Disentangling Hippocampal Shape Variations: A Study of Neurological Disorders Using Graph Variational Autoencoder with Contrastive Learning

This paper presents a comprehensive study focused on disentangling hippocampal shape variations from diffusion tensor imaging (DTI) datasets within the context of neurological disorders. Leveraging a Graph Variational Autoencoder (VAE) enhanced with Supervised Contrastive Learning, our approach aims to improve interpretability by disentangling two distinct latent variables corresponding to age and the presence of diseases. In our ablation study, we investigate a range of VAE architectures and contrastive loss functions, showcasing the enhanced disentanglement capabilities of our approach. This evaluation uses synthetic 3D torus mesh data and real 3D hippocampal mesh datasets derived from the DTI hippocampal dataset. Our supervised disentanglement model outperforms several state-of-the-art (SOTA) methods like attribute and guided VAEs in terms of disentanglement scores. Our model distinguishes between age groups and disease status in patients with Multiple Sclerosis (MS) using the hippocampus data. Our Graph VAE with Supervised Contrastive Learning shows the volume changes of the hippocampus of MS populations at different ages, and the result is consistent with the current neuroimaging literature. This research provides valuable insights into the relationship between neurological disorder and hippocampal shape changes in different age groups of MS populations using a Graph VAE with Supervised Contrastive loss.

ShadowSense: Unsupervised Domain Adaptation and Feature Fusion for Shadow-Agnostic Tree Crown Detection from RGB-Thermal Drone Imagery

Accurate detection of individual tree crowns from remote sensing data poses a significant challenge due to the dense nature of forest canopy and the presence of diverse environmental variations, e.g., overlapping canopies, occlusions, and varying lighting conditions. Additionally, the lack of data for training robust models adds another limitation in effectively studying complex forest conditions. This paper presents a novel method for detecting shadowed tree crowns and provides a challenging dataset comprising roughly 50k paired RGB-thermal images to facilitate future research for illumination-invariant detection. The proposed method (ShadowSense) is entirely self-supervised, leveraging domain adversarial training without source domain annotations for feature extraction and foreground feature alignment for feature pyramid networks to adapt domain-invariant representations by focusing on visible foreground regions, respectively. It then fuses complementary information of both modalities to effectively improve upon the predictions of an RGB-trained detector and boost the overall accuracy. Extensive experiments demonstrate the superiority of the proposed method over both the baseline RGB-trained detector and state-of-the-art techniques that rely on unsupervised domain adaptation or early image fusion. Our code and data are available: https://github.com/rudrakshkapil/ShadowSense

Predicting Ki67, ER, PR, and HER2 Statuses from H&E-stained Breast Cancer Images

Despite the advances in machine learning and digital pathology, it is not yet clear if machine learning methods can accurately predict molecular information merely from histomorphology. In a quest to answer this question, we built a large-scale dataset (185538 images) with reliable measurements for Ki67, ER, PR, and HER2 statuses. The dataset is composed of mirrored images of H\&E and corresponding images of immunohistochemistry (IHC) assays (Ki67, ER, PR, and HER2. These images are mirrored through registration. To increase reliability, individual pairs were inspected and discarded if artifacts were present (tissue folding, bubbles, etc). Measurements for Ki67, ER and PR were determined by calculating H-Score from image analysis. HER2 measurement is based on binary classification: 0 and 1+ (IHC scores representing a negative subset) vs 3+ (IHC score positive subset). Cases with IHC equivocal score (2+) were excluded. We show that a standard ViT-based pipeline can achieve prediction performances around 90% in terms of Area Under the Curve (AUC) when trained with a proper labeling protocol. Finally, we shed light on the ability of the trained classifiers to localize relevant regions, which encourages future work to improve the localizations. Our proposed dataset is publicly available: https://ihc4bc.github.io/

TMR-RD: Training-based Model Refinement and Representation Disagreement for Semi-Supervised Object Detection

