cardiac image interpretation has the potential to transform clinical practice in multiple ways including enabling low-cost serial assessment of cardiac function in the primary care and rural setting. We hypothesized that advances in computer vision could enable building a fully automated, scalable analysis pipeline for echocardiogram (echo) interpretation. Our approach entailed: 1) preprocessing; 2) convolutional neural networks (CNN) for view identification, image segmentation, and phasing of the cardiac cycle; 3) quantification of chamber volumes and left ventricular mass; 4) particle tracking to compute longitudinal strain; and 5) targeted disease detection. CNNs accurately identified views (e.g. 99% for apical 4-chamber) and segmented individual cardiac chambers. Cardiac structure measurements agreed with study report values (e.g. mean absolute deviations (MAD) of 7.7 mL/kg/m2 for left ventricular diastolic volume index, 2918 studies). We computed automated ejection fraction and longitudinal strain measurements (within 2 cohorts), which agreed with commercial software-derived values [for ejection fraction, MAD=5.3%, N=3101 studies; for strain, MAD=1.5% (n=197) and 1.6% (n=110)], and demonstrated applicability to serial monitoring of breast cancer patients for trastuzumab cardiotoxicity. Overall, we found that, compared to manual measurements, automated measurements had superior performance across seven internal consistency metrics with an average increase in the Spearman correlation coefficient of 0.05 (p=0.02). Finally, we developed disease detection algorithms for hypertrophic cardiomyopathy and cardiac amyloidosis, with C-statistics of 0.93 and 0.84, respectively. Our pipeline lays the groundwork for using automated interpretation to support point-of-care handheld cardiac ultrasound and large-scale analysis of the millions of echos archived within healthcare systems., Comment: 9 figures, 2 tables
- Published
- 2017
44. Phase I/II study to assess the clinical pharmacology and safety of single ascending and multiple subcutaneous doses of PF-06881894 in women with non-distantly metastatic breast cancer
- Author
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Yao, Hsuan-Ming, Jones, Sarah Ruta, Morales, Serafin, Moosavi, Shahrzad, Zhang, Jeffrey, Freyman, Amy, and Ottery, Faith D.
- Published
- 2021
- Full Text
- View/download PDF
45. Fully Automated Echocardiogram Interpretation in Clinical Practice
- Author
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Zhang, Jeffrey, Gajjala, Sravani, Agrawal, Pulkit, Tison, Geoffrey H, Hallock, Laura A, Beussink-Nelson, Lauren, Lassen, Mats H, Fan, Eugene, Aras, Mandar A, Jordan, ChaRandle, Fleischmann, Kirsten E, Melisko, Michelle, Qasim, Atif, Shah, Sanjiv J, Bajcsy, Ruzena, and Deo, Rahul C
- Subjects
Heart Disease ,Cardiovascular ,Bioengineering ,Amyloidosis ,Automation ,Cardiomyopathy ,Hypertrophic ,Deep Learning ,Echocardiography ,Humans ,Hypertension ,Pulmonary ,Image Interpretation ,Computer-Assisted ,Predictive Value of Tests ,Reproducibility of Results ,Stroke Volume ,Ventricular Function ,Left ,diagnosis ,echocardiography ,machine learning ,Cardiorespiratory Medicine and Haematology ,Clinical Sciences ,Public Health and Health Services ,Cardiovascular System & Hematology - Abstract
BackgroundAutomated cardiac image interpretation has the potential to transform clinical practice in multiple ways, including enabling serial assessment of cardiac function by nonexperts in primary care and rural settings. We hypothesized that advances in computer vision could enable building a fully automated, scalable analysis pipeline for echocardiogram interpretation, including (1) view identification, (2) image segmentation, (3) quantification of structure and function, and (4) disease detection.MethodsUsing 14 035 echocardiograms spanning a 10-year period, we trained and evaluated convolutional neural network models for multiple tasks, including automated identification of 23 viewpoints and segmentation of cardiac chambers across 5 common views. The segmentation output was used to quantify chamber volumes and left ventricular mass, determine ejection fraction, and facilitate automated determination