1.1k citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Carnegie Mellon UniversityUS3 papers
- Eli Lilly (United States)US3 papers
- Harvard UniversityUS3 papers
- New Jersey Institute of TechnologyUS3 papers
- Pfizer (United States)US3 papers
- United States Military AcademyUS3 papers
- University of WashingtonUS3 papers
- Centre National de la Recherche ScientifiqueFR2 papers
- Duke UniversityUS2 papers
- Janssen Research & Development (United States)US2 papers
- Nektar Therapeutics (United States)US2 papers
- New York UniversityUS2 papers
34 papers
Can Foundational Large Language Models Assist with Conducting Pharmaceuticals Manufacturing Investigations?
Hossein Salami, Brandye Smith-Goettler, Vijay Yadav
General purpose Large Language Models (LLM) such as the Generative Pretrained Transformer (GPT) and Large Language Model Meta AI (LLaMA) have attracted much attention in recent yea…
MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision
Jianning Li, Zongwei Zhou, Jiancheng Yang +154
Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from co…
Explainability of Traditional and Deep Learning Models on Longitudinal Healthcare Records
Lin Lee Cheong, Tesfagabir Meharizghi, Wynona Black +2
Recent advances in deep learning have led to interest in training deep learning models on longitudinal healthcare records to predict a range of medical events, with models demonstr…
Using HCI in Cross-Disciplinary Teams: A Case Study of Academic Collaboration in HCI-Health Teams in the US Using a Team Science Perspective
Elena Agapie, Shefali Haldar, Sharmaine Galvez Poblete
Human-centered computing research has been increasingly applied to address important challenges in the health domain. Conducting research in cross-disciplinary teams can come with…
Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments
Laurent Gatto, Ruedi Aebersold, Juergen Cox +18
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of pro…
Exact Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of Multimodality
Anna Terebus, Farid Manuchehrfar, Youfang Cao +1
Feed-forward loops (FFLs) are among the most ubiquitously found motifs of reaction networks in nature. However, little is known about their stochastic behavior and the variety of n…
Olympus: a benchmarking framework for noisy optimization and experiment planning
Florian Häse, Matteo Aldeghi, Riley J. Hickman +5
Research challenges encountered across science, engineering, and economics can frequently be formulated as optimization tasks. In chemistry and materials science, recent growth in…
Principal Stratum Strategy: Potential Role in Drug Development
Björn Bornkamp, Kaspar Rufibach, Jianchang Lin +6
A randomized trial allows estimation of the causal effect of an intervention compared to a control in the overall population and in subpopulations defined by baseline characteristi…
Assessing the Impact of COVID-19 on the Objective and Analysis of Oncology Clinical Trials -- Application of the Estimand Framework
Evgeny Degtyarev, Kaspar Rufibach, Yue Shentu +10
COVID-19 outbreak has rapidly evolved into a global pandemic. The impact of COVID-19 on patient journeys in oncology represents a new risk to interpretation of trial results and it…
Clinical Trial Drug Safety Assessment for Studies and Submissions Impacted by COVID-19
Mary Nilsson, Brenda Crowe, Greg Anglin +4
In this paper, we provide guidance on how standard safety analyses and reporting of clinical trial safety data may need to be modified, given the potential impact of the COVID-19 p…
Decision Making in Drug Development via Inference on Power
Geoffrey S Johnson
A typical power calculation is performed by replacing unknown population-level quantities in the power function with what is observed in external studies. Many authors and practiti…
Group Equivariant Generative Adversarial Networks
Neel Dey, Antong Chen, Soheil Ghafurian
Recent improvements in generative adversarial visual synthesis incorporate real and fake image transformation in a self-supervised setting, leading to increased stability and perce…
An efficient and accurate approximation to the distribution of quadratic forms of Gaussian variables
Hong Zhang, Judong Shen, Zheyang Wu
In computational and applied statistics, it is of great interest to get fast and accurate calculation for the distributions of the quadratic forms of Gaussian random variables. Thi…
Multiplicity for a Group Sequential Trial with Biomarker Subpopulations
Ting-Yu Chen, Jing Zhao, Linda Sun +1
Biomarker subpopulations have become increasingly important for drug development in targeted therapies. The use of biomarkers has the potential to facilitate more effective outcome…
A deep learning-facilitated radiomics solution for the prediction of lung lesion shrinkage in non-small cell lung cancer trials
Antong Chen, Jennifer Saouaf, Bo Zhou +6
Herein we propose a deep learning-based approach for the prediction of lung lesion response based on radiomic features extracted from clinical CT scans of patients in non-small cel…
The Reciprocal Bayesian LASSO
Himel Mallick, Rahim Alhamzawi, Erina Paul +1
A reciprocal LASSO (rLASSO) regularization employs a decreasing penalty function as opposed to conventional penalization approaches that use increasing penalties on the coefficient…
Sheared Amorphous Packings Display Two Separate Particle Transport Mechanisms
Dong Wang, Joshua A. Dijksman, Jonathan Bares +2
Shearing granular materials induces non-affine displacements. Such non-affine displacements have been studied extensively, and are known to correlate with plasticity and other mech…
Alternative Analysis Methods for Time to Event Endpoints under Non-proportional Hazards: A Comparative Analysis
Ray S. Lin, Ji Lin, Satrajit Roychoudhury +16
The log-rank test is most powerful under proportional hazards (PH). In practice, non-PH patterns are often observed in clinical trials, such as in immuno-oncology; therefore, alter…
Somatic mutations render human exome and pathogen DNA more similar
Ehsan Ebrahimzadeh, Maggie Engler, David Tse +2
Immunotherapy has recently shown important clinical successes in a substantial number of oncology indications. Additionally, the tumor somatic mutation load has been shown to assoc…
A multi-level convolutional LSTM model for the segmentation of left ventricle myocardium in infarcted porcine cine MR images
Dongqing Zhang, Ilknur Icke, Belma Dogdas +6
Automatic segmentation of left ventricle (LV) myocardium in cardiac short-axis cine MR images acquired on subjects with myocardial infarction is a challenging task, mainly because…
A Progressively-trained Scale-invariant and Boundary-aware Deep Neural Network for the Automatic 3D Segmentation of Lung Lesions
Bo Zhou, Randolph Crawford, Belma Dogdas +2
Volumetric segmentation of lesions on CT scans is important for many types of analysis, including lesion growth kinetic modeling in clinical trials and machine learning of radiomic…
Algebraic tests of general Gaussian latent tree models
Dennis Leung, Mathias Drton
We consider general Gaussian latent tree models in which the observed variables are not restricted to be leaves of the tree. Extending related recent work, we give a full semi-alge…
Probability-Scale Residuals in HIV/AIDS Research: Diagnostics and Inference
Bryan E. Shepherd, Qi Liu, Valentine Wanga +1
The probability-scale residual (PSR) is well defined across a wide variety of variable types and models, making it useful for studies of HIV/AIDS. In this manuscript, we highlight…
Characterizing Granular Networks Using Topological Metrics
Joshua A. Dijksman, Lenka Kovalcinova, Jie Ren +4
We carry out a direct comparison of experimental and numerical realizations of the exact same granular system as it undergoes shear jamming. We adjust the numerical methods used to…