Electronic health records and stratified psychiatry: bridge to precision treatment?

Development of an ML prediction model involves a multi-step process [11]. Briefly, labeled data are partitioned into training and test subsets. The data subsets undergo preprocessing to minimize the impact of dataset anomalies (e.g., missing values, outliers, redundant features) on the algorithm’s learning process. The algorithm is applied to the training data, learning the relationship between the features and predictive target. Performance is typically evaluated via cross-validation to estimate the model’s performance on new observations (internal validation). However, this only approximates a model’s ability to generalize to unseen data. Prediction models must demonstrate the ability to generalize to independent datasets (external validation) [12]. Ideally, external validation should occur in a separate study by a different analytic team [13]. Clinical validation involves assessing a model’s generalization to real world data as well as potential clinical utility and impact. Randomized cluster trials, for instance, evaluate groups of patients randomly assigned to receive care based on a model’s prediction versus care-as-usual.

Few examples exist of predictive ML models advancing to clinical validation in psychiatry, indicative of a sizeable translational gap. Delgadillo et al. compared the efficacy and cost of stratified care compared to stepped care for a psychological intervention for depression (n = 951 patients) in a cluster randomized trial [14]. The investigators previously developed a ML prediction model to classify patients as standard or complex cases using self-reported measures and sociodemographic information extracted from clinical records (n = 1512 patients) [15]. In the prospective trial, complex cases were matched to high-intensity treatment and standard cases to low-intensity treatment. Stratified care was associated with a 7% increase in the probability of improvement in depressive symptoms at a modest ~$140 increase in cost per patient [14].

Methodological flaws

What is driving this translational gap? Much of it may relate to challenges in generalizing models beyond their initial training data. There are no silver bullets in the development of ML prediction models and many potential pitfalls. The most common are overfitting and over-optimism due to insufficient training data, excess complexity improper (or lack of) cross-validation, and/or data leakage [16,17,18].

Most published ML studies in psychiatry suffer these methodological flaws [3,4,5]. Tornero-Costa et al. reviewed 153 ML applications in mental health and found only one study to be at low risk of bias by the Prediction model Risk Of Bias ASsessment Tool (PROBAST) criteria [3]. Approximately 37.3% of studies used a sample size of 150 or less to train models. Details on preprocessing were completely absent in 36.6% of studies and 47.7% lacked a description of data missingness. Only 13.7% of studies attempted external validation. Flaws in the analysis domain (e.g., attempts to control overfitting and optimism) contributed significantly to bias risk in most applications (90.8%). Furthermore, in 82.3% of the studies, data and developed model were not publicly accessible. Two other systematic reviews also found overall high risk of bias (>90%) among ML prediction studies, including poor reporting of preprocessing steps as well as low rates of internal and external validation [4, 5]. Meehan et al. additionally reported that only 22.7% of studies (of those meeting statistical standards) appropriately embedded feature selection within cross-validation to avoid data leakage [5].

The precise degree to which published ML prediction models overestimate their ability to generalize is difficult to estimate. In the area of prognosis prediction, Rosen et al. assessed 22 published prediction models of transition to psychosis in individuals at clinical high-risk [19]. Models were assessed for external validation from a multisite, naturalistic study. Only two models demonstrated “good” (AUC > = 0.7) performance and 9 models failed to achieve better than chance (AUC = 0.5) prediction. None of the models outperformed the clinician raters (AUC = 0.75) [19].

The model development process is vulnerable to human inductive biases, which can inflate model performance estimates due to unintentional errors or deliberate “gaming” for publication [17, 20]. Performance scores have become inappropriately prioritized in peer review due to erroneous higher = better assumptions. Most studies employ a single algorithm without justifying its selection or compare multiple algorithms’ performance on the same dataset, then select the best performing one (multiple testing issue) [17, 21]. Software packages like PyCaret (Python) offer the ability to “screen” the performance of a dozen or more algorithms on a dataset in a single step. This analytic flexibility creates risk, because even random data can be tuned to significance solely through manipulation of hyperparameters [17].

Low quality or biased training data

Methodological shortcomings offer only partial explanation for the observed translational gap. As the saying goes, “garbage in, garbage out.” Low quality, small, or biased training data can generate unreliable models with poor generalization to new observations or worse, make unfair predictions that adversely impact patients. Ideal ML training data is large, representative of the population of interest, complete (low missingness), balanced, and possesses accurate and consistent feature and predictive target labels or values (low noise). Per the systematic reviews above, these data quality criteria have been often neglected [3,4,5].

