Christopher R. King

Dingwen Li, Bing Xue, Christopher King et al.

Major postoperative complications are devastating to surgical patients. Some of these complications are potentially preventable via early predictions based on intraoperative data. However, intraoperative data comprise long and fine-grained multivariate time series, prohibiting the effective learning of accurate models. The large gaps associated with clinical events and protocols are usually ignored. Moreover, deep models generally lack transparency. Nevertheless, the interpretability is crucial to assist clinicians in planning for and delivering postoperative care and timely interventions. Towards this end, we propose a hierarchical model combining the strength of both attention and recurrent models for intraoperative time series. We further develop an explanation module for the hierarchical model to interpret the predictions by providing contributions of intraoperative data in a fine-grained manner. Experiments on a large dataset of 111,888 surgeries with multiple outcomes and an external high-resolution ICU dataset show that our model can achieve strong predictive performance (i.e., high accuracy) and offer robust interpretations (i.e., high transparency) for predicted outcomes based on intraoperative time series.

Sandhya Tripathi, Bradley A. Fritz, Mohamed Abdelhack et al.

An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable algorithms, especially in health care. We approach this issue in the common but difficult case of numeric features such as nearly Gaussian and binary features, where unit changes and variable shift make simple matching of univariate summaries unsuccessful. We develop two novel procedures to address this problem. First, we demonstrate multiple methods of "fingerprinting" a feature based on its associations to other features. In the setting of even modest prior information, this allows most shared features to be accurately identified. Second, we demonstrate a deep learning algorithm for translation between databases. Unlike prior approaches, our algorithm takes advantage of discovered mappings while identifying surrogates for unshared features and learning transformations. In synthetic and real-world experiments using two electronic health record databases, our algorithms outperform existing baselines for matching variable sets, while jointly learning to impute unshared or transformed variables.

Sandhya Tripathi, Bradley A Fritz, Michael S Avidan et al.

Although prediction models for delirium, a commonly occurring condition during general hospitalization or post-surgery, have not gained huge popularity, their algorithmic bias evaluation is crucial due to the existing association between social determinants of health and delirium risk. In this context, using MIMIC-III and another academic hospital dataset, we present some initial experimental evidence showing how sociodemographic features such as sex and race can impact the model performance across subgroups. With this work, our intent is to initiate a discussion about the intersectionality effects of old age, race and socioeconomic factors on the early-stage detection and prevention of delirium using ML.

Hao Liu, Muhan Zhang, Zehao Dong et al.

Rich Electronic Health Records (EHR), have created opportunities to improve clinical processes using machine learning methods. Prediction of the same patient events at different time horizons can have very different applications and interpretations; however, limited number of events in each potential time window hurts the effectiveness of conventional machine learning algorithms. We propose a novel time associated meta learning (TAML) method to make effective predictions at multiple future time points. We view time-associated disease prediction as classification tasks at multiple time points. Such closely-related classification tasks are an excellent candidate for model-based meta learning. To address the sparsity problem after task splitting, TAML employs a temporal information sharing strategy to augment the number of positive samples and include the prediction of related phenotypes or events in the meta-training phase. We demonstrate the effectiveness of TAML on multiple clinical datasets, where it consistently outperforms a range of strong baselines. We also develop a MetaEHR package for implementing both time-associated and time-independent few-shot prediction on EHR data.

Lecheng Kong, Christopher King, Bradley Fritz et al.

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good performance, but is often not as available as clinical text in real-world scenarios. We propose a \textbf{multi-view learning framework} that jointly learns from codes and text to combine the availability and forward-looking nature of text and better performance of ICD codes. The learned text embeddings can be used as inputs to predictive algorithms independent of the ICD codes during inference. Our approach uses a Graph Neural Network (GNN) to process ICD codes, and Bi-LSTM to process text. We apply Deep Canonical Correlation Analysis (DCCA) to enforce the two views to learn a similar representation of each patient. In experiments using planned surgical procedure text, our model outperforms BERT models fine-tuned to clinical data, and in experiments using diverse text in MIMIC-III, our model is competitive to a fine-tuned BERT at a tiny fraction of its computational effort.

Ronak Dedhiya, Siva Teja Kakileti, Goutham Deepu et al.

