Dialysis Patients' Social Networks and Living Donation Offers.

Rationale & Objective: Most living kidney donors are members of a hemodialysis patient's social network. Network members are divided into core members, those strongly connected to the patient and other members; and peripheral members, those weakly connected to the patient and other members. We identify how many hemodialysis patients' network members offered to become kidney donors, whether these offers were from core or peripheral network members, and whose offers the patients accepted. Study Design: A cross-sectional interviewer-administered hemodialysis patient social network survey. Setting & Participants: Prevalent hemodialysis patients in 2 facilities. Predictors: Network size and constraint, a donation from a peripheral network member. Outcomes: Number of living donor offers, accepting an offer. Analytical Approach: We performed egocentric network analyses for all participants. Poisson regression models evaluated associations between network measures and number of offers. Logistic regression models determined the associations between network factors and accepting a donation offer. Results: The mean age of the 106 participants was 60 years. Forty-five percent were female, and 75% self-identified as Black. Fifty-two percent of participants received at least one living donor offer (range 1-6); 42% of the offers were from peripheral members. Participants with larger networks received more offers (incident rate ratio [IRR], 1.26; 95% CI, 1.12-1.42; P = 0.001), including networks with more peripheral members (constraint, IRR, 0.97; 95% CI, 0.96-0.98; P < 0.001). Participants who received a peripheral member offer had 3.6 times greater odds of accepting an offer (OR, 3.56; 95% CI, 1.15-10.8; P = 0.02) than those who did not receive a peripheral member offer. Limitations: A small sample of only hemodialysis patients. Conclusions: Most participants received at least one living donor offer, often from peripheral network members. Future living donor interventions should focus on both core and peripheral network members.

The company we keep. Using hemodialysis social network data to classify patients' kidney transplant attitudes with machine learning algorithms.

BACKGROUND: Hemodialysis clinic patient social networks may reinforce positive and negative attitudes towards kidney transplantation. We examined whether a patient's position within the hemodialysis clinic social network could improve machine learning classification of the patient's positive or negative attitude towards kidney transplantation when compared to sociodemographic and clinical variables. METHODS: We conducted a cross-sectional social network survey of hemodialysis patients in two geographically and demographically different hemodialysis clinics. We evaluated whether machine learning logistic regression models using sociodemographic or network data best predicted the participant's transplant attitude. Models were evaluated for accuracy, precision, recall, and F1-score. RESULTS: The 110 surveyed participants' mean age was 60 ± 13 years old. Half (55%) identified as male, and 74% identified as Black. At facility 1, 69% of participants had a positive attitude towards transplantation whereas at facility 2, 45% of participants had a positive attitude. The machine learning logistic regression model using network data alone obtained a higher accuracy and F1 score than the sociodemographic and clinical data model (accuracy 65% ± 5% vs. 61% ± 7%, F1 score 76% ± 2% vs. 70% ± 7%). A model with a combination of both sociodemographic and network data had a higher accuracy of 74% ± 3%, and an F1-score of 81% ± 2%. CONCLUSION: Social network data improved the machine learning algorithm's ability to classify attitudes towards kidney transplantation, further emphasizing the importance of hemodialysis clinic social networks on attitudes towards transplant.

Optimizing clinical trials recruitment via deep learning.

OBJECTIVE: Clinical trials, prospective research studies on human participants carried out by a distributed team of clinical investigators, play a crucial role in the development of new treatments in health care. This is a complex and expensive process where investigators aim to enroll volunteers with predetermined characteristics, administer treatment(s), and collect safety and efficacy data. Therefore, choosing top-enrolling investigators is essential for efficient clinical trial execution and is 1 of the primary drivers of drug development cost. MATERIALS AND METHODS: To facilitate clinical trials optimization, we propose DeepMatch (DM), a novel approach that builds on top of advances in deep learning. DM is designed to learn from both investigator and trial-related heterogeneous data sources and rank investigators based on their expected enrollment performance on new clinical trials. RESULTS: Large-scale evaluation conducted on 2618 studies provides evidence that the proposed ranking-based framework improves the current state-of-the-art by up to 19% on ranking investigators and up to 10% on detecting top/bottom performers when recruiting investigators for new clinical trials. DISCUSSION: The extensive experimental section suggests that DM can provide substantial improvement over current industry standards in several regards: (1) the enrollment potential of the investigator list, (2) the time it takes to generate the list, and (3) data-informed decisions about new investigators. CONCLUSION: Due to the great significance of the problem at hand, related research efforts are set to shift the paradigm of how investigators are chosen for clinical trials, thereby optimizing and automating them and reducing the cost of new therapies.

