Kiran Kokilepersaud

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.

Seulgi Kim, Kiran Kokilepersaud, Mohit Prabhushankar et al.

Multi-modal fusion methods often suffer from two types of representation collapse: feature collapse where individual dimensions lose their discriminative power (as measured by eigenspectra), and modality collapse where one dominant modality overwhelms the other. Applications like human action anticipation that require fusing multifarious sensor data are hindered by both feature and modality collapse. However, existing methods attempt to counter feature collapse and modality collapse separately. This is because there is no unifying framework that efficiently addresses feature and modality collapse in conjunction. In this paper, we posit the utility of effective rank as an informative measure that can be utilized to quantify and counter both the representation collapses. We propose \textit{Rank-enhancing Token Fuser}, a theoretically grounded fusion framework that selectively blends less informative features from one modality with complementary features from another modality. We show that our method increases the effective rank of the fused representation. To address modality collapse, we evaluate modality combinations that mutually increase each others' effective rank. We show that depth maintains representational balance when fused with RGB, avoiding modality collapse. We validate our method on action anticipation, where we present \texttt{R3D}, a depth-informed fusion framework. Extensive experiments on NTURGBD, UTKinect, and DARai demonstrate that our approach significantly outperforms prior state-of-the-art methods by up to 3.74\%. Our code is available at: \href{https://github.com/olivesgatech/R3D}{https://github.com/olivesgatech/R3D}.

Kiran Kokilepersaud, Mohit Prabhushankar, Ghassan AlRegib

In seismic interpretation, pixel-level labels of various rock structures can be time-consuming and expensive to obtain. As a result, there oftentimes exists a non-trivial quantity of unlabeled data that is left unused simply because traditional deep learning methods rely on access to fully labeled volumes. To rectify this problem, contrastive learning approaches have been proposed that use a self-supervised methodology in order to learn useful representations from unlabeled data. However, traditional contrastive learning approaches are based on assumptions from the domain of natural images that do not make use of seismic context. In order to incorporate this context within contrastive learning, we propose a novel positive pair selection strategy based on the position of slices within a seismic volume. We show that the learnt representations from our method out-perform a state of the art contrastive learning methodology in a semantic segmentation task.

Zoe Fowler, Kiran Kokilepersaud, Mohit Prabhushankar et al.

This paper presents a novel approach to active learning that takes into account the non-independent and identically distributed (non-i.i.d.) structure of a clinical trial setting. There exists two types of clinical trials: retrospective and prospective. Retrospective clinical trials analyze data after treatment has been performed; prospective clinical trials collect data as treatment is ongoing. Typically, active learning approaches assume the dataset is i.i.d. when selecting training samples; however, in the case of clinical trials, treatment results in a dependency between the data collected at the current and past visits. Thus, we propose prospective active learning to overcome the limitations present in traditional active learning methods and apply it to disease detection in optical coherence tomography (OCT) images, where we condition on the time an image was collected to enforce the i.i.d. assumption. We compare our proposed method to the traditional active learning paradigm, which we refer to as retrospective in nature. We demonstrate that prospective active learning outperforms retrospective active learning in two different types of test settings.

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.

Kiran Kokilepersaud, Mohit Prabhushankar, Yavuz Yarici et al.

In this work, we present a methodology to shape a fisheye-specific representation space that reflects the interaction between distortion and semantic context present in this data modality. Fisheye data has the wider field of view advantage over other types of cameras, but this comes at the expense of high radial distortion. As a result, objects further from the center exhibit deformations that make it difficult for a model to identify their semantic context. While previous work has attempted architectural and training augmentation changes to alleviate this effect, no work has attempted to guide the model towards learning a representation space that reflects this interaction between distortion and semantic context inherent to fisheye data. We introduce an approach to exploit this relationship by first extracting distortion class labels based on an object's distance from the center of the image. We then shape a backbone's representation space with a weighted contrastive loss that constrains objects of the same semantic class and distortion class to be close to each other within a lower dimensional embedding space. This backbone trained with both semantic and distortion information is then fine-tuned within an object detection setting to empirically evaluate the quality of the learnt representation. We show this method leads to performance improvements by as much as 1.1% mean average precision over standard object detection strategies and .6% improvement over other state of the art representation learning approaches.

Kiran Kokilepersaud, Mohit Prabhushankar, Ghassan AlRegib

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.