Onchocerciasis is causing blindness in over half a million people in the world today. Drug development for the disease is crippled as there is no way of measuring effectiveness of the drug without an invasive procedure. Drug efficacy measurement through assessment of viability of onchocerca worms requires the patients to undergo nodulectomy which is invasive, expensive, time-consuming, skill-dependent, infrastructure dependent and lengthy process. In this paper, we discuss the first-ever study that proposes use of machine learning over thermal imaging to non-invasively and accurately predict the viability of worms. The key contributions of the paper are (i) a unique thermal imaging protocol along with pre-processing steps such as alignment, registration and segmentation to extract interpretable features (ii) extraction of relevant semantic features (iii) development of accurate classifiers for detecting the existence of viable worms in a nodule. When tested on a prospective test data of 30 participants with 48 palpable nodules, we achieved an Area Under the Curve (AUC) of 0.85.

Mohamed Abdelhack, Jiaming Zhang, Sandhya Tripathi et al.

Data missingness and quality are common problems in machine learning, especially for high-stakes applications such as healthcare. Developers often train machine learning models on carefully curated datasets using only high quality data; however, this reduces the utility of such models in production environments. We propose a novel neural network modification to mitigate the impacts of low quality and missing data which involves replacing the fixed weights of a fully-connected layer with a function of an additional input. This is inspired from neuromodulation in biological neural networks where the cortex can up- and down-regulate inputs based on their reliability and the presence of other data. In testing, with reliability scores as a modulating signal, models with modulating layers were found to be more robust against degradation of data quality, including additional missingness. These models are superior to imputation as they save on training time by completely skipping the imputation process and further allow the introduction of other data quality measures that imputation cannot handle. Our results suggest that explicitly accounting for reduced information quality with a modulating fully connected layer can enable the deployment of artificial intelligence systems in real-time applications.

Jonathan P. Epperlein, Roman Overko, Sergiy Zhuk et al.

Reinforcement learning (RL) algorithms aim to learn optimal decisions in unknown environments through experience of taking actions and observing the rewards gained. In some cases, the environment is not influenced by the actions of the RL agent, in which case the problem can be modeled as a contextual multi-armed bandit and lightweight myopic algorithms can be employed. On the other hand, when the RL agent's actions affect the environment, the problem must be modeled as a Markov decision process and more complex RL algorithms are required which take the future effects of actions into account. Moreover, in practice, it is often unknown from the outset whether or not the agent's actions will impact the environment and it is therefore not possible to determine which RL algorithm is most fitting. In this work, we propose to avoid this difficult decision entirely and incorporate a choice mechanism into our RL framework. Rather than assuming a specific problem structure, we use a probabilistic structure estimation procedure based on a likelihood-ratio (LR) test to make a more informed selection of learning algorithm. We derive a sufficient condition under which myopic policies are optimal, present an LR test for this condition, and derive a bound on the regret of our framework. We provide examples of real-world scenarios where our framework is needed and provide extensive simulations to validate our approach.

Sandhya Tripathi, Bradley A. Fritz, Mohamed Abdelhack et al.

With the current ongoing debate about fairness, explainability and transparency of machine learning models, their application in high-impact clinical decision-making systems must be scrutinized. We consider a real-life example of risk estimation before surgery and investigate the potential for bias or unfairness of a variety of algorithms. Our approach creates transparent documentation of potential bias so that the users can apply the model carefully. We augment a model-card like analysis using propensity scores with a decision-tree based guide for clinicians that would identify predictable shortcomings of the model. In addition to functioning as a guide for users, we propose that it can guide the algorithm development and informatics team to focus on data sources and structures that can address these shortcomings.

Zhicheng Cui, Bradley A Fritz, Christopher R King et al.

Logistic regression (LR) is widely used in clinical prediction because it is simple to deploy and easy to interpret. Nevertheless, being a linear model, LR has limited expressive capability and often has unsatisfactory performance. Generalized additive models (GAMs) extend the linear model with transformations of input features, though feature interaction is not allowed for all GAM variants. In this paper, we propose a factored generalized additive model (F-GAM) to preserve the model interpretability for targeted features while allowing a rich model for interaction with features fixed within the individual. We evaluate F-GAM on prediction of two targets, postoperative acute kidney injury and acute respiratory failure, from a single-center database. We find superior model performance of F-GAM in terms of AUPRC and AUROC compared to several other GAM implementations, random forests, support vector machine, and a deep neural network. We find that the model interpretability is good with results with high face validity.