Multimodal Data Fusion and Quantitative Analysis for Medical Applications

Medical big data is not only enormous in its size, but also heterogeneous and complex in its data structure, which makes conventional systems or algorithms difficult to process. These heterogeneous medical data include imaging data (e.g., Positron Emission Tomography (PET), Computerized Tomography (CT), Magnetic Resonance Imaging (MRI)), and non-imaging data (e.g., laboratory biomarkers, electronic medical records, and hand-written doctor notes). Multimodal data fusion is an emerging vital field to address this urgent challenge, aiming to process and analyze the complex, diverse and heterogeneous multimodal data. The fusion algorithms bring great potential in medical data analysis, by 1) taking advantage of complementary information from different sources (such as functional-structural complementarity of PET/CT images) and 2) exploiting consensus information that reflects the intrinsic essence (such as the genetic essence underlying medical imaging and clinical symptoms). Thus, multimodal data fusion benefits a wide range of quantitative medical applications, including personalized patient care, more optimal medical operation plan, and preventive public health. Though there has been extensive research on computational approaches for multimodal fusion, there are three major challenges of multimodal data fusion in quantitative medical applications, which are summarized as feature-level fusion, information-level fusion and knowledge-level fusion: • Feature-level fusion. The first challenge is to mine multimodal biomarkers from high-dimensional small-sample multimodal medical datasets, which hinders the effective discovery of informative multimodal biomarkers. Specifically, efficient dimension reduction algorithms are required to alleviate "curse of dimensionality" problem and address the criteria for discovering interpretable, relevant, non-redundant and generalizable multimodal biomarkers. • Information-level fusion. The second challenge is to exploit and interpret inter-modal and intra-modal information for precise clinical decisions. Although radiomics and multi-branch deep learning have been used for implicit information fusion guided with supervision of the labels, there is a lack of methods to explicitly explore inter-modal relationships in medical applications. Unsupervised multimodal learning is able to mine inter-modal relationship as well as reduce the usage of labor-intensive data and explore potential undiscovered biomarkers; however, mining discriminative information without label supervision is an upcoming challenge. Furthermore, the interpretation of complex non-linear cross-modal associations, especially in deep multimodal learning, is another critical challenge in information-level fusion, which hinders the exploration of multimodal interaction in disease mechanism. • Knowledge-level fusion. The third challenge is quantitative knowledge distillation from multi-focus regions on medical imaging. Although characterizing imaging features from single lesions using either feature engineering or deep learning methods have been investigated in recent years, both methods neglect the importance of inter-region spatial relationships. Thus, a topological profiling tool for multi-focus regions is in high demand, which is yet missing in current feature engineering and deep learning methods. Furthermore, incorporating domain knowledge with distilled knowledge from multi-focus regions is another challenge in knowledge-level fusion. To address the three challenges in multimodal data fusion, this thesis provides a multi-level fusion framework for multimodal biomarker mining, multimodal deep learning, and knowledge distillation from multi-focus regions. Specifically, our major contributions in this thesis include: • To address the challenges in feature-level fusion, we propose an Integrative Multimodal Biomarker Mining framework to select interpretable, relevant, non-redundant and generalizable multimodal biomarkers from high-dimensional small-sample imaging and non-imaging data for diagnostic and prognostic applications. The feature selection criteria including representativeness, robustness, discriminability, and non-redundancy are exploited by consensus clustering, Wilcoxon filter, sequential forward selection, and correlation analysis, respectively. SHapley Additive exPlanations (SHAP) method and nomogram are employed to further enhance feature interpretability in machine learning models. • To address the challenges in information-level fusion, we propose an Interpretable Deep Correlational Fusion framework, based on canonical correlation analysis (CCA) for 1) cohesive multimodal fusion of medical imaging and non-imaging data, and 2) interpretation of complex non-linear cross-modal associations. Specifically, two novel loss functions are proposed to optimize the discovery of informative multimodal representations in both supervised and unsupervised deep learning, by jointly learning inter-modal consensus and intra-modal discriminative information. An interpretation module is proposed to decipher the complex non-linear cross-modal association by leveraging interpretation methods in both deep learning and multimodal consensus learning. • To address the challenges in knowledge-level fusion, we proposed a Dynamic Topological Analysis framework, based on persistent homology, for knowledge distillation from inter-connected multi-focus regions in medical imaging and incorporation of domain knowledge. Different from conventional feature engineering and deep learning, our DTA framework is able to explicitly quantify inter-region topological relationships, including global-level geometric structure and community-level clusters. K-simplex Community Graph is proposed to construct the dynamic community graph for representing community-level multi-scale graph structure. The constructed dynamic graph is subsequently tracked with a novel Decomposed Persistence algorithm. Domain knowledge is incorporated into the Adaptive Community Profile, summarizing the tracked multi-scale community topology with additional customizable clinically important factors

