Developing robust movement decoders for local field potentials

textBrain Computer Interfaces (BCI) are devices that translate acquired neural signals to command and control signals. Applications of BCI include neural rehabilitation and neural prosthesis (thought controlled wheelchair, thought controlled speller etc.) to aid patients with disabilities and to augment human computer interaction. A successful practical BCI requires a faithful acquisition modality to record high quality neural signals; a signal processing system to construct appropriate features from these signals; and an algorithm to translate these features to appropriate outputs. Intracortical recordings like local field potentials provide reliable high SNR signals over long periods and suit BCI applications well. However, the non-stationarity of neural signals poses a challenge in robust decoding of subject behavior. Most BCI research focuses either on developing daily re-calibrated decoders that require exhaustive training sessions; or on providing cross-validation results. Such results ignore the variation of signal characteristics over different sessions and provide an optimistic estimate of BCI performance. Specifically, traditional BCI algorithms fail to perform at the same level on chronological data recordings. Neural signals are susceptible to variations in signal characteristics due to changes in subject behavior and learning, and variability in electrode characteristics due to tissue interactions. While training day-specific BCI overcomes signal variability, BCI re-training causes user frustration and exhaustion. This dissertation presents contributions to solve these challenges in BCI research. Specifically, we developed decoders trained on a single recording session and applied them on subsequently recorded sessions. This strategy evaluates BCI in a practical scenario with a potential to alleviate BCI user frustration without compromising performance. The initial part of the dissertation investigates extracting features that remain robust to changes in neural signal over several days of recordings. It presents a qualitative feature extraction technique based on ranking the instantaneous power of multichannel data. These qualitative features remain robust to outliers and changes in the baseline of neural recordings, while extracting discriminative information. These features form the foundation in developing robust decoders. Next, this dissertation presents a novel algorithm based on the hypothesis that multiple neural spatial patterns describe the variation in behavior. The presented algorithm outperforms the traditional methods in decoding over chronological recordings. Adapting such a decoder over multiple recording sessions (over 6 weeks) provided > 90% accuracy in decoding eight movement directions. In comparison, performance of traditional algorithms like Common Spatial Patterns deteriorates to 16% over the same time. Over time, adaptation reinforces some spatial patterns while diminishing others. Characterizing these spatial patterns reduces model complexity without user input, while retaining the same accuracy levels. Lastly, this dissertation provides an algorithm that overcomes the variation in recording quality. Chronic electrode implantation causes changes in signal-to-noise ratio (SNR) of neural signals. Thus, some signals and their corresponding features available during training become unavailable during testing and vice-versa. The proposed algorithm uses prior knowledge on spatial pattern evolution to estimate unknown neural features. This algorithm overcomes SNR variations and provides up to 93% decoding of eight movement directions over 6 weeks. Since model training requires only one session, this strategy reduces user frustration. In a practical closed-loop BCI, the user learns to produce stable spatial patterns, which improves performance of the proposed algorithms.Electrical and Computer Engineerin

End-to-End Tracking and Semantic Segmentation Using Recurrent Neural Networks

In this work we present a novel end-to-end framework for tracking and classifying a robot's surroundings in complex, dynamic and only partially observable real-world environments. The approach deploys a recurrent neural network to filter an input stream of raw laser measurements in order to directly infer object locations, along with their identity in both visible and occluded areas. To achieve this we first train the network using unsupervised Deep Tracking, a recently proposed theoretical framework for end-to-end space occupancy prediction. We show that by learning to track on a large amount of unsupervised data, the network creates a rich internal representation of its environment which we in turn exploit through the principle of inductive transfer of knowledge to perform the task of it's semantic classification. As a result, we show that only a small amount of labelled data suffices to steer the network towards mastering this additional task. Furthermore we propose a novel recurrent neural network architecture specifically tailored to tracking and semantic classification in real-world robotics applications. We demonstrate the tracking and classification performance of the method on real-world data collected at a busy road junction. Our evaluation shows that the proposed end-to-end framework compares favourably to a state-of-the-art, model-free tracking solution and that it outperforms a conventional one-shot training scheme for semantic classification

