Automatic Whole Slide Pathology Image Diagnosis Framework via Unit Stochastic Selection and Attention Fusion.

Pathology tissue slides are taken as the gold standard for the diagnosis of most cancer diseases. Automatic pathology slide diagnosis is still a challenging task for researchers because of the high-resolution, significant morphological variation, and ambiguity between malignant and benign regions in whole slide images (WSIs). In this study, we introduce a general framework to automatically diagnose different types of WSIs via unit stochastic selection and attention fusion. For example, a unit can denote a patch in a histopathology slide or a cell in a cytopathology slide. To be specific, we first train a unit-level convolutional neural network (CNN) to perform two tasks: constructing feature extractors for the units and for estimating a unit's non-benign probability. Then we use our novel stochastic selection algorithm to choose a small subset of units that are most likely to be non-benign, referred to as the Units Of Interest (UOI), as determined by the CNN. Next, we use the attention mechanism to fuse the representations of the UOI to form a fixed-length descriptor for the WSI's diagnosis. We evaluate the proposed framework on three datasets: histological thyroid frozen sections, histological colonoscopy tissue slides, and cytological cervical pap smear slides. The framework achieves diagnosis accuracies higher than 0.8 and AUC values higher than 0.85 in all three applications. Experiments demonstrate the generality and effectiveness of the proposed framework and its potentiality for clinical applications.

Fusing remote sensing data with spatiotemporal in situ samples for red tide (Karenia brevis) detection.

We present a novel method for detecting red tide (Karenia brevis) blooms off the west coast of Florida, driven by a neural network classifier that combines remote sensing data with spatiotemporally distributed in situ sample data. The network detects blooms over a 1-km grid, using seven ocean color features from the MODIS-Aqua satellite platform (2002-2021) and in situ sample data collected by the Florida Fish and Wildlife Conservation Commission and its partners. Model performance was demonstrably enhanced by two key innovations: depth normalization of satellite features and encoding of an in situ feature. The satellite features were normalized to adjust for depth-dependent bottom reflection effects in shallow coastal waters. The in situ data were used to engineer a feature that contextualizes recent nearby ground truth of K. brevis concentrations through a K-nearest neighbor spatiotemporal proximity weighting scheme. A rigorous experimental comparison revealed that our model outperforms existing remote detection methods presented in the literature and applied in practice. This classifier has strong potential to be operationalized to support more efficient monitoring and mitigation of future blooms, more accurate communication about their spatial extent and distribution, and a deeper scientific understanding of bloom dynamics, transport, drivers, and impacts in the region. This approach also has the potential to be adapted for the detection of other algal blooms in coastal waters. Integr Environ Assess Manag 2024;00:1-15. © 2024 SETAC.

Interactive thyroid whole slide image diagnostic system using deep representation.

BACKGROUND AND OBJECTIVES: The vast size of the histopathology whole slide image poses formidable challenges to its automatic diagnosis. With the goal of computer-aided diagnosis and the insights that suspicious regions are generally easy to identify in thyroid whole slide images (WSIs), we develop an interactive whole slide diagnostic system for thyroid frozen sections based on the suspicious regions preselected by pathologists. METHODS: We propose to generate feature representations for the suspicious regions via extracting and fusing patch features using deep neural networks. We then evaluate region classification and retrieval on four classifiers and three supervised hashing methods based on the feature representations. The code is released at https://github.com/PingjunChen/ThyroidInteractive. RESULTS: We evaluate the proposed system on 345 thyroid frozen sections and achieve 96.1% cross-validated classification accuracy, and retrieval mean average precision (MAP) of 0.972. CONCLUSIONS: With the participation of pathologists, the system possesses the following four notable advantages compared to directly handling whole slide images: 1) Reduced interference of irrelevant regions; 2) Alleviated computation and memory cost. 3) Fine-grained and precise suspicious region retrieval. 4) Cooperative relationship between pathologists and the diagnostic system. Additionally, experimental results demonstrate the potential of the proposed system on the practical thyroid frozen section diagnosis.

Hyperspectral tree crown classification using the multiple instance adaptive cosine estimator.

Tree species classification using hyperspectral imagery is a challenging task due to the high spectral similarity between species and large intra-species variability. This paper proposes a solution using the Multiple Instance Adaptive Cosine Estimator (MI-ACE) algorithm. MI-ACE estimates a discriminative target signature to differentiate between a pair of tree species while accounting for label uncertainty. Multi-class species classification is achieved by training a set of one-vs-one MI-ACE classifiers corresponding to the classification between each pair of tree species and a majority voting on the classification results from all classifiers. Additionally, the performance of MI-ACE does not rely on parameter settings that require tuning resulting in a method that is easy to use in application. Results presented are using training and testing data provided by a data analysis competition aimed at encouraging the development of methods for extracting ecological information through remote sensing obtained through participation in the competition. The experimental results using one-vs-one MI-ACE technique composed of a hierarchical classification, where a tree crown is first classified to one of the genus classes and one of the species classes. The species-level rank-1 classification accuracy is 86.4% and cross entropy is 0.9395 on the testing data, provided by the competition organizer, without the release of ground truth for testing data. Similarly, the same evaluation metrics are computed on the training data, where the rank-1 classification accuracy is 95.62% and the cross entropy is 0.2649. The results show that the presented approach can not only classify the majority species classes, but also classify the rare species classes.

