Kelly Peterson

Eamonn Kennedy, Shashank Vadlamani, Hannah M Lindsey et al.

An extensive library of symptom inventories has been developed over time to measure clinical symptoms, but this variety has led to several long standing issues. Most notably, results drawn from different settings and studies are not comparable, which limits reproducibility. Here, we present an artificial intelligence (AI) approach using semantic textual similarity (STS) to link symptoms and scores across previously incongruous symptom inventories. We tested the ability of four pre-trained STS models to screen thousands of symptom description pairs for related content - a challenging task typically requiring expert panels. Models were tasked to predict symptom severity across four different inventories for 6,607 participants drawn from 16 international data sources. The STS approach achieved 74.8% accuracy across five tasks, outperforming other models tested. This work suggests that incorporating contextual, semantic information can assist expert decision-making processes, yielding gains for both general and disease-specific clinical assessment.

Hannah Eyre, Alec B Chapman, Kelly S Peterson et al.

Despite impressive success of machine learning algorithms in clinical natural language processing (cNLP), rule-based approaches still have a prominent role. In this paper, we introduce medspaCy, an extensible, open-source cNLP library based on spaCy framework that allows flexible integration of rule-based and machine learning-based algorithms adapted to clinical text. MedspaCy includes a variety of components that meet common cNLP needs such as context analysis and mapping to standard terminologies. By utilizing spaCy's clear and easy-to-use conventions, medspaCy enables development of custom pipelines that integrate easily with other spaCy-based modules. Our toolkit includes several core components and facilitates rapid development of pipelines for clinical text.

Ognjen Rudovic, Yuria Utsumi, Ricardo Guerrero et al.

We introduce a novel personalized Gaussian Process Experts (pGPE) model for predicting per-subject ADAS-Cog13 cognitive scores -- a significant predictor of Alzheimer's Disease (AD) in the cognitive domain -- over the future 6, 12, 18, and 24 months. We start by training a population-level model using multi-modal data from previously seen subjects using a base Gaussian Process (GP) regression. Then, we personalize this model by adapting the base GP sequentially over time to a new (target) subject using domain adaptive GPs, and also by training subject-specific GP. While we show that these models achieve improved performance when selectively applied to the forecasting task (one performs better than the other on different subjects/visits), the average performance per model is suboptimal. To this end, we used the notion of meta learning in the proposed pGPE to design a regression-based weighting of these expert models, where the expert weights are optimized for each subject and his/her future visit. The results on a cohort of subjects from the ADNI dataset show that this newly introduced personalized weighting of the expert models leads to large improvements in accurately forecasting future ADAS-Cog13 scores and their fine-grained changes associated with the AD progression. This approach has potential to help identify at-risk patients early and improve the construction of clinical trials for AD.

Yuria Utsumi, Ognjen Rudovic, Kelly Peterson et al.

In this paper, we introduce the use of a personalized Gaussian Process model (pGP) to predict per-patient changes in ADAS-Cog13 -- a significant predictor of Alzheimer's Disease (AD) in the cognitive domain -- using data from each patient's previous visits, and testing on future (held-out) data. We start by learning a population-level model using multi-modal data from previously seen patients using a base Gaussian Process (GP) regression. The personalized GP (pGP) is formed by adapting the base GP sequentially over time to a new (target) patient using domain adaptive GPs. We extend this personalized approach to predict the values of ADAS-Cog13 over the future 6, 12, 18, and 24 months. We compare this approach to a GP model trained only on past data of the target patients (tGP), as well as to a new approach that combines pGP with tGP. We find that the new approach, combining pGP with tGP, leads to large improvements in accurately forecasting future ADAS-Cog13 scores.

Kelly Peterson, Ognjen Rudovic, Ricardo Guerrero et al.

In this paper, we introduce the use of a personalized Gaussian Process model (pGP) to predict the key metrics of Alzheimer's Disease progression (MMSE, ADAS-Cog13, CDRSB and CS) based on each patient's previous visits. We start by learning a population-level model using multi-modal data from previously seen patients using the base Gaussian Process (GP) regression. Then, this model is adapted sequentially over time to a new patient using domain adaptive GPs to form the patient's pGP. We show that this new approach, together with an auto-regressive formulation, leads to significant improvements in forecasting future clinical status and cognitive scores for target patients when compared to modeling the population with traditional GPs.