Semi-supervised object detection (SSOD) can incorporate limited labeled data and large amounts of unlabeled data to improve the performance and generalization of existing object detectors. Despite many advances, recent SSOD methods are still challenged by noisy/misleading pseudo-labels, classical exponential moving average (EMA) strategy, and the consensus of Teacher-Student models in the latter stages of training. This paper proposes a novel training-based model refinement (TMR) stage and a simple yet effective representation disagreement (RD) strategy to address the limitations of classical EMA and the consensus problem. The TMR stage of Teacher-Student models optimizes the lightweight scaling operation to refine the model's weights and prevent overfitting or forgetting learned patterns from unlabeled data. Meanwhile, the RD strategy helps keep these models diverged to encourage the student model to explore complementary representations. In addition, we use cascade regression to generate more reliable pseudo-labels for supervising the student model. Extensive experiments demonstrate the superior performance of our approach over state-of-the-art SSOD methods. Specifically, the proposed approach outperforms the Unbiased-Teacher method by an average mAP margin of 4.6% and 5.3% when using partially-labeled and fully-labeled data on the MS-COCO dataset, respectively.

Document Image Cleaning using Budget-Aware Black-Box Approximation

Recent work has shown that by approximating the behaviour of a non-differentiable black-box function using a neural network, the black-box can be integrated into a differentiable training pipeline for end-to-end training. This methodology is termed "differentiable bypass,'' and a successful application of this method involves training a document preprocessor to improve the performance of a black-box OCR engine. However, a good approximation of an OCR engine requires querying it for all samples throughout the training process, which can be computationally and financially expensive. Several zeroth-order optimization (ZO) algorithms have been proposed in black-box attack literature to find adversarial examples for a black-box model by computing its gradient in a query-efficient manner. However, the query complexity and convergence rate of such algorithms makes them infeasible for our problem. In this work, we propose two sample selection algorithms to train an OCR preprocessor with less than 10% of the original system's OCR engine queries, resulting in more than 60% reduction of the total training time without significant loss of accuracy. We also show an improvement of 4% in the word-level accuracy of a commercial OCR engine with only 2.5% of the total queries and a 32x reduction in monetary cost. Further, we propose a simple ranking technique to prune 30% of the document images from the training dataset without affecting the system's performance.

Towards Early Prediction of Human iPSC Reprogramming Success

This paper presents advancements in automated early-stage prediction of the success of reprogramming human induced pluripotent stem cells (iPSCs) as a potential source for regenerative cell therapies.The minuscule success rate of iPSC-reprogramming of around $ 0.01% $ to $ 0.1% $ makes it labor-intensive, time-consuming, and exorbitantly expensive to generate a stable iPSC line. Since that requires culturing of millions of cells and intense biological scrutiny of multiple clones to identify a single optimal clone. The ability to reliably predict which cells are likely to establish as an optimal iPSC line at an early stage of pluripotency would therefore be ground-breaking in rendering this a practical and cost-effective approach to personalized medicine. Temporal information about changes in cellular appearance over time is crucial for predicting its future growth outcomes. In order to generate this data, we first performed continuous time-lapse imaging of iPSCs in culture using an ultra-high resolution microscope. We then annotated the locations and identities of cells in late-stage images where reliable manual identification is possible. Next, we propagated these labels backwards in time using a semi-automated tracking system to obtain labels for early stages of growth. Finally, we used this data to train deep neural networks to perform automatic cell segmentation and classification. Our code and data are available at https://github.com/abhineet123/ipsc_prediction.

Weakly Supervised Realtime Dynamic Background Subtraction

Background subtraction is a fundamental task in computer vision with numerous real-world applications, ranging from object tracking to video surveillance. Dynamic backgrounds poses a significant challenge here. Supervised deep learning-based techniques are currently considered state-of-the-art for this task. However, these methods require pixel-wise ground-truth labels, which can be time-consuming and expensive. In this work, we propose a weakly supervised framework that can perform background subtraction without requiring per-pixel ground-truth labels. Our framework is trained on a moving object-free sequence of images and comprises two networks. The first network is an autoencoder that generates background images and prepares dynamic background images for training the second network. The dynamic background images are obtained by thresholding the background-subtracted images. The second network is a U-Net that uses the same object-free video for training and the dynamic background images as pixel-wise ground-truth labels. During the test phase, the input images are processed by the autoencoder and U-Net, which generate background and dynamic background images, respectively. The dynamic background image helps remove dynamic motion from the background-subtracted image, enabling us to obtain a foreground image that is free of dynamic artifacts. To demonstrate the effectiveness of our method, we conducted experiments on selected categories of the CDnet 2014 dataset and the I2R dataset. Our method outperformed all top-ranked unsupervised methods. We also achieved better results than one of the two existing weakly supervised methods, and our performance was similar to the other. Our proposed method is online, real-time, efficient, and requires minimal frame-level annotation, making it suitable for a wide range of real-world applications.

