348 research outputs found

    On the Utility of Representation Learning Algorithms for Myoelectric Interfacing

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    Electrical activity produced by muscles during voluntary movement is a reflection of the firing patterns of relevant motor neurons and, by extension, the latent motor intent driving the movement. Once transduced via electromyography (EMG) and converted into digital form, this activity can be processed to provide an estimate of the original motor intent and is as such a feasible basis for non-invasive efferent neural interfacing. EMG-based motor intent decoding has so far received the most attention in the field of upper-limb prosthetics, where alternative means of interfacing are scarce and the utility of better control apparent. Whereas myoelectric prostheses have been available since the 1960s, available EMG control interfaces still lag behind the mechanical capabilities of the artificial limbs they are intended to steer—a gap at least partially due to limitations in current methods for translating EMG into appropriate motion commands. As the relationship between EMG signals and concurrent effector kinematics is highly non-linear and apparently stochastic, finding ways to accurately extract and combine relevant information from across electrode sites is still an active area of inquiry.This dissertation comprises an introduction and eight papers that explore issues afflicting the status quo of myoelectric decoding and possible solutions, all related through their use of learning algorithms and deep Artificial Neural Network (ANN) models. Paper I presents a Convolutional Neural Network (CNN) for multi-label movement decoding of high-density surface EMG (HD-sEMG) signals. Inspired by the successful use of CNNs in Paper I and the work of others, Paper II presents a method for automatic design of CNN architectures for use in myocontrol. Paper III introduces an ANN architecture with an appertaining training framework from which simultaneous and proportional control emerges. Paper Iv introduce a dataset of HD-sEMG signals for use with learning algorithms. Paper v applies a Recurrent Neural Network (RNN) model to decode finger forces from intramuscular EMG. Paper vI introduces a Transformer model for myoelectric interfacing that do not need additional training data to function with previously unseen users. Paper vII compares the performance of a Long Short-Term Memory (LSTM) network to that of classical pattern recognition algorithms. Lastly, paper vIII describes a framework for synthesizing EMG from multi-articulate gestures intended to reduce training burden

    Detection of entangled states supported by reinforcement learning

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    Discrimination of entangled states is an important element of quantum enhanced metrology. This typically requires low-noise detection technology. Such a challenge can be circumvented by introducing nonlinear readout process. Traditionally, this is realized by reversing the very dynamics that generates the entangled state, which requires a full control over the system evolution. In this work, we present nonlinear readout of highly entangled states by employing reinforcement learning (RL) to manipulate the spin-mixing dynamics in a spin-1 atomic condensate. The RL found results in driving the system towards an unstable fixed point, whereby the (to be sensed) phase perturbation is amplified by the subsequent spin-mixing dynamics. Working with a condensate of 10900 {87}^Rb atoms, we achieve a metrological gain of 6.97 dB beyond the classical precision limit. Our work would open up new possibilities in unlocking the full potential of entanglement caused quantum enhancement in experiments

    Cancer Subtyping Detection using Biomarker Discovery in Multi-Omics Tensor Datasets

