Human activity recognition using magnetic induction-based motion signals and deep recurrent neural networks.
Ontology highlight
ABSTRACT:
SUBMITTER: Golestani N
PROVIDER: S-EPMC7096402 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
Publications
Human activity recognition using magnetic induction-based motion signals and deep recurrent neural networks.
Golestani Negar N Moghaddam Mahta M
Nature communications 20200325 1
Recognizing human physical activities using wireless sensor networks has attracted significant research interest due to its broad range of applications, such as healthcare, rehabilitation, athletics, and senior monitoring. There are critical challenges inherent in designing a sensor-based activity recognition system operating in and around a lossy medium such as the human body to gain a trade-off among power consumption, cost, computational complexity, and accuracy. We introduce an innovative wi ...[more]
Similar Datasets
Project description:The discovery and development of novel pharmaceuticals is an area of active research mainly due to the large investments required and long payback times. As of 2016, the development of a novel drug candidate required up to $ USD 2.6 billion in investment for only 10% rate of approval by the FDA. To help decreasing the costs associated with the process, a number of in silico approaches have been developed with relatively low success due to limited predicting performance. Here, we introduced a machine learning-based algorithm as an alternative for a more accurate search of new pharmacological candidates, which takes advantage of Recurrent Neural Networks (RNN) for active molecule prediction within large databases. Our approach, termed PharmaNet was implemented here to search for ligands against specific cell receptors within 102 targets of the DUD-E database, which contains 22886 active molecules. PharmaNet comprises three main phases. First, a SMILES representation of the molecule is converted into a raw molecular image. Second, a convolutional encoder processes the data to obtain a fingerprint molecular image that is finally analyzed by a Recurrent Neural Network (RNN). This approach enables precise predictions of the molecules' target on the basis of the feature extraction, the sequence analysis and the relevant information filtered out throughout the process. Molecule Target prediction is a highly unbalanced detection problem and therefore, we propose that an adequate evaluation metric of performance is the area under the Normalized Average Precision (NAP) curve. PharmaNet largely surpasses the previous state-of-the-art method with 97.7% in the Receiver Operating Characteristic curve (ROC-AUC) and 65.5% in the NAP curve. We obtained a perfect performance for human farnesyl pyrophosphate synthase (FPPS), which is a potential target for antimicrobial and anticancer treatments. We decided to test PharmaNet for activity prediction against FPPS by searching in the CHEMBL data set. We obtained three (3) potential inhibitors that were further validated through both molecular docking and in silico toxicity prediction. Most importantly, one of this candidates, CHEMBL2007613, was predicted as a potential antiviral due to its involvement on the PCDH17 pathway, which has been reported to be related to viral infections.
| S-EPMC8075191 | biostudies-literature
Project description:MOTIVATION:Messenger RNA subcellular localization mechanisms play a crucial role in post-transcriptional gene regulation. This trafficking is mediated by trans-acting RNA-binding proteins interacting with cis-regulatory elements called zipcodes. While new sequencing-based technologies allow the high-throughput identification of RNAs localized to specific subcellular compartments, the precise mechanisms at play, and their dependency on specific sequence elements, remain poorly understood. RESULTS:We introduce RNATracker, a novel deep neural network built to predict, from their sequence alone, the distributions of mRNA transcripts over a predefined set of subcellular compartments. RNATracker integrates several state-of-the-art deep learning techniques (e.g. CNN, LSTM and attention layers) and can make use of both sequence and secondary structure information. We report on a variety of evaluations showing RNATracker's strong predictive power, which is significantly superior to a variety of baseline predictors. Despite its complexity, several aspects of the model can be isolated to yield valuable, testable mechanistic hypotheses, and to locate candidate zipcode sequences within transcripts. AVAILABILITY AND IMPLEMENTATION:Code and data can be accessed at https://www.github.com/HarveyYan/RNATracker. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
| S-EPMC6612824 | biostudies-other
Project description:The ability to manipulate domains underpins function in applications of ferroelectrics. While there have been demonstrations of controlled nanoscale manipulation of domain structures to drive emergent properties, such approaches lack an internal feedback loop required for automatic manipulation. Here, using a deep sequence-to-sequence autoencoder we automate the extraction of latent features of nanoscale ferroelectric switching from piezoresponse force spectroscopy of tensile-strained PbZr0.2Ti0.8O3 with a hierarchical domain structure. We identify characteristic behavior in the piezoresponse and cantilever resonance hysteresis loops, which allows for the classification and quantification of nanoscale-switching mechanisms. Specifically, we identify elastic hardening events which are associated with the nucleation and growth of charged domain walls. This work demonstrates the efficacy of unsupervised neural networks in learning features of a material's physical response from nanoscale multichannel hyperspectral imagery and provides new capabilities in leveraging in operando spectroscopies that could enable the automated manipulation of nanoscale structures in materials.