EHR data share many of the same quality issues impacting data collected explicitly for research, as well as some unique challenges that have deterred its use for ML in the past [22,23,24]. EHR data are highly heterogenous, encompassing both structured and unstructured elements. Structured data is collected through predefined fields (e.g., demographics, diagnoses, lab results, medications, sensor readings). Unstructured data is effectively everything else, including imaging and text. Extracting meaningful features from unstructured EHR data is non-trivial and often requires supervised and unsupervised ML techniques.

The quality of EHR data can vary by physician and clinical site. Quality challenges with EHR data that can adversely impact ML models for stratified psychiatry include:

Selection bias

EHR populations are non-random samples, which may create differences between the training data population and the target population [25]. Patients with more severe symptoms or treatment resistance may be frequently referred. Factors other than need for treatment (e.g., insurance status, referral, specialty clinics) can lead to systematic overrepresentation or underrepresentation of certain groups or disorders in the data. Marginalized populations, such as racial and ethnic minorities, for example, face barriers to accessing care and may be absent in the data [26]. When an algorithm trains on data that is not diverse, the certainty of the model’s predictions is questionable for unrepresented groups (high epistemic uncertainty) [27]. This may lead to unfair predictions (algorithmic bias) [28].


Missing data are common in EHRs. The impacts of missing data on model performance can be severe, especially when the data are missing not at random or missing at random but with a high proportion of missing values [29]. Furthermore, the frequency of records can vary substantially by patient. One individual may have multiple records in a period, others may have none [30]. Does absence of a diagnosis indicate true lack of a disorder or simply reflect that the patient received care elsewhere during a given interval? Structured self-reported patient outcome measures (e.g., psychometric measures) are often missing or incomplete [31].

Inaccurate features and targets

Feature and target labels or values provide the ground truth for learning. Inaccuracies and missingness generate noise, which can hinder effective learning. The lineage of a given data element is important in considering its reliability and validity. For example, a patient’s diagnoses may be extracted from clinical notes, encounter/billing data, or problem lists (often not dated or updated) [32]. In some cases, the evaluating practitioner enters the encounter-associated diagnostic codes; in other instances, these are abstracted by a medical billing agent, creating uncertainty.


Imaging and sensor-based data may be collected using different acquisition parameters and equipment, leading to variability in measurements across EHRs and over time [33]. Data may be collected using different coding systems (e.g., DSM, ICD), the criteria for which also change over time. These issues can hinder external validation as well as contribute to data drift with the potential for deterioration in model performance [34].

Imbalanced data

When data are imbalanced, ML classification models may be more likely to predict the majority class, resulting in a high accuracy but low sensitivity or specificity for the minority class [35]. The consequences of data imbalance can be severe, particularly when the minority class is the most clinically relevant (e.g., patients with suicidal ideation who go on to attempt, adverse drug reactions).

Temporal dynamics

Patient records represent a sequence of events over time [36]. Diagnostic clarification may create conflicts (e.g., depression later revealed to be bipolar disorder), depending on the forward and lookback windows used to create a dataset. Failure to appropriately account for the longitudinal nature of a patient’s clinical course can contribute to data leakage. Temporal data leakage occurs when future information is inadvertently used to make predictions for past events (e.g., including a future co-morbidity when predicting response to past treatment). Feature leakage occurs when variables expose information about the prediction target.

Empirical evidence indicates that preprocessing techniques can just as easily mitigate as exacerbate underlying data quality and bias issues. For example, missing data may be handled by complete case analysis (i.e., removal of observations with missing features) or imputation [37]. If data are not missing completely at random, deletion may eliminate key individuals [29]. Fernando et al. found that records containing missing data tended to be “fairer” than complete records and that their removal could contribute to algorithmic bias [38]. In the case of imputation, if the estimated values do not accurately represent the true underlying data, replacing “missing” values may inject error (e.g., imputing scores for psychometric scale items absent due to skip logic) and impact feature selection [39].

EHR data often require the creation of proxy features and outcomes to capture concepts (e.g., continuous prescription refills as an indicator of treatment effectiveness) or to reduce feature and label noise [40, 41]. No standards currently exist to guide such decisions or their reporting, creating high risk for bias. For example, if attempting to determine cannabis use when a patient was treated with a given antidepressant, one could check for a DSM/ICD diagnosis in their encounters or problem list, mine clinical notes to see whether use was endorsed/denied, or examine urine toxicology for positive/negative results. Each choice carries a different degree of uncertainty. Absence of evidence does not indicate evidence of absence [42], although studies often make that assumption.

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