From Nano to Macro: Overview of the IEEE Bio Image and Signal Processing Technical Committee

The Bio Image and Signal Processing (BISP) Technical Committee (TC) of the IEEE Signal Processing Society (SPS) promotes activities within the broad technical field of biomedical image and signal processing. Areas of interest include medical and biological imaging, digital pathology, molecular imaging, microscopy, and associated computational imaging, image analysis, and image-guided treatment, alongside physiological signal processing, computational biology, and bioinformatics. BISP has 40 members and covers a wide range of EDICS, including CIS-MI: Medical Imaging, BIO-MIA: Medical Image Analysis, BIO-BI: Biological Imaging, BIO: Biomedical Signal Processing, BIO-BCI: Brain/Human-Computer Interfaces, and BIO-INFR: Bioinformatics. BISP plays a central role in the organization of the IEEE International Symposium on Biomedical Imaging (ISBI) and contributes to the technical sessions at the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), and the IEEE International Conference on Image Processing (ICIP). In this paper, we provide a brief history of the TC, review the technological and methodological contributions its community delivered, and highlight promising new directions we anticipate

Adaptive and Topological Deep Learning with applications to Neuroscience

Deep Learning and neuroscience have developed a two way relationship with each informing the other. Neural networks, the main tools at the heart of Deep Learning, were originally inspired by connectivity in the brain and have now proven to be critical to state-of-the-art computational neuroscience methods. This dissertation explores this relationship, first, by developing an adaptive sampling method for a neural network-based partial different equation solver and then by developing a topological deep learning framework for neural spike decoding. We demonstrate that our adaptive scheme is convergent and more accurate than DGM -- as long as the residual mirrors the local error -- at the same number of training steps and using the same or less number of training points. We present a multitude of tests applied to selected PDEs discussing the robustness of our scheme. Next, we further illustrate the partnership between deep learning and neuroscience by decoding neural activity using a novel neural network architecture developed to exploit the underlying connectivity of the data by employing tools from Topological Data Analysis. Neurons encode information like external stimuli or allocentric location by generating firing patterns where specific ensembles of neurons fire simultaneously for one value. Understanding, representing, and decoding these neural structures require models that encompass higher order connectivity than traditional graph-based models may provide. Our framework combines unsupervised simplicial complex discovery with the power of deep learning via a new architecture we develop herein called a simplicial convolutional recurrent neural network (SCRNN). Simplicial complexes, topological spaces that use not only vertices and edges but also higher-dimensional objects, naturally generalize graphs and capture more than just pairwise relationships. The effectiveness and versatility of the SCRNN is demonstrated on head direction data to test its performance and then applied to grid cell datasets with the task to automatically predict trajectories

Deriving and Exploiting Situational Information in Speech: Investigations in a Simulated Search and Rescue Scenario

The need for automatic recognition and understanding of speech is emerging in tasks involving the processing of large volumes of natural conversations. In application domains such as Search and Rescue, exploiting automated systems for extracting mission-critical information from speech communications has the potential to make a real difference. Spoken language understanding has commonly been approached by identifying units of meaning (such as sentences, named entities, and dialogue acts) for providing a basis for further discourse analysis. However, this fine-grained identification of fundamental units of meaning is sensitive to high error rates in the automatic transcription of noisy speech. This thesis demonstrates that topic segmentation and identification techniques can be employed for information extraction from spoken conversations by being robust to such errors. Two novel topic-based approaches are presented for extracting situational information within the search and rescue context. The first approach shows that identifying the changes in the context and content of first responders' report over time can provide an estimation of their location. The second approach presents a speech-based topological map estimation technique that is inspired, in part, by automatic mapping algorithms commonly used in robotics. The proposed approaches are evaluated on a goal-oriented conversational speech corpus, which has been designed and collected based on an abstract communication model between a first responder and a task leader during a search process. Results have confirmed that a highly imperfect transcription of noisy speech has limited impact on the information extraction performance compared with that obtained on the transcription of clean speech data. This thesis also shows that speech recognition accuracy can benefit from rescoring its initial transcription hypotheses based on the derived high-level location information. A new two-pass speech decoding architecture is presented. In this architecture, the location estimation from a first decoding pass is used to dynamically adapt a general language model which is used for rescoring the initial recognition hypotheses. This decoding strategy has resulted in a statistically significant gain in the recognition accuracy of the spoken conversations in high background noise. It is concluded that the techniques developed in this thesis can be extended to more application domains that deal with large volumes of natural spoken conversations