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    This thesis begins with a thorough review of research trends from 2015 to 2022, examining the challenges and issues related to biomarker discovery in multi-omics datasets. The review covers areas of application, proposed methodologies, evaluation criteria used to assess performance, as well as limitations and drawbacks that require further investigation and improvement. This comprehensive overview serves to provide a deeper understanding of the current state of research in this field and the opportunities for future research. It will be particularly useful for those who are interested in this area of study and seeking to expand their knowledge. In the second part of this thesis, a novel methodology is proposed for the identification of significant biomarkers in a multi-omics colon cancer dataset. The integration of clinical features with biomarker discovery has the potential to facilitate the early identification of mortality risk and the development of personalized therapies for a range of diseases, including cancer and stroke. Recent advancements in “omics� technologies have opened up new avenues for researchers to identify disease biomarkers through system-level analysis. Machine learning methods, particularly those based on tensor decomposition techniques, have gained popularity due to the challenges associated with integrative analysis of multi-omics data owing to the complexity of biological systems. Despite extensive efforts towards discovering disease-associated biomolecules by analyzing data from various “omics� experiments, such as genomics, transcriptomics, and metabolomics, the poor integration of diverse forms of 'omics' data has made the integrative analysis of multi-omics data a daunting task. Our research includes ANOVA simultaneous component analysis (ASCA) and Tucker3 modeling to analyze a multivariate dataset with an underlying experimental design. By comparing the spaces spanned by different model components we showed how the two methods can be used for confirmatory analysis and provide complementary information. we demonstrated the novel use of ASCA to analyze the residuals of Tucker3 models to find the optimum one. Increasing the model complexity to more factors removed the last remaining ASCA detectable structure in the residuals. Bootstrap analysis of the core matrix values of the Tucker3 models used to check that additional triads of eigenvectors were needed to describe the remaining structure in the residuals. Also, we developed a new simple, novel strategy for aligning Tucker3 bootstrap models with the Tucker3 model of the original data so that eigenvectors of the three modes, the order of the values in the core matrix, and their algebraic signs match the original Tucker3 model without the need for complicated bookkeeping strategies or performing rotational transformations. Additionally, to avoid getting an overparameterized Tucker3 model, we used the bootstrap method to determine 95% confidence intervals of the loadings and core values. Also, important variables for classification were identified by inspection of loading confidence intervals. The experimental results obtained using the colon cancer dataset demonstrate that our proposed methodology is effective in improving the performance of biomarker discovery in a multi-omics cancer dataset. Overall, our study highlights the potential of integrating multi-omics data with machine learning methods to gain deeper insights into the complex biological mechanisms underlying cancer and other diseases. The experimental results using NIH colon cancer dataset demonstrate that the successful application of our proposed methodology in cancer subtype classification provides a foundation for further investigation into its utility in other disease areas

    A primer on correlation-based dimension reduction methods for multi-omics analysis

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    The continuing advances of omic technologies mean that it is now more tangible to measure the numerous features collectively reflecting the molecular properties of a sample. When multiple omic methods are used, statistical and computational approaches can exploit these large, connected profiles. Multi-omics is the integration of different omic data sources from the same biological sample. In this review, we focus on correlation-based dimension reduction approaches for single omic datasets, followed by methods for pairs of omics datasets, before detailing further techniques for three or more omic datasets. We also briefly detail network methods when three or more omic datasets are available and which complement correlation-oriented tools. To aid readers new to this area, these are all linked to relevant R packages that can implement these procedures. Finally, we discuss scenarios of experimental design and present road maps that simplify the selection of appropriate analysis methods. This review will guide researchers navigate the emerging methods for multi-omics and help them integrate diverse omic datasets appropriately and embrace the opportunity of population multi-omics.Comment: 30 pages, 2 figures, 6 table

    Spherical and Hyperbolic Toric Topology-Based Codes On Graph Embedding for Ising MRF Models: Classical and Quantum Topology Machine Learning

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    The paper introduces the application of information geometry to describe the ground states of Ising models by utilizing parity-check matrices of cyclic and quasi-cyclic codes on toric and spherical topologies. The approach establishes a connection between machine learning and error-correcting coding. This proposed approach has implications for the development of new embedding methods based on trapping sets. Statistical physics and number geometry applied for optimize error-correcting codes, leading to these embedding and sparse factorization methods. The paper establishes a direct connection between DNN architecture and error-correcting coding by demonstrating how state-of-the-art architectures (ChordMixer, Mega, Mega-chunk, CDIL, ...) from the long-range arena can be equivalent to of block and convolutional LDPC codes (Cage-graph, Repeat Accumulate). QC codes correspond to certain types of chemical elements, with the carbon element being represented by the mixed automorphism Shu-Lin-Fossorier QC-LDPC code. The connections between Belief Propagation and the Permanent, Bethe-Permanent, Nishimori Temperature, and Bethe-Hessian Matrix are elaborated upon in detail. The Quantum Approximate Optimization Algorithm (QAOA) used in the Sherrington-Kirkpatrick Ising model can be seen as analogous to the back-propagation loss function landscape in training DNNs. This similarity creates a comparable problem with TS pseudo-codeword, resembling the belief propagation method. Additionally, the layer depth in QAOA correlates to the number of decoding belief propagation iterations in the Wiberg decoding tree. Overall, this work has the potential to advance multiple fields, from Information Theory, DNN architecture design (sparse and structured prior graph topology), efficient hardware design for Quantum and Classical DPU/TPU (graph, quantize and shift register architect.) to Materials Science and beyond.Comment: 71 pages, 42 Figures, 1 Table, 1 Appendix. arXiv admin note: text overlap with arXiv:2109.08184 by other author

