Cari Whyne

Hamidreza Aftabi, Faye Yu, Brooke Switzer et al.

Predicting long-term bone remodeling after mandibular reconstruction would be of great clinical benefit, yet standard generative models struggle to maintain trajectory-level consistency and anatomical fidelity over long horizons. We introduce OsteoFlow, a flow-based framework predicting Year-1 post-operative CT scans from Day-5 scans. Our core contribution is Lyapunov-guided trajectory distillation: Unlike one-step distillation, our method distills a continuous trajectory over transport time from a registration-derived stationary velocity field teacher. Combined with a resection-aware image loss, this enforces geometric correspondence without sacrificing generative capacity. Evaluated on 344 paired regions of interest, OsteoFlow significantly outperforms state of-the-art baselines, reducing mean absolute error in the surgical resection zone by ~20%. This highlights the promise of trajectory distillation for long-term prediction. Code is available on GitHub: OsteoFlow.

Geoff Klein, Michael Hardisty, Cari Whyne et al.

Vertebral detection and segmentation are critical steps for treatment planning in spine surgery and radiation therapy. Accurate identification and segmentation are complicated in imaging that does not include the full spine, in cases with variations in anatomy (T13 and/or L6 vertebrae), and in the presence of fracture or hardware. This paper proposes VertDetect, a fully automated end-to-end 3D vertebral instance segmentation Convolutional Neural Network (CNN) model to predict vertebral level labels and segmentations for all vertebrae present in a CT scan. The utilization of a shared CNN backbone provides the detection and segmentation branches of the network with feature maps containing both spinal and vertebral level information. A Graph Convolutional Network (GCN) layer is used to improve vertebral labelling by using the known structure of the spine. This model achieved a Dice Similarity Coefficient (DSC) of 0.883 (95% CI, 0.843-0.906) and 0.882 (95% CI, 0.835-0.909) in the VerSe 2019 and 0.868 (95\% CI, 0.834-0.890) and 0.869 (95\% CI, 0.832-0.891) in the VerSe 2020 public and hidden test sets, respectively. This model achieved state-of-the-art performance for an end-to-end architecture, whose design facilitates the extraction of features that can be subsequently used for downstream tasks.

David M. Burns, Cari M. Whyne

Seglearn is an open-source python package for machine learning time series or sequences using a sliding window segmentation approach. The implementation provides a flexible pipeline for tackling classification, regression, and forecasting problems with multivariate sequence and contextual data. This package is compatible with scikit-learn and is listed under scikit-learn Related Projects. The package depends on numpy, scipy, and scikit-learn. Seglearn is distributed under the BSD 3-Clause License. Documentation includes a detailed API description, user guide, and examples. Unit tests provide a high degree of code coverage.

David M. Burns, Cari M. Whyne

A significant challenge for a supervised learning approach to inertial human activity recognition is the heterogeneity of data between individual users, resulting in very poor performance of impersonal algorithms for some subjects. We present an approach to personalized activity recognition based on deep embeddings derived from a fully convolutional neural network. We experiment with both categorical cross entropy loss and triplet loss for training the embedding, and describe a novel triplet loss function based on subject triplets. We evaluate these methods on three publicly available inertial human activity recognition data sets (MHEALTH, WISDM, and SPAR) comparing classification accuracy, out-of-distribution activity detection, and embedding generalization to new activities. The novel subject triplet loss provides the best performance overall, and all personalized deep embeddings out-perform our baseline personalized engineered feature embedding and an impersonal fully convolutional neural network classifier.