Novel Architectures and Optimization Algorithms for Training Neural Networks and Applications

The two main areas of Deep Learning are Unsupervised and Supervised Learning. Unsupervised Learning studies a class of data processing problems in which only descriptions of objects are known, without label information. Generative Adversarial Networks (GANs) have become among the most widely used unsupervised neural net models. GAN combines two neural nets, generative and discriminative, that work simultaneously. We introduce a new family of discriminator loss functions that adopts a weighted sum of real and fake parts, which we call adaptive weighted loss functions. Using the gradient information, we can adaptively choose weights to train a discriminator in the direction that benefits the GAN\u27s stability. Also, we propose several improvements to the GAN training schemes. One is self-correcting optimization for training a GAN discriminator on Speech Enhancement tasks, which helps avoid ``harmful\u27\u27 training directions for parts of the discriminator loss. The other improvement is a consistency loss, which targets the inconsistency in time and time-frequency domains caused by Fourier Transforms. Contrary to Unsupervised Learning, Supervised Learning uses labels for each object, and it is required to find the relationship between objects and labels. Building computing methods to interpret and represent human language automatically is known as Natural Language Processing which includes tasks such as word prediction, machine translation, etc. In this area, we propose a novel Neumann-Cayley Gated Recurrent Unit (NC-GRU) architecture based on a Neumann series-based Scaled Cayley transformation. The NC-GRU uses orthogonal matrices to prevent exploding gradient problems and enhance long-term memory on various prediction tasks. In addition, we propose using our newly introduced NC-GRU unit inside Neural Nets model to create neural molecular fingerprints. Integrating novel NC-GRU fingerprints and Multi-Task Deep Neural Networks schematics help to improve the performance of several molecular-related tasks. We also introduce a new normalization method - Assorted-Time Normalization, that helps to preserve information from multiple consecutive time steps and normalize using them in Recurrent Nets like architectures. Finally, we propose a Symmetry Structured Convolutional Neural Network (SCNN), an architecture with 2D structured symmetric features over spatial dimensions, that generates and preserves the symmetry structure in the network\u27s convolutional layers

EMG-to-Speech: Direct Generation of Speech from Facial Electromyographic Signals

The general objective of this work is the design, implementation, improvement and evaluation of a system that uses surface electromyographic (EMG) signals and directly synthesizes an audible speech output: EMG-to-speech

Computer analysis of children's non-native English speech for language learning and assessment

Children's ASR appears to be more challenging than adults' and it's even more difficult when it comes to non-native children's speech. This research investigates different techniques to compensate for the effects of non-native and children on the performance of ASR systems. The study mainly utilises hybrid DNN-HMM systems with conventional DNNs, LSTMs and more advanced TDNN models. This work uses the CALL-ST corpus and TLT-school corpus to study children's non-native English speech. Initially, data augmentation was explored on the CALL-ST corpus to address the lack of data problem using the AMI corpus and PF-STAR German corpus. Feature selection, acoustic model adaptation and selection were also investigated on CALL-ST. More aspects of the ASR system, including pronunciation modelling, acoustic modelling, language modelling and system fusion, were explored on the TLT-school corpus as this corpus has a bigger amount of data. Then, the relationships between the CALL-ST and TLT-school corpora were studied and utilised to improve ASR performance. The other part of the present work is text processing for non-native children's English speech. We focused on providing accept/reject feedback to learners based on the text generated by the ASR system from learners' spoken responses. A rule-based and a machine learning-based system were proposed for making the judgement, several aspects of the systems were evaluated. The influence of the ASR system on the text processing system was explored

Dynamical Networks of Social Influence: Modern Trends and Perspectives

Dynamics and control of processes over social networks, such as the evolution of opinions, social influence and interpersonal appraisals, diffusion of information and misinformation, emergence and dissociation of communities, are now attracting significant attention from the broad research community that works on systems, control, identification and learning. To provide an introduction to this rapidly developing area, a Tutorial Session was included into the program of IFAC World Congress 2020. This paper provides a brief summary of the three tutorial lectures, covering the most “mature” directions in analysis of social networks and dynamics over them: 1) formation of opinions under social influence; 2) identification and learning for analysis of a network’s structure; 3) dynamics of interpersonal appraisals