Recent Progress in Transformer-based Medical Image Analysis

The transformer is primarily used in the field of natural language processing. Recently, it has been adopted and shows promise in the computer vision (CV) field. Medical image analysis (MIA), as a critical branch of CV, also greatly benefits from this state-of-the-art technique. In this review, we first recap the core component of the transformer, the attention mechanism, and the detailed structures of the transformer. After that, we depict the recent progress of the transformer in the field of MIA. We organize the applications in a sequence of different tasks, including classification, segmentation, captioning, registration, detection, enhancement, localization, and synthesis. The mainstream classification and segmentation tasks are further divided into eleven medical image modalities. A large number of experiments studied in this review illustrate that the transformer-based method outperforms existing methods through comparisons with multiple evaluation metrics. Finally, we discuss the open challenges and future opportunities in this field. This task-modality review with the latest contents, detailed information, and comprehensive comparison may greatly benefit the broad MIA community.Comment: Computers in Biology and Medicine Accepte

Articulatory Copy Synthesis Based on the Speech Synthesizer VocalTractLab

Articulatory copy synthesis (ACS), a subarea of speech inversion, refers to the reproduction of natural utterances and involves both the physiological articulatory processes and their corresponding acoustic results. This thesis proposes two novel methods for the ACS of human speech using the articulatory speech synthesizer VocalTractLab (VTL) to address or mitigate the existing problems of speech inversion, such as non-unique mapping, acoustic variation among different speakers, and the time-consuming nature of the process. The first method involved finding appropriate VTL gestural scores for given natural utterances using a genetic algorithm. It consisted of two steps: gestural score initialization and optimization. In the first step, gestural scores were initialized using the given acoustic signals with speech recognition, grapheme-to-phoneme (G2P), and a VTL rule-based method for converting phoneme sequences to gestural scores. In the second step, the initial gestural scores were optimized by a genetic algorithm via an analysis-by-synthesis (ABS) procedure that sought to minimize the cosine distance between the acoustic features of the synthetic and natural utterances. The articulatory parameters were also regularized during the optimization process to restrict them to reasonable values. The second method was based on long short-term memory (LSTM) and convolutional neural networks, which were responsible for capturing the temporal dependence and the spatial structure of the acoustic features, respectively. The neural network regression models were trained, which used acoustic features as inputs and produced articulatory trajectories as outputs. In addition, to cover as much of the articulatory and acoustic space as possible, the training samples were augmented by manipulating the phonation type, speaking effort, and the vocal tract length of the synthetic utterances. Furthermore, two regularization methods were proposed: one based on the smoothness loss of articulatory trajectories and another based on the acoustic loss between original and predicted acoustic features. The best-performing genetic algorithms and convolutional LSTM systems (evaluated in terms of the difference between the estimated and reference VTL articulatory parameters) obtained average correlation coefficients of 0.985 and 0.983 for speaker-dependent utterances, respectively, and their reproduced speech achieved recognition accuracies of 86.25% and 64.69% for speaker-independent utterances of German words, respectively. When applied to German sentence utterances, as well as English and Mandarin Chinese word utterances, the neural network based ACS systems achieved recognition accuracies of 73.88%, 52.92%, and 52.41%, respectively. The results showed that both of these methods not only reproduced the articulatory processes but also reproduced the acoustic signals of reference utterances. Moreover, the regularization methods led to more physiologically plausible articulatory processes and made the estimated articulatory trajectories be more articulatorily preferred by VTL, thus reproducing more natural and intelligible speech. This study also found that the convolutional layers, when used in conjunction with batch normalization layers, automatically learned more distinctive features from log power spectrograms. Furthermore, the neural network based ACS systems trained using German data could be generalized to the utterances of other languages

On Improving Generalization of CNN-Based Image Classification with Delineation Maps Using the CORF Push-Pull Inhibition Operator

Deployed image classification pipelines are typically dependent on the images captured in real-world environments. This means that images might be affected by different sources of perturbations (e.g. sensor noise in low-light environments). The main challenge arises by the fact that image quality directly impacts the reliability and consistency of classification tasks. This challenge has, hence, attracted wide interest within the computer vision communities. We propose a transformation step that attempts to enhance the generalization ability of CNN models in the presence of unseen noise in the test set. Concretely, the delineation maps of given images are determined using the CORF push-pull inhibition operator. Such an operation transforms an input image into a space that is more robust to noise before being processed by a CNN. We evaluated our approach on the Fashion MNIST data set with an AlexNet model. It turned out that the proposed CORF-augmented pipeline achieved comparable results on noise-free images to those of a conventional AlexNet classification model without CORF delineation maps, but it consistently achieved significantly superior performance on test images perturbed with different levels of Gaussian and uniform noise

Introduction to Facial Micro Expressions Analysis Using Color and Depth Images: A Matlab Coding Approach (Second Edition, 2023)

The book attempts to introduce a gentle introduction to the field of Facial Micro Expressions Recognition (FMER) using Color and Depth images, with the aid of MATLAB programming environment. FMER is a subset of image processing and it is a multidisciplinary topic to analysis. So, it requires familiarity with other topics of Artifactual Intelligence (AI) such as machine learning, digital image processing, psychology and more. So, it is a great opportunity to write a book which covers all of these topics for beginner to professional readers in the field of AI and even without having background of AI. Our goal is to provide a standalone introduction in the field of MFER analysis in the form of theorical descriptions for readers with no background in image processing with reproducible Matlab practical examples. Also, we describe any basic definitions for FMER analysis and MATLAB library which is used in the text, that helps final reader to apply the experiments in the real-world applications. We believe that this book is suitable for students, researchers, and professionals alike, who need to develop practical skills, along with a basic understanding of the field. We expect that, after reading this book, the reader feels comfortable with different key stages such as color and depth image processing, color and depth image representation, classification, machine learning, facial micro-expressions recognition, feature extraction and dimensionality reduction. The book attempts to introduce a gentle introduction to the field of Facial Micro Expressions Recognition (FMER) using Color and Depth images, with the aid of MATLAB programming environment.Comment: This is the second edition of the boo