Matthew J. McDermott

Matthew McDermott, Anand Dighe, Peter Szolovits et al. · harvard

Objective: Reflex testing protocols allow clinical laboratories to perform second line diagnostic tests on existing specimens based on the results of initially ordered tests. Reflex testing can support optimal clinical laboratory test ordering and diagnosis. In current clinical practice, reflex testing typically relies on simple "if-then" rules; however, this limits their scope since most test ordering decisions involve more complexity than a simple rule will allow. Here, using the analyte ferritin as an example, we propose an alternative machine learning-based approach to "smart" reflex testing with a wider scope and greater impact than traditional rule-based approaches. Methods: Using patient data, we developed a machine learning model to predict whether a patient getting CBC testing will also have ferritin testing ordered, consider applications of this model to "smart" reflex testing, and evaluate the model by comparing its performance to possible rule-based approaches. Results: Our underlying machine learning models performed moderately well in predicting ferritin test ordering and demonstrated greater suitability to reflex testing than rule-based approaches. Using chart review, we demonstrate that our model may improve ferritin test ordering. Finally, as a secondary goal, we demonstrate that ferritin test results are missing not at random (MNAR), a finding with implications for unbiased imputation of missing test results. Conclusions: Machine learning may provide a foundation for new types of reflex testing with enhanced benefits for clinical diagnosis and laboratory utilization management.

Matthew McDermott, Jason Rife

Distribution-to-distribution (D2D) point cloud registration techniques such as the Normal Distributions Transform (NDT) can align point clouds sampled from unstructured scenes and provide accurate bounds of their own solution error covariance -- an important feature for safety-of-life navigation tasks. D2D methods rely on the assumption of a static scene and are therefore susceptible to bias from range-shadowing, self-occlusion, moving objects, and distortion artifacts as the recording device moves between frames. Deep Learning-based approaches can achieve higher accuracy in dynamic scenes by relaxing these constraints, however, DNNs produce uninterpretable solutions which can be problematic from a safety perspective. In this paper, we propose a method of down-sampling LIDAR point clouds to exclude voxels that violate the assumption of a static scene and introduce error to the D2D scan matching process. Our approach uses a solution consistency filter -- identifying and suppressing voxels where D2D contributions disagree with local estimates from a PointNet-based registration network. Our results show that this technique provides significant benefits in registration accuracy, and is particularly useful in scenes containing dense foliage.

Thomas Sounack, Joshua Davis, Brigitte Durieux et al.

Encoder-based transformer models are central to biomedical and clinical Natural Language Processing (NLP), as their bidirectional self-attention makes them well-suited for efficiently extracting structured information from unstructured text through discriminative tasks. However, encoders have seen slower development compared to decoder models, leading to limited domain adaptation in biomedical and clinical settings. We introduce BioClinical ModernBERT, a domain-adapted encoder that builds on the recent ModernBERT release, incorporating long-context processing and substantial improvements in speed and performance for biomedical and clinical NLP. BioClinical ModernBERT is developed through continued pretraining on the largest biomedical and clinical corpus to date, with over 53.5 billion tokens, and addresses a key limitation of prior clinical encoders by leveraging 20 datasets from diverse institutions, domains, and geographic regions, rather than relying on data from a single source. It outperforms existing biomedical and clinical encoders on four downstream tasks spanning a broad range of use cases. We release both base (150M parameters) and large (396M parameters) versions of BioClinical ModernBERT, along with training checkpoints to support further research.