Deep Active Learning Explored Across Diverse Label Spaces

abstract: Deep learning architectures have been widely explored in computer vision and have depicted commendable performance in a variety of applications. A fundamental challenge in training deep networks is the requirement of large amounts of labeled training data. While gathering large quantities of unlabeled data is cheap and easy, annotating the data is an expensive process in terms of time, labor and human expertise. Thus, developing algorithms that minimize the human effort in training deep models is of immense practical importance. Active learning algorithms automatically identify salient and exemplar samples from large amounts of unlabeled data and can augment maximal information to supervised learning models, thereby reducing the human annotation effort in training machine learning models. The goal of this dissertation is to fuse ideas from deep learning and active learning and design novel deep active learning algorithms. The proposed learning methodologies explore diverse label spaces to solve different computer vision applications. Three major contributions have emerged from this work; (i) a deep active framework for multi-class image classication, (ii) a deep active model with and without label correlation for multi-label image classi- cation and (iii) a deep active paradigm for regression. Extensive empirical studies on a variety of multi-class, multi-label and regression vision datasets corroborate the potential of the proposed methods for real-world applications. Additional contributions include: (i) a multimodal emotion database consisting of recordings of facial expressions, body gestures, vocal expressions and physiological signals of actors enacting various emotions, (ii) four multimodal deep belief network models and (iii) an in-depth analysis of the effect of transfer of multimodal emotion features between source and target networks on classification accuracy and training time. These related contributions help comprehend the challenges involved in training deep learning models and motivate the main goal of this dissertation.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201

Multimodal Machine Learning in Image-Based and Clinical Biomedicine: Survey and Prospects

Machine learning (ML) applications in medical artificial intelligence (AI) systems have shifted from traditional and statistical methods to increasing application of deep learning models. This survey navigates the current landscape of multimodal ML, focusing on its profound impact on medical image analysis and clinical decision support systems. Emphasizing challenges and innovations in addressing multimodal representation, fusion, translation, alignment, and co-learning, the paper explores the transformative potential of multimodal models for clinical predictions. It also highlights the need for principled assessments and practical implementation of such models, bringing attention to the dynamics between decision support systems and healthcare providers and personnel. Despite advancements, challenges such as data biases and the scarcity of "big data" in many biomedical domains persist. We conclude with a discussion on principled innovation and collaborative efforts to further the mission of seamless integration of multimodal ML models into biomedical practice

Deep Learning in Single-Cell Analysis

Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.Comment: 77 pages, 11 figures, 15 tables, deep learning, single-cell analysi

New ideas and trends in deep multimodal content understanding: a review

The focus of this survey is on the analysis of two modalities of multimodal deep learning: image and text. Unlike classic reviews of deep learning where monomodal image classifiers such as VGG, ResNet and Inception module are central topics, this paper will examine recent multimodal deep models and structures, including auto-encoders, generative adversarial nets and their variants. These models go beyond the simple image classifiers in which they can do uni-directional (e.g. image captioning, image generation) and bi-directional (e.g. cross-modal retrieval, visual question answering) multimodal tasks. Besides, we analyze two aspects of the challenge in terms of better content understanding in deep multimodal applications. We then introduce current ideas and trends in deep multimodal feature learning, such as feature embedding approaches and objective function design, which are crucial in overcoming the aforementioned challenges. Finally, we include several promising directions for future research.Computer Systems, Imagery and Medi