Crown-CAM: Reliable Visual Explanations for Tree Crown Detection in Aerial Images

Visual explanation of "black-box" models has enabled researchers and experts in artificial intelligence (AI) to exploit the localization abilities of such methods to a much greater extent. Despite most of the developed visual explanation methods applied to single object classification problems, they are not well-explored in the detection task, where the challenges may go beyond simple coarse area-based discrimination. This is of particular importance when a detector should face several objects with different scales from various viewpoints or if the objects of interest are absent. In this paper, we propose CrownCAM to generate reliable visual explanations for the challenging and dynamic problem of tree crown detection in aerial images. It efficiently provides fine-grain localization of tree crowns and non-contextual background suppression for scenarios with highly dense forest trees in the presence of potential distractors or scenes without tree crowns. Additionally, two Intersection over Union (IoU)-based metrics are introduced that can effectively quantify both the accuracy and inaccuracy of generated visual explanations with respect to regions with or without tree crowns in the image. Empirical evaluations demonstrate that the proposed Crown-CAM outperforms the Score-CAM, Augmented ScoreCAM, and Eigen-CAM methods by an average IoU margin of 8.7, 5.3, and 21.7 (and 3.3, 9.8, and 16.5) respectively in improving the accuracy (and decreasing inaccuracy) of visual explanations on the challenging NEON tree crown dataset.

Early Detection of Bark Beetle Attack Using Remote Sensing and Machine Learning: A Review

Bark beetle outbreaks can result in a devastating impact on forest ecosystem processes, biodiversity, forest structure and function, and economies. Accurate and timely detection of bark beetle infestations is crucial to mitigate further damage, develop proactive forest management activities, and minimize economic losses. Incorporating remote sensing (RS) data with machine learning (ML) (or deep learning (DL)) can provide a great alternative to the current approaches that rely on aerial surveys and field surveys, which are impractical over vast geographical regions. This paper provides a comprehensive review of past and current advances in the early detection of bark beetle-induced tree mortality from three key perspectives: bark beetle & host interactions, RS, and ML/DL. We parse recent literature according to bark beetle species & attack phases, host trees, study regions, imagery platforms & sensors, spectral/spatial/temporal resolutions, spectral signatures, spectral vegetation indices (SVIs), ML approaches, learning schemes, task categories, models, algorithms, classes/clusters, features, and DL networks & architectures. This review focuses on challenging early detection, discussing current challenges and potential solutions. Our literature survey suggests that the performance of current ML methods is limited (less than 80%) and depends on various factors, including imagery sensors & resolutions, acquisition dates, and employed features & algorithms/networks. A more promising result from DL networks and then the random forest (RF) algorithm highlighted the potential to detect subtle changes in visible, thermal, and short-wave infrared (SWIR) spectral regions.

Unsupervised diffeomorphic cardiac image registration using parameterization of the deformation field

This study proposes an end-to-end unsupervised diffeomorphic deformable registration framework based on moving mesh parameterization. Using this parameterization, a deformation field can be modeled with its transformation Jacobian determinant and curl of end velocity field. The new model of the deformation field has three important advantages; firstly, it relaxes the need for an explicit regularization term and the corresponding weight in the cost function. The smoothness is implicitly embedded in the solution which results in a physically plausible deformation field. Secondly, it guarantees diffeomorphism through explicit constraints applied to the transformation Jacobian determinant to keep it positive. Finally, it is suitable for cardiac data processing, since the nature of this parameterization is to define the deformation field in terms of the radial and rotational components. The effectiveness of the algorithm is investigated by evaluating the proposed method on three different data sets including 2D and 3D cardiac MRI scans. The results demonstrate that the proposed framework outperforms existing learning-based and non-learning-based methods while generating diffeomorphic transformations.