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.

This paper provides a comprehensive review of past and current advances in the early detection of bark beetle-induced tree mortality from three primary perspectives: bark beetle & host interactions, RS, and ML/DL. In contrast to prior efforts, this review encompasses all RS systems and emphasizes ML/DL methods to investigate their strengths and weaknesses. We parse existing literature based on multi- or hyper-spectral analyses and distill their knowledge based on: bark beetle species & attack phases with a primary emphasis on early stages of attacks, host trees, study regions, RS 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. Although DL-based methods and the random forest (RF) algorithm showed promising results, highlighting their potential to detect subtle changes across visible, thermal, and short-wave infrared (SWIR) spectral regions, they still have limited effectiveness and high uncertainties. To inspire novel solutions to these shortcomings, we delve into the principal challenges & opportunities from different perspectives, enabling a deeper understanding of the current state of research and guiding future research directions.

Semi-supervised object detection (SSOD) aims to improve the performance and generalization of existing object detectors by utilizing limited labeled data and extensive unlabeled data. Despite many advances, recent SSOD methods are still challenged by inadequate model refinement using the classical exponential moving average (EMA) strategy, the consensus of Teacher-Student models in the latter stages of training (i.e., losing their distinctiveness), and noisy/misleading pseudo-labels. 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 additional patterns in unlabeled data. Our approach can be integrated into established SSOD methods and is empirically validated using two baseline methods, with and without cascade regression, to generate more reliable pseudo-labels. Extensive experiments demonstrate the superior performance of our approach over state-of-the-art SSOD methods. Specifically, the proposed approach outperforms the baseline Unbiased-Teacher-v2 (& Unbiased-Teacher-v1) method by an average mAP margin of 2.23, 2.1, and 3.36 (& 2.07, 1.9, and 3.27) on COCO-standard, COCO-additional, and Pascal VOC datasets, respectively.

Visual explanation of ``black-box'' models allows researchers in explainable artificial intelligence (XAI) to interpret the model's decisions in a human-understandable manner. In this paper, we propose interpretable class activation mapping for tree crown detection (Crown-CAM) that overcomes inaccurate localization & computational complexity of previous methods while generating reliable visual explanations for the challenging and dynamic problem of tree crown detection in aerial images. It consists of an unsupervised selection of activation maps, computation of local score maps, and non-contextual background suppression to efficiently provide fine-grain localization of tree crowns in scenarios with dense forest trees or scenes without tree crowns. Additionally, two Intersection over Union (IoU)-based metrics are introduced to effectively quantify both the accuracy and inaccuracy of generated explanations with respect to regions with or even without tree crowns in the image. Empirical evaluations demonstrate that the proposed Crown-CAM outperforms the Score-CAM, Augmented Score-CAM, 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.

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.

Abstract--Machine learning researchers have long noted a trade-off between interpretability and prediction performance. On the one hand, traditional models are often interpretable to humans but they cannot achieve high prediction performances. At the opposite end of the spectrum, deep models can achieve state-of-the-art performances in many tasks. However, deep models' predictions are known to be uninterpretable to humans. In this paper we present a framework that shortens the gap between the two aforementioned groups of methods. Given an artificial neural network (ANN), our method finds a Gaussian process (GP) whose predictions almost match those of the ANN. As GPs are highly interpretable, we use the trained GP to explain the ANN's decisions. We use our method to explain ANNs' decisions on may datasets. The explanations provide intriguing insights about the ANNs' decisions. With the best of our knowledge, our inference formulation for GPs is the first one in which an ANN and a similarly behaving Gaussian process naturally appear. Furthermore, we examine some of the known theoretical conditions under which an ANN is interpretable by GPs. Some of those theoretical conditions are too restrictive for modern architectures. However, we hypothesize that only a subset of those theoretical conditions are sufficient. Finally, we implement our framework as a publicly available tool called GPEX. Given any pytorch feed-forward module, GPEX allows users to interpret any ANN subcomponent of the module effortlessly and without having to be involved in the inference algorithm.

Output encoding often leads to superior accuracies in various machine learning tasks. In this paper we look at a significant task of cell detection/localization from microscopy images as a test case for output encoding. Since the output space is sparse for the cell detection problem (only a few pixel locations are cell centers), we employ compressed sensing (CS)-based output encoding here. Using random projections, CS converts the sparse, output pixel space into dense and short (i.e., compressed) vectors. As a regressor, we use deep convolutional neural net (CNN) to predict the compressed vectors. Then applying a $L_1$-norm recovery algorithm to the predicted vectors, we recover sparse cell locations in the output pixel space. We demonstrate CS-based output encoding provides us with the opportunity to do ensemble averaging to boost detection/localization scores. We experimentally demonstrate that the proposed CNN + CS framework (referred to as CNNCS) is competitive or better than the state-of-the-art methods on benchmark datasets for microscopy cell detection. In the AMIDA13 MICCAI grand competition, we achieve the 3rd highest F1-score in all the 17 participated teams.