The accurate classification of lymphoma subtypes using hematoxylin and eosin (H&E)-stained tissue is complicated by the wide range of morphological features these cancers can exhibit. We present LymphoML - an interpretable machine learning method that identifies morphologic features that correlate with lymphoma subtypes. Our method applies steps to process H&E-stained tissue microarray cores, segment nuclei and cells, compute features encompassing morphology, texture, and architecture, and train gradient-boosted models to make diagnostic predictions. LymphoML's interpretable models, developed on a limited volume of H&E-stained tissue, achieve non-inferior diagnostic accuracy to pathologists using whole-slide images and outperform black box deep-learning on a dataset of 670 cases from Guatemala spanning 8 lymphoma subtypes. Using SHapley Additive exPlanation (SHAP) analysis, we assess the impact of each feature on model prediction and find that nuclear shape features are most discriminative for DLBCL (F1-score: 78.7%) and classical Hodgkin lymphoma (F1-score: 74.5%). Finally, we provide the first demonstration that a model combining features from H&E-stained tissue with features from a standardized panel of 6 immunostains results in a similar diagnostic accuracy (85.3%) to a 46-stain panel (86.1%).
Self-supervised learning (SSL) enables label efficient training for machine learning models. This is essential for domains such as medical imaging, where labels are costly and time-consuming to curate. However, the most effective supervised or SSL strategy for transferring models to different healthcare systems or novel tasks is not well understood. In this work, we systematically experiment with a variety of supervised and self-supervised pretraining strategies using multimodal datasets of medical images (chest X-rays) and text (radiology reports). We then evaluate their performance on data from two external institutions with diverse sets of tasks. In addition, we experiment with different transfer learning strategies to effectively adapt these pretrained models to new tasks and healthcare systems. Our empirical results suggest that multimodal SSL gives substantial gains over unimodal SSL in performance across new healthcare systems and tasks, comparable to models pretrained with full supervision. We demonstrate additional performance gains with models further adapted to the new dataset and task, using multimodal domain-adaptive pretraining (DAPT), linear probing then finetuning (LP-FT), and both methods combined. We offer suggestions for alternative models to use in scenarios where not all of these additions are feasible. Our results provide guidance for improving the generalization of medical image interpretation models to new healthcare systems and novel tasks.
Machine learning (ML) research has generally focused on models, while the most prominent datasets have been employed for everyday ML tasks without regard for the breadth, difficulty, and faithfulness of these datasets to the underlying problem. Neglecting the fundamental importance of datasets has caused major problems involving data cascades in real-world applications and saturation of dataset-driven criteria for model quality, hindering research growth. To solve this problem, we present DataPerf, a benchmark package for evaluating ML datasets and dataset-working algorithms. We intend it to enable the "data ratchet," in which training sets will aid in evaluating test sets on the same problems, and vice versa. Such a feedback-driven strategy will generate a virtuous loop that will accelerate development of data-centric AI. The MLCommons Association will maintain DataPerf.
How can we effectively leverage the domain knowledge from remote sensing to better segment agriculture land cover from satellite images? In this paper, we propose a novel, model-agnostic, data-fusion approach for vegetation-related computer vision tasks. Motivated by the various Vegetation Indices (VIs), which are introduced by domain experts, we systematically reviewed the VIs that are widely used in remote sensing and their feasibility to be incorporated in deep neural networks. To fully leverage the Near-Infrared channel, the traditional Red-Green-Blue channels, and Vegetation Index or its variants, we propose a Generalized Vegetation Index (GVI), a lightweight module that can be easily plugged into many neural network architectures to serve as an additional information input. To smoothly train models with our GVI, we developed an Additive Group Normalization (AGN) module that does not require extra parameters of the prescribed neural networks. Our approach has improved the IoUs of vegetation-related classes by 0.9-1.3 percent and consistently improves the overall mIoU by 2 percent on our baseline.