Contributions to statistical analysis methods for neural spiking activity

With the technical advances in neuroscience experiments in the past few decades, we have seen a massive expansion in our ability to record neural activity. These advances enable neuroscientists to analyze more complex neural coding and communication properties, and at the same time, raise new challenges for analyzing neural spiking data, which keeps growing in scale, dimension, and complexity. This thesis proposes several new statistical methods that advance statistical analysis approaches for neural spiking data, including sequential Monte Carlo (SMC) methods for efficient estimation of neural dynamics from membrane potential threshold crossings, state-space models using multimodal observation processes, and goodness-of-fit analysis methods for neural marked point process models. In a first project, we derive a set of iterative formulas that enable us to simulate trajectories from stochastic, dynamic neural spiking models that are consistent with a set of spike time observations. We develop a SMC method to simultaneously estimate the parameters of the model and the unobserved dynamic variables from spike train data. We investigate the performance of this approach on a leaky integrate-and-fire model. In another project, we define a semi-latent state-space model to estimate information related to the phenomenon of hippocampal replay. Replay is a recently discovered phenomenon where patterns of hippocampal spiking activity that typically occur during exploration of an environment are reactivated when an animal is at rest. This reactivation is accompanied by high frequency oscillations in hippocampal local field potentials. However, methods to define replay mathematically remain undeveloped. In this project, we construct a novel state-space model that enables us to identify whether replay is occurring, and if so to estimate the movement trajectories consistent with the observed neural activity, and to categorize the content of each event. The state-space model integrates information from the spiking activity from the hippocampal population, the rhythms in the local field potential, and the rat's movement behavior. Finally, we develop a new, general time-rescaling theorem for marked point processes, and use this to develop a general goodness-of-fit framework for neural population spiking models. We investigate this approach through simulation and a real data application

Developing implant technologies and evaluating brain-machine interfaces using information theory

Brain-machine interfaces (BMIs) hold promise for restoring motor functions in severely paralyzed individuals. Invasive BMIs are capable of recording signals from individual neurons and typically provide the highest signal-to-noise ratio. Despite many efforts in the scientific community, BMI technology is still not reliable enough for widespread clinical application. The most prominent challenges include biocompatibility, stability, longevity, and lack of good models for informed signal processing and BMI comparison. To address the problem of low signal quality of chronic probes, in the first part of the thesis one such design, the Neurotrophic Electrode, was modified by increasing its channel capacity to form a Neurotrophic Array (NA). Specifically, single wires were replaced with stereotrodes and the total number of recording wires was increased. This new array design was tested in a rhesus macaque performing a delayed saccade task. The NA recorded little single unit spiking activity, and its local field potentials (LFPs) correlated with presented visual stimuli and saccade locations better than did extracted spikes. The second part of the thesis compares the NA to the Utah Array (UA), the only other micro-array approved for chronic implantation in a human brain. The UA recorded significantly more spiking units, which had larger amplitudes than NA spikes. This was likely due to differences in the array geometry and construction. LFPs on the NA electrodes were more correlated with each other than those on the UA. These correlations negatively impacted the NA's information capacity when considering more than one recording site. The final part of this dissertation applies information theory to develop objective measures of BMI performance. Currently, decoder information transfer rate (ITR) is the most popular BMI information performance metric. However, it is limited by the selected decoding algorithm and does not represent the full task information embedded in the recorded neural signal. A review of existing methods to estimate ITR is presented, and these methods are interpreted within a BMI context. A novel Gaussian mixture Monte Carlo method is developed to produce good ITR estimates with a low number of trials and high number of dimensions, as is typical for BMI applications

Machine Learning for Physiological Time Series: Representing and Controlling Blood Glucose for Diabetes Management

Type 1 diabetes is a chronic health condition affecting over one million patients in the US, where blood glucose (sugar) levels are not well regulated by the body. Researchers have sought to use physiological data (e.g., blood glucose measurements) collected from wearable devices to manage this disease, either by forecasting future blood glucose levels for predictive alarms, or by automating insulin delivery for blood glucose management. However, the application of machine learning (ML) to these data is hampered by latent context, limited supervision and complex temporal dependencies. To address these challenges, we develop and evaluate novel ML approaches in the context of i) representing physiological time series, particularly for forecasting blood glucose values and ii) decision making for when and how much insulin to deliver. When learning representations, we leverage the structure of the physiological sequence as an implicit information stream. In particular, we a) incorporate latent context when predicting adverse events by jointly modeling patterns in the data and the context those patterns occurred under, b) propose novel types of self-supervision to handle limited data and c) propose deep models that predict functions underlying trajectories to encode temporal dependencies. In the context of decision making, we use reinforcement learning (RL) for blood glucose management. Through the use of an FDA-approved simulator of the glucoregulatory system, we achieve strong performance using deep RL with and without human intervention. However, the success of RL typically depends on realistic simulators or experimental real-world deployment, neither of which are currently practical for problems in health. Thus, we propose techniques for leveraging imperfect simulators and observational data. Beyond diabetes, representing and managing physiological signals is an important problem. By adapting techniques to better leverage the structure inherent in the data we can help overcome these challenges.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/163134/1/ifox_1.pd