of longitudinal strain through speckle tracking. Results were evaluated through comparison to manual segmentation and measurements from 8666 echocardiograms obtained during the routine clinical workflow. Finally, we developed models to detect 3 diseases: hypertrophic cardiomyopathy, cardiac amyloid, and pulmonary arterial hypertension.ResultsConvolutional neural networks accurately identified views (eg, 96% for parasternal long axis), including flagging partially obscured cardiac chambers, and enabled the segmentation of individual cardiac chambers. The resulting cardiac structure measurements agreed with study report values (eg, median absolute deviations of 15% to 17% of observed values for left ventricular mass, left ventricular diastolic volume, and left atrial volume). In terms of function, we computed automated ejection fraction and longitudinal strain measurements (within 2 cohorts), which agreed with commercial software-derived values (for ejection fraction, median absolute deviation=9.7% of observed, N=6407 studies; for strain, median absolute deviation=7.5%, n=419, and 9.0%, n=110) and demonstrated applicability to serial monitoring of patients with breast cancer for trastuzumab cardiotoxicity. Overall, we found automated measurements to be comparable or superior to manual measurements across 11 internal consistency metrics (eg, the correlation of left atrial and ventricular volumes). Finally, we trained convolutional neural networks to detect hypertrophic cardiomyopathy, cardiac amyloidosis, and pulmonary arterial hypertension with C statistics of 0.93, 0.87, and 0.85, respectively.ConclusionsOur pipeline lays the groundwork for using automated interpretation to support serial patient tracking and scalable analysis of millions of echocardiograms archived within healthcare systems.
- Published
- 2018
46. Me-LLaMA: Foundation Large Language Models for Medical Applications
- Author
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Xie, Qianqian, primary, Chen, Qingyu, additional, Chen, Aokun, additional, Peng, Cheng, additional, Hu, Yan, additional, Lin, Fongci, additional, Peng, Xueqing, additional, Huang, Jimin, additional, Zhang, Jeffrey, additional, Keloth, Vipina, additional, Zhou, Xinyu, additional, He, Huan, additional, Ohno-Machado, Lucila, additional, Wu, Yonghui, additional, Xu, Hua, additional, and Bian, Jiang, additional
- Published
- 2024
- Full Text
- View/download PDF
47. How short peptides can disassemble ultra-stable tau fibrils extracted from Alzheimer’s disease brain by a strain-relief mechanism
- Author
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Eisenberg, David, primary, Hou, Ke, additional, Ge, Peng, additional, Sawaya, Michael, additional, Dolinsky, Joshua, additional, Yang, Yuan, additional, Jiang, Yi Xiao, additional, Lutter, Liisa, additional, Boyer, David, additional, Cheng, Xinyi, additional, Pi, Justin, additional, Zhang, Jeffrey, additional, Lu, Jiahui, additional, Yang, Shixin, additional, Yu, Zhiheng, additional, and Feigon, Juli, additional
- Published
- 2024
- Full Text
- View/download PDF
48. Corrigendum to “Proximal causal inference without uniqueness assumptions” [Statistics and Probability Letters 198 (2023) 1-8/109836]
- Author
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Zhang, Jeffrey, primary, Li, Wei, additional, Miao, Wang, additional, and Tchetgen, Eric Tchetgen, additional
- Published
- 2024
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49. Sensitivity analysis for matched observational studies with continuous exposures and binary outcomes
- Author
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Zhang, Jeffrey, primary, Small, Dylan S, additional, and Heng, Siyu, additional
- Published
- 2024
- Full Text
- View/download PDF
50. A Preliminary Analysis of Oral Edaravone-treated Patients with Amyotrophic Lateral Sclerosis Enrolled in a US-based Administrative Claims Database (S3.005)
- Author
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Ciepielewska, Malgorzata, primary, Zhang, Jeffrey, additional, Liu, Ying, additional, and Da Silva, Polina, additional
- Published
- 2024
- Full Text
- View/download PDF
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