Mohit Prabhushankar, Kiran Kokilepersaud, Jorge Quesada et al.

Crowdsourcing annotations has created a paradigm shift in the availability of labeled data for machine learning. Availability of large datasets has accelerated progress in common knowledge applications involving visual and language data. However, specialized applications that require expert labels lag in data availability. One such application is fault segmentation in subsurface imaging. Detecting, tracking, and analyzing faults has broad societal implications in predicting fluid flows, earthquakes, and storing excess atmospheric CO$_2$. However, delineating faults with current practices is a labor-intensive activity that requires precise analysis of subsurface imaging data by geophysicists. In this paper, we propose the $\texttt{CRACKS}$ dataset to detect and segment faults in subsurface images by utilizing crowdsourced resources. We leverage Amazon Mechanical Turk to obtain fault delineations from sections of the Netherlands North Sea subsurface images from (i) $26$ novices who have no exposure to subsurface data and were shown a video describing and labeling faults, (ii) $8$ practitioners who have previously interacted and worked on subsurface data, (iii) one geophysicist to label $7636$ faults in the region. Note that all novices, practitioners, and the expert segment faults on the same subsurface volume with disagreements between and among the novices and practitioners. Additionally, each fault annotation is equipped with the confidence level of the annotator. The paper provides benchmarks on detecting and segmenting the expert labels, given the novice and practitioner labels. Additional details along with the dataset links and codes are available at $\href{https://alregib.ece.gatech.edu/cracks-crowdsourcing-resources-for-analysis-and-categorization-of-key-subsurface-faults/}{link}$.

Kiran Kokilepersaud, Seulgi Kim, Mohit Prabhushankar et al.

In this paper, we propose an algorithm that can be used on top of a wide variety of self-supervised (SSL) approaches to take advantage of hierarchical structures that emerge during training. SSL approaches typically work through some invariance term to ensure consistency between similar samples and a regularization term to prevent global dimensional collapse. Dimensional collapse refers to data representations spanning a lower-dimensional subspace. Recent work has demonstrated that the representation space of these algorithms gradually reflects a semantic hierarchical structure as training progresses. Data samples of the same hierarchical grouping tend to exhibit greater dimensional collapse locally compared to the dataset as a whole due to sharing features in common with each other. Ideally, SSL algorithms would take advantage of this hierarchical emergence to have an additional regularization term to account for this local dimensional collapse effect. However, the construction of existing SSL algorithms does not account for this property. To address this, we propose an adaptive algorithm that performs a weighted decomposition of the denominator of the InfoNCE loss into two terms: local hierarchical and global collapse regularization respectively. This decomposition is based on an adaptive threshold that gradually lowers to reflect the emerging hierarchical structure of the representation space throughout training. It is based on an analysis of the cosine similarity distribution of samples in a batch. We demonstrate that this hierarchical emergence exploitation (HEX) approach can be integrated across a wide variety of SSL algorithms. Empirically, we show performance improvements of up to 5.6% relative improvement over baseline SSL approaches on classification accuracy on Imagenet with 100 epochs of training.

Kiran Kokilepersaud, Mohit Prabhushankar, Ghassan AlRegib et al.

In this paper, we propose a novel selection strategy for contrastive learning for medical images. On natural images, contrastive learning uses augmentations to select positive and negative pairs for the contrastive loss. However, in the medical domain, arbitrary augmentations have the potential to distort small localized regions that contain the biomarkers we are interested in detecting. A more intuitive approach is to select samples with similar disease severity characteristics, since these samples are more likely to have similar structures related to the progression of a disease. To enable this, we introduce a method that generates disease severity labels for unlabeled OCT scans on the basis of gradient responses from an anomaly detection algorithm. These labels are used to train a supervised contrastive learning setup to improve biomarker classification accuracy by as much as 6% above self-supervised baselines for key indicators of Diabetic Retinopathy.

Yavuz Yarici, Kiran Kokilepersaud, Mohit Prabhushankar et al.