The first Agriculture-Vision Challenge aims to encourage research in developing novel and effective algorithms for agricultural pattern recognition from aerial images, especially for the semantic segmentation task associated with our challenge dataset. Around 57 participating teams from various countries compete to achieve state-of-the-art in aerial agriculture semantic segmentation. The Agriculture-Vision Challenge Dataset was employed, which comprises of 21,061 aerial and multi-spectral farmland images. This paper provides a summary of notable methods and results in the challenge. Our submission server and leaderboard will continue to open for researchers that are interested in this challenge dataset and task; the link can be found here.
Identifying patients who will be discharged within 24 hours can improve hospital resource management and quality of care. We studied this problem using eight years of Electronic Health Records (EHR) data from Stanford Hospital. We fit models to predict 24 hour discharge across the entire inpatient population. The best performing models achieved an area under the receiver-operator characteristic curve (AUROC) of 0.85 and an AUPRC of 0.53 on a held out test set. This model was also well calibrated. Finally, we analyzed the utility of this model in a decision theoretic framework to identify regions of ROC space in which using the model increases expected utility compared to the trivial always negative or always positive classifiers.
Personalized probabilistic forecasts of time to event (such as mortality) can be crucial in decision making, especially in the clinical setting. Inspired by ideas from the meteorology literature, we approach this problem through the paradigm of maximizing sharpness of prediction distributions, subject to calibration. In regression problems, it has been shown that optimizing the continuous ranked probability score (CRPS) instead of maximum likelihood leads to sharper prediction distributions while maintaining calibration. We introduce the Survival-CRPS, a generalization of the CRPS to the time to event setting, and present right-censored and interval-censored variants. To holistically evaluate the quality of predicted distributions over time to event, we present the Survival-AUPRC evaluation metric, an analog to area under the precision-recall curve. We apply these ideas by building a recurrent neural network for mortality prediction, using an Electronic Health Record dataset covering millions of patients. We demonstrate significant benefits in models trained by the Survival-CRPS objective instead of maximum likelihood.
Improving the quality of end-of-life care for hospitalized patients is a priority for healthcare organizations. Studies have shown that physicians tend to over-estimate prognoses, which in combination with treatment inertia results in a mismatch between patients wishes and actual care at the end of life. We describe a method to address this problem using Deep Learning and Electronic Health Record (EHR) data, which is currently being piloted, with Institutional Review Board approval, at an academic medical center. The EHR data of admitted patients are automatically evaluated by an algorithm, which brings patients who are likely to benefit from palliative care services to the attention of the Palliative Care team. The algorithm is a Deep Neural Network trained on the EHR data from previous years, to predict all-cause 3-12 month mortality of patients as a proxy for patients that could benefit from palliative care. Our predictions enable the Palliative Care team to take a proactive approach in reaching out to such patients, rather than relying on referrals from treating physicians, or conduct time consuming chart reviews of all patients. We also present a novel interpretation technique which we use to provide explanations of the model's predictions.
We present Deep Voice, a production-quality text-to-speech system constructed entirely from deep neural networks. Deep Voice lays the groundwork for truly end-to-end neural speech synthesis. The system comprises five major building blocks: a segmentation model for locating phoneme boundaries, a grapheme-to-phoneme conversion model, a phoneme duration prediction model, a fundamental frequency prediction model, and an audio synthesis model. For the segmentation model, we propose a novel way of performing phoneme boundary detection with deep neural networks using connectionist temporal classification (CTC) loss. For the audio synthesis model, we implement a variant of WaveNet that requires fewer parameters and trains faster than the original. By using a neural network for each component, our system is simpler and more flexible than traditional text-to-speech systems, where each component requires laborious feature engineering and extensive domain expertise. Finally, we show that inference with our system can be performed faster than real time and describe optimized WaveNet inference kernels on both CPU and GPU that achieve up to 400x speedups over existing implementations.