Models, code, and papers for "Albee Y":

A Semi-Supervised Machine Learning Approach to Detecting Recurrent Metastatic Breast Cancer Cases Using Linked Cancer Registry and Electronic Medical Record Data

Jan 17, 2019
Albee Y. Ling, Allison W. Kurian, Jennifer L. Caswell-Jin, George W. Sledge Jr., Nigam H. Shah, Suzanne R. Tamang

Objectives: Most cancer data sources lack information on metastatic recurrence. Electronic medical records (EMRs) and population-based cancer registries contain complementary information on cancer treatment and outcomes, yet are rarely used synergistically. To enable detection of metastatic breast cancer (MBC), we applied a semi-supervised machine learning framework to linked EMR-California Cancer Registry (CCR) data. Materials and Methods: We studied 11,459 female patients treated at Stanford Health Care who received an incident breast cancer diagnosis from 2000-2014. The dataset consisted of structured data and unstructured free-text clinical notes from EMR, linked to CCR, a component of the Surveillance, Epidemiology and End Results (SEER) database. We extracted information on metastatic disease from patient notes to infer a class label and then trained a regularized logistic regression model for MBC classification. We evaluated model performance on a gold standard set of set of 146 patients. Results: There are 495 patients with de novo stage IV MBC, 1,374 patients initially diagnosed with Stage 0-III disease had recurrent MBC, and 9,590 had no evidence of metastatis. The median follow-up time is 96.3 months (mean 97.8, standard deviation 46.7). The best-performing model incorporated both EMR and CCR features. The area under the receiver-operating characteristic curve=0.925 [95% confidence interval: 0.880-0.969], sensitivity=0.861, specificity=0.878 and overall accuracy=0.870. Discussion and Conclusion: A framework for MBC case detection combining EMR and CCR data achieved good sensitivity, specificity and discrimination without requiring expert-labeled examples. This approach enables population-based research on how patients die from cancer and may identify novel predictors of cancer recurrence.

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Combining Parameter Identification and Trajectory Optimization: Real-time Planning for Information Gain

Jun 06, 2019
Keenan Albee, Monica Ekal, Rodrigo Ventura, Richard Linares

Robotic systems often operate with uncertainties in their dynamics, for example, unknown inertial properties. Broadly, there are two approaches for controlling uncertain systems: design robust controllers in spite of uncertainty, or characterize a system before attempting to control it. This paper proposes a middle-ground approach, making trajectory progress while also accounting for gaining information about the system. More specifically, it combines excitation trajectories which are usually intended to optimize information gain for an estimator, with goal-driven trajectory optimization metrics. For this purpose, a measure of information gain is incorporated (using the Fisher Information Matrix) in a real-time planning framework to produce trajectories favorable for estimation. At the same time, the planner receives stable parameter updates from the estimator, enhancing the system model. An implementation of this learn-as-you-go approach utilizing an Unscented Kalman Filter (UKF) and Nonlinear Model Predictive Controller (NMPC) is demonstrated in simulation. Results for cases with and without information gain and online parameter updates in the system model are presented.

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