The high cost of annotating data makes self-supervised approaches, such as contrastive learning methods, appealing for Human Activity Recognition (HAR). Effective contrastive learning relies on selecting informative positive and negative samples. However, HAR sensor signals are subject to significant domain shifts caused by subject variability. These domain shifts hinder model generalization to unseen subjects by embedding subject-specific variations rather than activity-specific features. As a result, human activity recognition models trained with contrastive learning often struggle to generalize to new subjects. We introduce Subject-Invariant Contrastive Learning (SICL), a simple yet effective loss function to improve generalization in human activity recognition. SICL re-weights negative pairs drawn from the same subject to suppress subject-specific cues and emphasize activity-specific information. We evaluate our loss function on three public benchmarks: UTD-MHAD, MMAct, and DARai. We show that SICL improves performance by up to 11% over traditional contrastive learning methods. Additionally, we demonstrate the adaptability of our loss function across various settings, including multiple self-supervised methods, multimodal scenarios, and supervised learning frameworks.

Kiran Kokilepersaud, Mohit Prabhushankar, Ghassan AlRegib

A key factor in effective Self-Supervised learning (SSL) is preventing dimensional collapse, where higher-dimensional representation spaces ($R$) span a lower-dimensional subspace. Therefore, SSL optimization strategies involve guiding a model to produce $R$ with a higher dimensionality ($H(R)$) through objectives that encourage decorrelation of features or sample uniformity in $R$. A higher $H(R)$ indicates that $R$ has greater feature diversity which is useful for generalization to downstream tasks. Alongside dimensionality optimization, SSL algorithms also utilize a projection head that maps $R$ into an embedding space $Z$. Recent work has characterized the projection head as a filter of noisy or irrelevant features from the SSL objective by reducing the mutual information $I(R;Z)$. Therefore, the current literature's view is that a good SSL representation space should have a high $H(R)$ and a low $I(R;Z)$. However, this view of SSL is lacking in terms of an understanding of the underlying training dynamics that influences the relationship between both terms. Our analysis shows that the best performing SSL models do not have the highest $H(R)$ nor the lowest $I(R;Z)$, but effectively arrive at a balance between both. To take advantage of this analysis, we introduce AdaDim, a training strategy that leverages SSL training dynamics by adaptively balancing between increasing $H(R)$ through feature decorrelation and sample uniformity as well as gradual regularization of $I(R;Z)$ as training progresses. We show performance improvements of up to 3% over common SSL baselines despite our method not utilizing expensive techniques such as queues, clustering, predictor networks, or student-teacher architectures.

Yavuz Yarici, Kiran Kokilepersaud, Mohit Prabhushankar et al.

Self-supervised models create representation spaces that lack clear semantic meaning. This interpretability problem of representations makes traditional explainability methods ineffective in this context. In this paper, we introduce a novel method to analyze representation spaces using three key perceptual components: color, shape, and texture. We employ selective masking of these components to observe changes in representations, resulting in distinct importance maps for each. In scenarios, where labels are absent, these importance maps provide more intuitive explanations as they are integral to the human visual system. Our approach enhances the interpretability of the representation space, offering explanations that resonate with human visual perception. We analyze how different training objectives create distinct representation spaces using perceptual components. Additionally, we examine the representation of images across diverse image domains, providing insights into the role of these components in different contexts.

Kiran Kokilepersaud, Yavuz Yarici, Mohit Prabhushankar et al.

In this work, we propose a novel supervised contrastive loss that enables the integration of taxonomic hierarchy information during the representation learning process. A supervised contrastive loss operates by enforcing that images with the same class label (positive samples) project closer to each other than images with differing class labels (negative samples). The advantage of this approach is that it directly penalizes the structure of the representation space itself. This enables greater flexibility with respect to encoding semantic concepts. However, the standard supervised contrastive loss only enforces semantic structure based on the downstream task (i.e. the class label). In reality, the class label is only one level of a \emph{hierarchy of different semantic relationships known as a taxonomy}. For example, the class label is oftentimes the species of an animal, but between different classes there are higher order relationships such as all animals with wings being ``birds". We show that by explicitly accounting for these relationships with a weighting penalty in the contrastive loss we can out-perform the supervised contrastive loss. Additionally, we demonstrate the adaptability of the notion of a taxonomy by integrating our loss into medical and noise-based settings that show performance improvements by as much as 7%.

Kiran Kokilepersaud, Stephanie Trejo Corona, Mohit Prabhushankar et al.

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 by using the 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. We also expand on this concept by proposing a method that uses a linear combination of clinical contrastive losses. We benchmark our methods against state of the art self-supervised methods in a novel setting with biomarkers of varying granularity. We show performance improvements by as much as 5\% in total biomarker detection AUROC.