Unveiling the frontiers of deep learning: innovations shaping diverse domains

Deep learning (DL) enables the development of computer models that are capable of learning, visualizing, optimizing, refining, and predicting data. In recent years, DL has been applied in a range of fields, including audio-visual data processing, agriculture, transportation prediction, natural language, biomedicine, disaster management, bioinformatics, drug design, genomics, face recognition, and ecology. To explore the current state of deep learning, it is necessary to investigate the latest developments and applications of deep learning in these disciplines. However, the literature is lacking in exploring the applications of deep learning in all potential sectors. This paper thus extensively investigates the potential applications of deep learning across all major fields of study as well as the associated benefits and challenges. As evidenced in the literature, DL exhibits accuracy in prediction and analysis, makes it a powerful computational tool, and has the ability to articulate itself and optimize, making it effective in processing data with no prior training. Given its independence from training data, deep learning necessitates massive amounts of data for effective analysis and processing, much like data volume. To handle the challenge of compiling huge amounts of medical, scientific, healthcare, and environmental data for use in deep learning, gated architectures like LSTMs and GRUs can be utilized. For multimodal learning, shared neurons in the neural network for all activities and specialized neurons for particular tasks are necessary.Comment: 64 pages, 3 figures, 3 table

A Review of Deep Learning Techniques for Speech Processing

The field of speech processing has undergone a transformative shift with the advent of deep learning. The use of multiple processing layers has enabled the creation of models capable of extracting intricate features from speech data. This development has paved the way for unparalleled advancements in speech recognition, text-to-speech synthesis, automatic speech recognition, and emotion recognition, propelling the performance of these tasks to unprecedented heights. The power of deep learning techniques has opened up new avenues for research and innovation in the field of speech processing, with far-reaching implications for a range of industries and applications. This review paper provides a comprehensive overview of the key deep learning models and their applications in speech-processing tasks. We begin by tracing the evolution of speech processing research, from early approaches, such as MFCC and HMM, to more recent advances in deep learning architectures, such as CNNs, RNNs, transformers, conformers, and diffusion models. We categorize the approaches and compare their strengths and weaknesses for solving speech-processing tasks. Furthermore, we extensively cover various speech-processing tasks, datasets, and benchmarks used in the literature and describe how different deep-learning networks have been utilized to tackle these tasks. Additionally, we discuss the challenges and future directions of deep learning in speech processing, including the need for more parameter-efficient, interpretable models and the potential of deep learning for multimodal speech processing. By examining the field's evolution, comparing and contrasting different approaches, and highlighting future directions and challenges, we hope to inspire further research in this exciting and rapidly advancing field

Surrogate-assisted parallel tempering for Bayesian neural learning

Due to the need for robust uncertainty quantification, Bayesian neural learning has gained attention in the era of deep learning and big data. Markov Chain Monte-Carlo (MCMC) methods typically implement Bayesian inference which faces several challenges given a large number of parameters, complex and multimodal posterior distributions, and computational complexity of large neural network models. Parallel tempering MCMC addresses some of these limitations given that they can sample multimodal posterior distributions and utilize high-performance computing. However, certain challenges remain given large neural network models and big data. Surrogate-assisted optimization features the estimation of an objective function for models which are computationally expensive. In this paper, we address the inefficiency of parallel tempering MCMC for large-scale problems by combining parallel computing features with surrogate assisted likelihood estimation that describes the plausibility of a model parameter value, given specific observed data. Hence, we present surrogate-assisted parallel tempering for Bayesian neural learning for simple to computationally expensive models. Our results demonstrate that the methodology significantly lowers the computational cost while maintaining quality in decision making with Bayesian neural networks. The method has applications for a Bayesian inversion and uncertainty quantification for a broad range of numerical models.Comment: Engineering Applications of Artificial Intelligenc

MER 2023: Multi-label Learning, Modality Robustness, and Semi-Supervised Learning

Over the past few decades, multimodal emotion recognition has made remarkable progress with the development of deep learning. However, existing technologies are difficult to meet the demand for practical applications. To improve the robustness, we launch a Multimodal Emotion Recognition Challenge (MER 2023) to motivate global researchers to build innovative technologies that can further accelerate and foster research. For this year's challenge, we present three distinct sub-challenges: (1) MER-MULTI, in which participants recognize both discrete and dimensional emotions; (2) MER-NOISE, in which noise is added to test videos for modality robustness evaluation; (3) MER-SEMI, which provides large amounts of unlabeled samples for semi-supervised learning. In this paper, we test a variety of multimodal features and provide a competitive baseline for each sub-challenge. Our system achieves 77.57% on the F1 score and 0.82 on the mean squared error (MSE) for MER-MULTI, 69.82% on the F1 score and 1.12 on MSE for MER-NOISE, and 86.75% on the F1 score for MER-SEMI, respectively. Baseline code is available at https://github.com/zeroQiaoba/MER2023-Baseline