Similarly, in Figure 1c), the CST clinical label for two separate patients with visually dissimlar OCT scans is shown.

Clinical practitioners use all available data modalities for diagnosing and treating eye diseases like Diabetic Retinopathy (DR) or Diabetic Macular Edema (DME).

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.

Deep learning models have achieved great success in automating skin lesion diagnosis. However, the ethnic disparity in these models' predictions needs to be addressed before deploying them. We introduce a novel approach, PatchAlign, to enhance skin condition image classification accuracy and fairness by aligning with clinical text representations of skin conditions. PatchAlign uses Graph Optimal Transport (GOT) Loss as a regularizer to perform cross-domain alignment. The representations obtained are robust and generalize well across skin tones, even with limited training samples. To reduce the effect of noise and artifacts in clinical dermatology images, we propose a learnable Masked Graph Optimal Transport for cross-domain alignment that further improves fairness metrics. We compare our model to the state-of-the-art FairDisCo on two skin lesion datasets with different skin types: Fitzpatrick17k and Diverse Dermatology Images (DDI). PatchAlign enhances the accuracy of skin condition image classification by 2.8% (in-domain) and 6.2% (out-domain) on Fitzpatrick17k, and 4.2% (in-domain) on DDI compared to FairDisCo. Additionally, it consistently improves the fairness of true positive rates across skin tones. The source code for the implementation is available at the following GitHub repository: https://github.com/aayushmanace/PatchAlign24, enabling easy reproduction and further experimentation.

There is considerable interest in predicting the pathogenicity of protein variants in human genes. Due to the sparsity of high quality labels, recent approaches turn to \textit{unsupervised} learning, using Multiple Sequence Alignments (MSAs) to train generative models of natural sequence variation within each gene. These generative models then predict variant likelihood as a proxy to evolutionary fitness. In this work we instead combine this evolutionary principle with pretrained protein language models (LMs), which have already shown promising results in predicting protein structure and function. Instead of training separate models per-gene, we find that a single protein LM trained on broad sequence datasets can score pathogenicity for any gene variant zero-shot, without MSAs or finetuning. We call this unsupervised approach \textbf{VELM} (Variant Effect via Language Models), and show that it achieves scoring performance comparable to the state of the art when evaluated on clinically labeled variants of disease-related genes.

This paper presents a novel positive and negative set selection strategy for contrastive learning of medical images based on labels that can be extracted from clinical data. In the medical field, there exists a variety of labels for data that serve different purposes at different stages of a diagnostic and treatment process. Clinical labels and biomarker labels are two examples. In general, clinical labels are easier to obtain in larger quantities because they are regularly collected during routine clinical care, while biomarker labels require expert analysis and interpretation to obtain. Within the field of ophthalmology, previous work has shown that clinical values exhibit correlations with biomarker structures that manifest within optical coherence tomography (OCT) scans. We exploit this relationship between clinical and biomarker data to improve performance for biomarker classification. This is accomplished by leveraging the larger amount of clinical data as pseudo-labels for our data without biomarker labels in order to choose positive and negative instances for training a backbone network with a supervised contrastive loss. In this way, a backbone network learns a representation space that aligns with the clinical data distribution available. Afterwards, we fine-tune the network trained in this manner with the smaller amount of biomarker labeled data with a cross-entropy loss in order to classify these key indicators of disease directly from OCT scans. Our method is shown to outperform state of the art self-supervised methods by as much as 5% in terms of accuracy on individual biomarker detection.

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.

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.

We present an approach to domain adaptation, addressing the case where data from the source domain is abundant, labelled data from the target domain is limited or non-existent, and a small amount of paired source-target data is available. The method is designed for developing deep learning models that detect the presence of medical conditions based on data from consumer-grade portable biosensors. It addresses some of the key problems in this area, namely, the difficulty of acquiring large quantities of clinically labelled data from the biosensor, and the noise and ambiguity that can affect the clinical labels. The idea is to pre-train an expressive model on a large dataset of labelled recordings from a sensor modality for which data is abundant, and then to adapt the model's lower layers so that its predictions on the target modality are similar to the original model's on paired examples from the source modality. We show that the pre-trained model's predictions provide a substantially better learning signal than the clinician-provided labels, and that this teacher-student technique significantly outperforms both a naive application of supervised deep learning and a label-supervised version of domain adaptation on a synthetic dataset and in a real-world case study on sleep apnea. By reducing the volume of data required and obviating the need for labels, our approach should reduce the cost associated with developing high-performance deep learning models for biosensors.