강인한 음성인식을 위한 DNN 기반 음향 모델링

학위논문 (박사)-- 서울대학교 대학원 : 공과대학 전기·컴퓨터공학부, 2019. 2. 김남수.본 논문에서는 강인한 음성인식을 위해서 DNN을 활용한 음향 모델링 기법들을 제안한다. 본 논문에서는 크게 세 가지의 DNN 기반 기법을 제안한다. 첫 번째는 DNN이 가지고 있는 잡음 환경에 대한 강인함을 보조 특징 벡터들을 통하여 최대로 활용하는 음향 모델링 기법이다. 이러한 기법을 통하여 DNN은 왜곡된 음성, 깨끗한 음성, 잡음 추정치, 그리고 음소 타겟과의 복잡한 관계를 보다 원활하게 학습하게 된다. 본 기법은 Aurora-5 DB 에서 기존의 보조 잡음 특징 벡터를 활용한 모델 적응 기법인 잡음 인지 학습 (noise-aware training, NAT) 기법을 크게 뛰어넘는 성능을 보였다. 두 번째는 DNN을 활용한 다 채널 특징 향상 기법이다. 기존의 다 채널 시나리오에서는 전통적인 신호 처리 기법인 빔포밍 기법을 통하여 향상된 단일 소스 음성 신호를 추출하고 그를 통하여 음성인식을 수행한다. 우리는 기존의 빔포밍 중에서 가장 기본적 기법 중 하나인 delay-and-sum (DS) 빔포밍 기법과 DNN을 결합한 다 채널 특징 향상 기법을 제안한다. 제안하는 DNN은 중간 단계 특징 벡터를 활용한 공동 학습 기법을 통하여 왜곡된 다 채널 입력 음성 신호들과 깨끗한 음성 신호와의 관계를 효과적으로 표현한다. 제안된 기법은 multichannel wall street journal audio visual (MC-WSJAV) corpus에서의 실험을 통하여, 기존의 다채널 향상 기법들보다 뛰어난 성능을 보임을 확인하였다. 마지막으로, 불확정성 인지 학습 (Uncertainty-aware training, UAT) 기법이다. 위에서 소개된 기법들을 포함하여 강인한 음성인식을 위한 기존의 DNN 기반 기법들은 각각의 네트워크의 타겟을 추정하는데 있어서 결정론적인 추정 방식을 사용한다. 이는 추정치의 불확정성 문제 혹은 신뢰도 문제를 야기한다. 이러한 문제점을 극복하기 위하여 제안하는 UAT 기법은 확률론적인 변화 추정을 학습하고 수행할 수 있는 뉴럴 네트워크 모델인 변화 오토인코더 (variational autoencoder, VAE) 모델을 사용한다. UAT는 왜곡된 음성 특징 벡터와 음소 타겟과의 관계를 매개하는 강인한 은닉 변수를 깨끗한 음성 특징 벡터 추정치의 분포 정보를 이용하여 모델링한다. UAT의 은닉 변수들은 딥 러닝 기반 음향 모델에 최적화된 uncertainty decoding (UD) 프레임워크로부터 유도된 최대 우도 기준에 따라서 학습된다. 제안된 기법은 Aurora-4 DB와 CHiME-4 DB에서 기존의 DNN 기반 기법들을 크게 뛰어넘는 성능을 보였다.In this thesis, we propose three acoustic modeling techniques for robust automatic speech recognition (ASR). Firstly, we propose a DNN-based acoustic modeling technique which makes the best use of the inherent noise-robustness of DNN is proposed. By applying this technique, the DNN can automatically learn the complicated relationship among the noisy, clean speech and noise estimate to phonetic target smoothly. The proposed method outperformed noise-aware training (NAT), i.e., the conventional auxiliary-feature-based model adaptation technique in Aurora-5 DB. The second method is multi-channel feature enhancement technique. In the general multi-channel speech recognition scenario, the enhanced single speech signal source is extracted from the multiple inputs using beamforming, i.e., the conventional signal-processing-based technique and the speech recognition process is performed by feeding that source into the acoustic model. We propose the multi-channel feature enhancement DNN algorithm by properly combining the delay-and-sum (DS) beamformer, which is one of the conventional beamforming techniques and DNN. Through the experiments using multichannel wall street journal audio visual (MC-WSJ-AV) corpus, it has been shown that the proposed method outperformed the conventional multi-channel feature enhancement techniques. Finally, uncertainty-aware training (UAT) technique is proposed. The most of the existing DNN-based techniques including the techniques introduced above, aim to optimize the point estimates of the targets (e.g., clean features, and acoustic model parameters). This tampers with the reliability of the estimates. In order to overcome this issue, UAT employs a modified structure of variational autoencoder (VAE), a neural network model which learns and performs stochastic variational inference (VIF). UAT models the robust latent variables which intervene the mapping between the noisy observed features and the phonetic target using the distributive information of the clean feature estimates. The proposed technique outperforms the conventional DNN-based techniques on Aurora-4 and CHiME-4 databases.Abstract i Contents iv List of Figures ix List of Tables xiii 1 Introduction 1 2 Background 9 2.1 Deep Neural Networks . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2 Experimental Database . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.2.1 Aurora-4 DB . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.2.2 Aurora-5 DB . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 2.2.3 MC-WSJ-AV DB . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.2.4 CHiME-4 DB . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 3 Two-stage Noise-aware Training for Environment-robust Speech Recognition 25 iii 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 3.2 Noise-aware Training . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 3.3 Two-stage NAT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 3.3.1 Lower DNN . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 3.3.2 Upper DNN . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 3.3.3 Joint Training . . . . . . . . . . . . . . . . . . . . . . . . . . 35 3.4 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 3.4.1 GMM-HMM System . . . . . . . . . . . . . . . . . . . . . . . 37 3.4.2 Training and Structures of DNN-based Techniques . . . . . . 37 3.4.3 Performance Evaluation . . . . . . . . . . . . . . . . . . . . . 40 3.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 4 DNN-based Feature Enhancement for Robust Multichannel Speech Recognition 45 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 4.2 Observation Model in Multi-Channel Reverberant Noisy Environment 49 4.3 Proposed Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 4.3.1 Lower DNN . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 4.3.2 Upper DNN and Joint Training . . . . . . . . . . . . . . . . . 54 4.4 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 4.4.1 Recognition System and Feature Extraction . . . . . . . . . . 56 4.4.2 Training and Structures of DNN-based Techniques . . . . . . 58 4.4.3 Dropout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 4.4.4 Performance Evaluation . . . . . . . . . . . . . . . . . . . . . 62 4.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 iv 5 Uncertainty-aware Training for DNN-HMM System using Varia- tional Inference 67 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 5.2 Uncertainty Decoding for Noise Robustness . . . . . . . . . . . . . . 72 5.3 Variational Autoencoder . . . . . . . . . . . . . . . . . . . . . . . . . 77 5.4 VIF-based uncertainty-aware Training . . . . . . . . . . . . . . . . . 83 5.4.1 Clean Uncertainty Network . . . . . . . . . . . . . . . . . . . 91 5.4.2 Environment Uncertainty Network . . . . . . . . . . . . . . . 93 5.4.3 Prediction Network and Joint Training . . . . . . . . . . . . . 95 5.5 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 5.5.1 Experimental Setup: Feature Extraction and ASR System . . 96 5.5.2 Network Structures . . . . . . . . . . . . . . . . . . . . . . . . 98 5.5.3 Eects of CUN on the Noise Robustness . . . . . . . . . . . . 104 5.5.4 Uncertainty Representation in Dierent SNR Condition . . . 105 5.5.5 Result of Speech Recognition . . . . . . . . . . . . . . . . . . 112 5.5.6 Result of Speech Recognition with LSTM-HMM . . . . . . . 114 5.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 6 Conclusions 127 Bibliography 131 요약 145Docto