Yash-yee Logan

Mohit Prabhushankar, Kiran Kokilepersaud, Yash-yee Logan et al.

Clinical diagnosis of the eye is performed over multifarious data modalities including scalar clinical labels, vectorized biomarkers, two-dimensional fundus images, and three-dimensional Optical Coherence Tomography (OCT) scans. Clinical practitioners use all available data modalities for diagnosing and treating eye diseases like Diabetic Retinopathy (DR) or Diabetic Macular Edema (DME). Enabling usage of machine learning algorithms within the ophthalmic medical domain requires research into the relationships and interactions between all relevant data over a treatment period. Existing datasets are limited in that they neither provide data nor consider the explicit relationship modeling between the data modalities. In this paper, we introduce the Ophthalmic Labels for Investigating Visual Eye Semantics (OLIVES) dataset that addresses the above limitation. This is the first OCT and near-IR fundus dataset that includes clinical labels, biomarker labels, disease labels, and time-series patient treatment information from associated clinical trials. The dataset consists of 1268 near-IR fundus images each with at least 49 OCT scans, and 16 biomarkers, along with 4 clinical labels and a disease diagnosis of DR or DME. In total, there are 96 eyes' data averaged over a period of at least two years with each eye treated for an average of 66 weeks and 7 injections. We benchmark the utility of OLIVES dataset for ophthalmic data as well as provide benchmarks and concrete research directions for core and emerging machine learning paradigms within medical image analysis.

Yash-yee Logan, Ryan Benkert, Ahmad Mustafa et al.

This paper considers making active learning more sensible from a medical perspective. In practice, a disease manifests itself in different forms across patient cohorts. Existing frameworks have primarily used mathematical constructs to engineer uncertainty or diversity-based methods for selecting the most informative samples. However, such algorithms do not present themselves naturally as usable by the medical community and healthcare providers. Thus, their deployment in clinical settings is very limited, if any. For this purpose, we propose a framework that incorporates clinical insights into the sample selection process of active learning that can be incorporated with existing algorithms. Our medically interpretable active learning framework captures diverse disease manifestations from patients to improve generalization performance of OCT classification. After comprehensive experiments, we report that incorporating patient insights within the active learning framework yields performance that matches or surpasses five commonly used paradigms on two architectures with a dataset having imbalanced patient distributions. Also, the framework integrates within existing medical practices and thus can be used by healthcare providers.

Kiran Kokilepersaud, Yash-Yee Logan, Ryan Benkert et al.

In this paper, we introduce the FOCAL (Ford-OLIVES Collaboration on Active Learning) dataset which enables the study of the impact of annotation-cost within a video active learning setting. Annotation-cost refers to the time it takes an annotator to label and quality-assure a given video sequence. A practical motivation for active learning research is to minimize annotation-cost by selectively labeling informative samples that will maximize performance within a given budget constraint. However, previous work in video active learning lacks real-time annotation labels for accurately assessing cost minimization and instead operates under the assumption that annotation-cost scales linearly with the amount of data to annotate. This assumption does not take into account a variety of real-world confounding factors that contribute to a nonlinear cost such as the effect of an assistive labeling tool and the variety of interactions within a scene such as occluded objects, weather, and motion of objects. FOCAL addresses this discrepancy by providing real annotation-cost labels for 126 video sequences across 69 unique city scenes with a variety of weather, lighting, and seasonal conditions. We also introduce a set of conformal active learning algorithms that take advantage of the sequential structure of video data in order to achieve a better trade-off between annotation-cost and performance while also reducing floating point operations (FLOPS) overhead by at least 77.67%. We show how these approaches better reflect how annotations on videos are done in practice through a sequence selection framework. We further demonstrate the advantage of these approaches by introducing two performance-cost metrics and show that the best conformal active learning method is cheaper than the best traditional active learning method by 113 hours.