    Mass spectral imaging of clinical samples using deep learning

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    A better interpretation of tumour heterogeneity and variability is vital for the improvement of novel diagnostic techniques and personalized cancer treatments. Tumour tissue heterogeneity is characterized by biochemical heterogeneity, which can be investigated by unsupervised metabolomics. Mass Spectrometry Imaging (MSI) combined with Machine Learning techniques have generated increasing interest as analytical and diagnostic tools for the analysis of spatial molecular patterns in tissue samples. Considering the high complexity of data produced by the application of MSI, which can consist of many thousands of spectral peaks, statistical analysis and in particular machine learning and deep learning have been investigated as novel approaches to deduce the relationships between the measured molecular patterns and the local structural and biological properties of the tissues. Machine learning have historically been divided into two main categories: Supervised and Unsupervised learning. In MSI, supervised learning methods may be used to segment tissues into histologically relevant areas e.g. the classification of tissue regions in H&E (Haemotoxylin and Eosin) stained samples. Initial classification by an expert histopathologist, through visual inspection enables the development of univariate or multivariate models, based on tissue regions that have significantly up/down-regulated ions. However, complex data may result in underdetermined models, and alternative methods that can cope with high dimensionality and noisy data are required. Here, we describe, apply, and test a novel diagnostic procedure built using a combination of MSI and deep learning with the objective of delineating and identifying biochemical differences between cancerous and non-cancerous tissue in metastatic liver cancer and epithelial ovarian cancer. The workflow investigates the robustness of single (1D) to multidimensional (3D) tumour analyses and also highlights possible biomarkers which are not accessible from classical visual analysis of the H&E images. The identification of key molecular markers may provide a deeper understanding of tumour heterogeneity and potential targets for intervention.Open Acces

    Deep Learning Techniques for Multi-Dimensional Medical Image Analysis

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    Space-Invariant Projection in Streaming Network Embedding

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    Newly arriving nodes in dynamics networks would gradually make the node embedding space drifted and the retraining of node embedding and downstream models indispensable. An exact threshold size of these new nodes, below which the node embedding space will be predicatively maintained, however, is rarely considered in either theory or experiment. From the view of matrix perturbation theory, a threshold of the maximum number of new nodes that keep the node embedding space approximately equivalent is analytically provided and empirically validated. It is therefore theoretically guaranteed that as the size of newly arriving nodes is below this threshold, embeddings of these new nodes can be quickly derived from embeddings of original nodes. A generation framework, Space-Invariant Projection (SIP), is accordingly proposed to enables arbitrary static MF-based embedding schemes to embed new nodes in dynamics networks fast. The time complexity of SIP is linear with the network size. By combining SIP with four state-of-the-art MF-based schemes, we show that SIP exhibits not only wide adaptability but also strong empirical performance in terms of efficiency and efficacy on the node classification task in three real datasets

    Nesting optimization with adversarial games, meta-learning, and deep equilibrium models