A Gaussian Mixture Model Representation of Endmember Variability in Hyperspectral Unmixing.

Hyperspectral unmixing while considering endmember variability is usually performed by the normal compositional model, where the endmembers for each pixel are assumed to be sampled from unimodal Gaussian distributions. However, in real applications, the distribution of a material is often not Gaussian. In this paper, we use Gaussian mixture models (GMM) to represent endmember variability. We show, given the GMM starting premise, that the distribution of the mixed pixel (under the linear mixing model) is also a GMM (and this is shown from two perspectives). The first perspective originates from random variable transformations and gives a conditional density function of the pixels given the abundances and GMM parameters. With proper smoothness and sparsity prior constraints on the abundances, the conditional density function leads to a standard maximum a posteriori (MAP ) problem which can be solved using generalized expectation maximization. The second perspective originates from marginalizing over the endmembers in the GMM, which provides us with a foundation to solve for the endmembers at each pixel. Hence, compared to the other distribution based methods, our model can not only estimate the abundances and distribution parameters, but also the distinct endmember set for each pixel. We tested the proposed GMM on several synthetic and real datasets, and showed its potential by comparing it to current popular methods.

A spatial compositional model for linear unmixing and endmember uncertainty estimation.

The normal compositional model (NCM) has been extensively used in hyperspectral unmixing. However, previous research has mostly focused on estimation of endmembers and/or their variability, based on the assumption that the pixels are independent random variables. In this paper, we show that this assumption does not hold if all the pixels are generated by a fixed endmember set. This introduces another concept, endmember uncertainty, which is related to whether the pixels fit into the endmember simplex. To further develop this idea, we derive the NCM from the ground up without the pixel independence assumption, along with (i) using different noise levels at different wavelengths and (ii) using a spatial and sparsity promoting prior for the abundances. The resulting new formulation is called the spatial compositional model (SCM) to better differentiate it from the NCM. The SCM maximum a posteriori (MAP) objective leads to an optimization problem featuring noise weighted least-squares minimization for unmixing. The problem is solved by projected gradient descent, resulting in an algorithm that estimates endmembers, abundances, noise variances, and endmember uncertainty simultaneously. We compared SCM with current state-of-the-art algorithms on synthetic and real images. The results show that SCM can in the main provide more accurate endmembers and abundances. Moreover, the estimated uncertainty can serve as a prediction of endmember error under certain conditions.

Twenty years of mixture of experts.

In this paper, we provide a comprehensive survey of the mixture of experts (ME). We discuss the fundamental models for regression and classification and also their training with the expectation-maximization algorithm. We follow the discussion with improvements to the ME model and focus particularly on the mixtures of Gaussian process experts. We provide a review of the literature for other training methods, such as the alternative localized ME training, and cover the variational learning of ME in detail. In addition, we describe the model selection literature which encompasses finding the optimum number of experts, as well as the depth of the tree. We present the advances in ME in the classification area and present some issues concerning the classification model. We list the statistical properties of ME, discuss how the model has been modified over the years, compare ME to some popular algorithms, and list several applications. We conclude our survey with future directions and provide a list of publicly available datasets and a list of publicly available software that implement ME. Finally, we provide examples for regression and classification. We believe that the study described in this paper will provide quick access to the relevant literature for researchers and practitioners who would like to improve or use ME, and that it will stimulate further studies in ME.

Generalized encoding and decoding operators for lattice-based associative memories.

During the 1990s Ritter, introduced a new family of associative memories based on lattice algebra instead of linear algebra. These memories provide unlimited storage capacity, unlike linear-correlation-based models. The canonical lattice-based memories, however, are susceptible to noise in the initial input data. In this brief, we present novel methods of encoding and decoding lattice-based memories using two families of ordered weighted average (OWA) operators. The result is a greater robustness to distortion in the initial input data, and a greater understanding of the effect of the choice of encoding and decoding operators on the behavior of the system, with the tradeoff that the time complexity for encoding is increased.

RKF-PCA: robust kernel fuzzy PCA.

Principal component analysis (PCA) is a mathematical method that reduces the dimensionality of the data while retaining most of the variation in the data. Although PCA has been applied in many areas successfully, it suffers from sensitivity to noise and is limited to linear principal components. The noise sensitivity problem comes from the least-squares measure used in PCA and the limitation to linear components originates from the fact that PCA uses an affine transform defined by eigenvectors of the covariance matrix and the mean of the data. In this paper, a robust kernel PCA method that extends the kernel PCA and uses fuzzy memberships is introduced to tackle the two problems simultaneously. We first introduce an iterative method to find robust principal components, called Robust Fuzzy PCA (RF-PCA), which has a connection with robust statistics and entropy regularization. The RF-PCA method is then extended to a non-linear one, Robust Kernel Fuzzy PCA (RKF-PCA), using kernels. The modified kernel used in the RKF-PCA satisfies the Mercer's condition, which means that the derivation of the K-PCA is also valid for the RKF-PCA. Formal analyses and experimental results suggest that the RKF-PCA is an efficient non-linear dimension reduction method and is more noise-robust than the original kernel PCA.