Towards realizing the vision of precision medicine: AI based prediction of clinical drug response.

Accurate and individualized prediction of response to therapies is central to precision medicine. However, because of the generally complex and multifaceted nature of clinical drug response, realizing this vision is highly challenging, requiring integrating different data types from the same individual into one prediction model. We used the anti-epileptic drug brivaracetam as a case study and combine a hybrid data/knowledge-driven feature extraction with machine learning to systematically integrate clinical and genetic data from a clinical discovery dataset (n = 235 patients). We constructed a model that successfully predicts clinical drug response [area under the curve (AUC) = 0.76] and show that even with limited sample size, integrating high-dimensional genetics data with clinical data can inform drug response prediction. After further validation on data collected from an independently conducted clinical study (AUC = 0.75), we extensively explore our model to gain insights into the determinants of drug response, and identify various clinical and genetic characteristics predisposing to poor response. Finally, we assess the potential impact of our model on clinical trial design and demonstrate that, by enriching for probable responders, significant reductions in clinical study sizes may be achieved. To our knowledge, our model represents the first retrospectively validated machine learning model linking drug mechanism of action and the genetic, clinical and demographic background in epilepsy patients to clinical drug response. Hence, it provides a blueprint for how machine learning-based multimodal data integration can act as a driver in achieving the goals of precision medicine in fields such as neurology.

Predicting drug-resistant epilepsy - A machine learning approach based on administrative claims data.

Patients with drug-resistant epilepsy (DRE) are at high risk of morbidity and mortality, yet their referral to specialist care is frequently delayed. The ability to identify patients at high risk of DRE at the time of treatment initiation, and to subsequently steer their treatment pathway toward more personalized interventions, has high clinical utility. Here, we aim to demonstrate the feasibility of developing algorithms for predicting DRE using machine learning methods. Longitudinal, intersected data sourced from US pharmacy, medical, and adjudicated hospital claims from 1,376,756 patients from 2006 to 2015 were analyzed; 292,892 met inclusion criteria for epilepsy, and 38,382 were classified as having DRE using a proxy measure for drug resistance. Patients were characterized using 1270 features reflecting demographics, comorbidities, medications, procedures, epilepsy status, and payer status. Data from 175,735 randomly selected patients were used to train three algorithms and from the remainder to assess the trained models' predictive power. A model with only age and sex was used as a benchmark. The best model, random forest, achieved an area under the receiver operating characteristic curve (95% confidence interval [CI]) of 0.764 (0.759, 0.770), compared with 0.657 (0.651, 0.663) for the benchmark model. Moreover, predicted probabilities for DRE were well-calibrated with the observed frequencies in the data. The model predicted drug resistance approximately 2 years before patients in the test dataset had failed two antiepileptic drugs (AEDs). Machine learning models constructed using claims data predicted which patients are likely to fail ≥3 AEDs and are at risk of developing DRE at the time of the first AED prescription. The use of such models can ensure that patients with predicted DRE receive specialist care with potentially more aggressive therapeutic interventions from diagnosis, to help reduce the serious sequelae of DRE.

Changing the approach to treatment choice in epilepsy using big data.

PURPOSE: A UCB-IBM collaboration explored the application of machine learning to large claims databases to construct an algorithm for antiepileptic drug (AED) choice for individual patients. METHODS: Claims data were collected between January 2006 and September 2011 for patients with epilepsy > 16 years of age. A subset of patient claims with a valid index date of AED treatment change (new, add, or switch) were used to train the AED prediction model by retrospectively evaluating an index date treatment for subsequent treatment change. Based on the trained model, a model-predicted AED regimen with the lowest likelihood of treatment change was assigned to each patient in the group of test claims, and outcomes were evaluated to test model validity. RESULTS: The model had 72% area under receiver operator characteristic curve, indicating good predictive power. Patients who were given the model-predicted AED regimen had significantly longer survival rates (time until a treatment change event) and lower expected health resource utilization on average than those who received another treatment. The actual prescribed AED regimen at the index date matched the model-predicted AED regimen in only 13% of cases; there were large discrepancies in the frequency of use of certain AEDs/combinations between model-predicted AED regimens and those actually prescribed. CONCLUSIONS: Chances of treatment success were improved if patients received the model-predicted treatment. Using the model's prediction system may enable personalized, evidence-based epilepsy care, accelerating the match between patients and their ideal therapy, thereby delivering significantly better health outcomes for patients and providing health-care savings by applying resources more efficiently. Our goal will be to strengthen the predictive power of the model by integrating diverse data sets and potentially moving to prospective data collection.

Newer antiepileptic drug use and other factors decreasing hospital encounters.

A retrospective analysis was conducted in one claims database and was confirmed in a second independent database (covering both commercial and government insurance plans between 11/2009 and 9/2011) for the understanding of factors influencing antiepileptic drug (AED) use and the role of AEDs and other health-care factors in hospital encounters. In both datasets, epilepsy cases were identified by AED use and epilepsy diagnosis coding. Variables analyzed for effect on hospitalization rates were as follows: (1) use of first-generation AEDs or second-generation AEDs, (2) treatment changes, and (3) factors that may affect AED choice. Lower rates of epilepsy-related hospital encounters (encounters with an epilepsy diagnosis code) were associated with use of second-generation AEDs, deliberate treatment changes, and treatment by a neurologist. Epilepsy-related hospital encounters were more frequent for patients not receiving an AED and for those with greater comorbidities. On average, patients taking ≥1 first-generation AED experienced epilepsy-related hospitalizations every 684days, while those taking ≥1second-generation AED were hospitalized every 1001days (relative risk reduction of 31%, p<0.01). Prescriptions for second-generation AEDs were more common among neurologists and among physicians near an epilepsy center. Use of second-generation AEDs, access to specialty care, and deliberate efforts to change medications following epilepsy-related hospital encounters improved outcomes of epilepsy treatment based on average time between epilepsy-related hospital encounters. These factors may be enhanced by public health policies, private insurance reimbursement policies, and education of patients and physicians.