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    Nested optimization, whereby an optimization problem is constrained by the solutions of other optimization problems, has recently seen a surge in its application to Deep Learning. While the study of such problems started nearly a century ago in the context of market theory, many of the algorithms developed since do not scale to modern Deep Learning applications. In this thesis, I push the understanding and applicability of nested optimization to three machine learning domains: 1) adversarial games, 2) meta-learning and 3) deep equilibrium models. For each domain, I tackle a particular goal. In 1) I adversarially learn model compression, in the case where training data isn't available, in 2) I meta-learn hyperparameters for long optimization processes without introducing greediness, and in 3) I use deep equilibrium models to improve temporal coherence in video landmark detection. The first part of my thesis deals with casting model compression as an adversarial game. Performing knowledge transfer from a large teacher network to a smaller student is a popular task in deep learning. However, due to growing dataset sizes and stricter privacy regulations, it is increasingly common not to have access to the data that was used to train the teacher. I propose a novel method which trains a student to match the predictions of its teacher without using any data or metadata. This is achieved by nesting the training optimization of the student with that of an adversarial generator, which searches for images on which the student poorly matches the teacher. These images are used to train the student in an online fashion. The student closely approximates its teacher for simple datasets like SVHN, and on CIFAR10 I improve on the state-of-the-art for few-shot distillation (with 100100 images per class), despite using no data. Finally, I also propose a metric to quantify the degree of belief matching between teacher and student in the vicinity of decision boundaries, and observe a significantly higher match between the zero-shot student and the teacher, than between a student distilled with real data and the teacher. The second part of my thesis deals with meta-learning hyperparameters in the case when the nested optimization to be differentiated is itself solved by many gradient steps. Gradient-based hyperparameter optimization has earned a widespread popularity in the context of few-shot meta-learning, but remains broadly impractical for tasks with long horizons (many gradient steps), due to memory scaling and gradient degradation issues. A common workaround is to learn hyperparameters online, but this introduces greediness which comes with a significant performance drop. I propose forward-mode differentiation with sharing (FDS), a simple and efficient algorithm which tackles memory scaling issues with forward-mode differentiation, and gradient degradation issues by sharing hyperparameters that are contiguous in time. I provide theoretical guarantees about the noise reduction properties of my algorithm, and demonstrate its efficiency empirically by differentiating through 104\sim 10^4 gradient steps of unrolled optimization. I consider large hyperparameter search ranges on CIFAR-10 where I significantly outperform greedy gradient-based alternatives, while achieving ×20\times 20 speedups compared to the state-of-the-art black-box methods. The third part of my thesis deals with converting deep equilibrium models to a form of nested optimization in order to perform robust video landmark detection. Cascaded computation, whereby predictions are recurrently refined over several stages, has been a persistent theme throughout the development of landmark detection models. I show that the recently proposed deep equilibrium model (DEQ) can be naturally adapted to this form of computation, given appropriate regularization. My landmark model achieves state-of-the-art performance on the challenging WFLW facial landmark dataset, reaching 3.923.92 normalized mean error with fewer parameters and a training memory cost of O(1)\mathcal{O}(1) in the number of recurrent modules. Furthermore, I show that DEQs are particularly suited for landmark detection in videos. In this setting, it is typical to train on still images due to the lack of labeled videos. This can lead to a ``flickering'' effect at inference time on video, whereby a model can rapidly oscillate between different plausible solutions across consecutive frames. I show that the DEQ root solving problem can be turned into a constrained optimization problem in a way that emulates recurrence at inference time, despite not having access to temporal data at training time. I call this "Recurrence without Recurrence'', and demonstrate that it helps reduce landmark flicker by introducing a new metric, and contributing a new facial landmark video dataset targeting landmark uncertainty. On the hard subset of this new dataset, made up of 500500 videos, my model improves the accuracy and temporal coherence by 1010 and 13%13\% respectively, compared to the strongest previously published model using a hand-tuned conventional filter

    Machine Learning and Its Application to Reacting Flows

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    This open access book introduces and explains machine learning (ML) algorithms and techniques developed for statistical inferences on a complex process or system and their applications to simulations of chemically reacting turbulent flows. These two fields, ML and turbulent combustion, have large body of work and knowledge on their own, and this book brings them together and explain the complexities and challenges involved in applying ML techniques to simulate and study reacting flows. This is important as to the world’s total primary energy supply (TPES), since more than 90% of this supply is through combustion technologies and the non-negligible effects of combustion on environment. Although alternative technologies based on renewable energies are coming up, their shares for the TPES is are less than 5% currently and one needs a complete paradigm shift to replace combustion sources. Whether this is practical or not is entirely a different question, and an answer to this question depends on the respondent. However, a pragmatic analysis suggests that the combustion share to TPES is likely to be more than 70% even by 2070. Hence, it will be prudent to take advantage of ML techniques to improve combustion sciences and technologies so that efficient and “greener” combustion systems that are friendlier to the environment can be designed. The book covers the current state of the art in these two topics and outlines the challenges involved, merits and drawbacks of using ML for turbulent combustion simulations including avenues which can be explored to overcome the challenges. The required mathematical equations and backgrounds are discussed with ample references for readers to find further detail if they wish. This book is unique since there is not any book with similar coverage of topics, ranging from big data analysis and machine learning algorithm to their applications for combustion science and system design for energy generation
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