Modeling Healthcare Quality via Compact Representations of Electronic Health Records.

Increased availability of Electronic Health Record (EHR) data provides unique opportunities for improving the quality of health services. In this study, we couple EHRs with the advanced machine learning tools to predict three important parameters of healthcare quality. More specifically, we describe how to learn low-dimensional vector representations of patient conditions and clinical procedures in an unsupervised manner, and generate feature vectors of hospitalized patients useful for predicting their length of stay, total incurred charges, and mortality rates. In order to learn vector representations, we propose to employ state-of-the-art language models specifically designed for modeling co-occurrence of diseases and applied clinical procedures. The proposed model is trained on a large-scale EHR database comprising more than 35 million hospitalizations in California over a period of nine years. We compared the proposed approach to several alternatives and evaluated their effectiveness by measuring accuracy of regression and classification models used for three predictive tasks considered in this study. Our model outperformed the baseline models on all tasks, indicating a strong potential of the proposed approach for advancing quality of the healthcare system.

Patient-specific early classification of multivariate observations.

Early classification of time series has been receiving a lot of attention recently. In this paper we present a model, which we call the Early Classification Model (ECM), that allows for early, accurate and patient-specific classification of multivariate observations. ECM is comprised of an integration of the widely used Hidden Markov Model (HMM) and Support Vector Machine (SVM) models. It attained very promising results on the datasets we tested it on: in one set of experiments based on a published dataset of response to drug therapy in Multiple Sclerosis patients, ECM used only an average of 40% of a time series and was able to outperform some of the baseline models, which needed the full time series for classification. In the set of experiments tested on a sepsis therapy dataset, ECM was able to surpass the standard threshold-based method and the state-of-the-art method for early classification of multivariate time series.

Casting a Wider Net: Data Driven Discovery of Proxies for Target Diagnoses.

BACKGROUND: The Hospital Readmissions Reduction Program (HRRP) introduced in October 2012 as part of the Affordable Care Act (ACA), ties hospital reimbursement rates to adjusted 30-day readmissions and mortality performance for a small set of target diagnoses. There is growing concern and emerging evidence that use of a small set of target diagnoses to establish reimbursement rates can lead to unstable results that are susceptible to manipulation (gaming) by hospitals. METHODS: We propose a novel approach to identifying co-occurring diagnoses and procedures that can themselves serve as a proxy indicator of the target diagnosis. The proposed approach constructs a Markov Blanket that allows a high level of performance, in terms of predictive accuracy and scalability, along with interpretability of obtained results. In order to scale to a large number of co-occuring diagnoses (features) and hospital discharge records (samples), our approach begins with Google's PageRank algorithm and exploits the stability of obtained results to rank the contribution of each diagnosis/procedure in terms of presence in a Markov Blanket for outcome prediction. RESULTS: Presence of target diagnoses acute myocardial infarction (AMI), congestive heart failure (CHF), pneumonia (PN), and Sepsis in hospital discharge records for Medicare and Medicaid patients in California and New York state hospitals (2009-2011), were predicted using models trained on a subset of California state hospitals (2003-2008). Using repeated holdout evaluation, we used ~30,000,000 hospital discharge records and analyzed the stability of the proposed approach. Model performance was measured using the Area Under the ROC Curve (AUC) metric, and importance and contribution of single features to the final result. The results varied from AUC=0.68 (with SE<1e-4) for PN on cross validation datasets to AUC=0.94, with (SE<1e-7) for Sepsis on California hospitals (2009 - 2011), while the stability of features was consistently better with more training data for each target diagnosis. Prediction accuracy for considered target diagnoses approaches or exceeds accuracy estimates for discharge record data. CONCLUSIONS: This paper presents a novel approach to identifying a small subset of relevant diagnoses and procedures that approximate the Markov Blanket for target diagnoses. Accuracy and interpretability of results demonstrate the potential of our approach.

Improving sequence alignments for intrinsically disordered proteins.

Here we analyze sequence alignments for intrinsically disordered proteins. For 55 disordered protein families we measure the performance of different scoring matrices and propose one adjusted to disordered regions. An iterative algorithm of realigning sequences and recalculating matrices is designed and tested. For each matrix we also test a wide range of gap penalties. Results show an improvement in the ability to detect and discriminate related disordered proteins whose average sequence identity with the other family members is below 50%.