| S-EPMC6805893 | biostudies-literature
Project description:Early identification of individuals at risk of developing Alzheimer's disease (AD) dementia is important for developing disease-modifying therapies. In this study, given multimodal AD markers and clinical diagnosis of an individual from one or more timepoints, we seek to predict the clinical diagnosis, cognition and ventricular volume of the individual for every month (indefinitely) into the future. We proposed and applied a minimal recurrent neural network (minimalRNN) model to data from The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) challenge, comprising longitudinal data of 1677 participants (Marinescu et al., 2018) from the Alzheimer's Disease Neuroimaging Initiative (ADNI). We compared the performance of the minimalRNN model and four baseline algorithms up to 6 years into the future. Most previous work on predicting AD progression ignore the issue of missing data, which is a prevalent issue in longitudinal data. Here, we explored three different strategies to handle missing data. Two of the strategies treated the missing data as a "preprocessing" issue, by imputing the missing data using the previous timepoint ("forward filling") or linear interpolation ("linear filling). The third strategy utilized the minimalRNN model itself to fill in the missing data both during training and testing ("model filling"). Our analyses suggest that the minimalRNN with "model filling" compared favorably with baseline algorithms, including support vector machine/regression, linear state space (LSS) model, and long short-term memory (LSTM) model. Importantly, although the training procedure utilized longitudinal data, we found that the trained minimalRNN model exhibited similar performance, when using only 1 input timepoint or 4 input timepoints, suggesting that our approach might work well with just cross-sectional data. An earlier version of our approach was ranked 5th (out of 53 entries) in the TADPOLE challenge in 2019. The current approach is ranked 2nd out of 63 entries as of June 3rd, 2020.
| S-EPMC7797176 | biostudies-literature
Project description:The cerebral cortex predicts visual motion to adapt human behavior to surrounding objects moving in real time. Although the underlying mechanisms are still unknown, predictive coding is one of the leading theories. Predictive coding assumes that the brain's internal models (which are acquired through learning) predict the visual world at all times and that errors between the prediction and the actual sensory input further refine the internal models. In the past year, deep neural networks based on predictive coding were reported for a video prediction machine called PredNet. If the theory substantially reproduces the visual information processing of the cerebral cortex, then PredNet can be expected to represent the human visual perception of motion. In this study, PredNet was trained with natural scene videos of the self-motion of the viewer, and the motion prediction ability of the obtained computer model was verified using unlearned videos. We found that the computer model accurately predicted the magnitude and direction of motion of a rotating propeller in unlearned videos. Surprisingly, it also represented the rotational motion for illusion images that were not moving physically, much like human visual perception. While the trained network accurately reproduced the direction of illusory rotation, it did not detect motion components in negative control pictures wherein people do not perceive illusory motion. This research supports the exciting idea that the mechanism assumed by the predictive coding theory is one of basis of motion illusion generation. Using sensory illusions as indicators of human perception, deep neural networks are expected to contribute significantly to the development of brain research.
| S-EPMC5863044 | biostudies-literature
Project description:Acoustic signals serve communication within and across species throughout the animal kingdom. Studying the genetics, evolution, and neurobiology of acoustic communication requires annotating acoustic signals: segmenting and identifying individual acoustic elements like syllables or sound pulses. To be useful, annotations need to be accurate, robust to noise, and fast. We here introduce DeepAudioSegmenter (DAS), a method that annotates acoustic signals across species based on a deep-learning derived hierarchical presentation of sound. We demonstrate the accuracy, robustness, and speed of DAS using acoustic signals with diverse characteristics from insects, birds, and mammals. DAS comes with a graphical user interface for annotating song, training the network, and for generating and proofreading annotations. The method can be trained to annotate signals from new species with little manual annotation and can be combined with unsupervised methods to discover novel signal types. DAS annotates song with high throughput and low latency for experimental interventions in realtime. Overall, DAS is a universal, versatile, and accessible tool for annotating acoustic communication signals.
| S-EPMC8560090 | biostudies-literature
Project description:Artificial neural networks (ANN) have become the mainstream acoustic modeling technique for large vocabulary automatic speech recognition (ASR). A conventional ANN features a multi-layer architecture that requires massive amounts of computation. The brain-inspired spiking neural networks (SNN) closely mimic the biological neural networks and can operate on low-power neuromorphic hardware with spike-based computation. Motivated by their unprecedented energy-efficiency and rapid information processing capability, we explore the use of SNNs for speech recognition. In this work, we use SNNs for acoustic modeling and evaluate their performance on several large vocabulary recognition scenarios. The experimental results demonstrate competitive ASR accuracies to their ANN counterparts, while require only 10 algorithmic time steps and as low as 0.68 times total synaptic operations to classify each audio frame. Integrating the algorithmic power of deep SNNs with energy-efficient neuromorphic hardware, therefore, offer an attractive solution for ASR applications running locally on mobile and embedded devices.
| S-EPMC7090229 | biostudies-literature
Project description:In recent years, hand gesture recognition (HGR) technologies that use electromyography (EMG) signals have been of considerable interest in developing human-machine interfaces. Most state-of-the-art HGR approaches are based mainly on supervised machine learning (ML). However, the use of reinforcement learning (RL) techniques to classify EMGs is still a new and open research topic. Methods based on RL have some advantages such as promising classification performance and online learning from the user's experience. In this work, we propose a user-specific HGR system based on an RL-based agent that learns to characterize EMG signals from five different hand gestures using Deep Q-network (DQN) and Double-Deep Q-Network (Double-DQN) algorithms. Both methods use a feed-forward artificial neural network (ANN) for the representation of the agent policy. We also performed additional tests by adding a long-short-term memory (LSTM) layer to the ANN to analyze and compare its performance. We performed experiments using training, validation, and test sets from our public dataset, EMG-EPN-612. The final accuracy results demonstrate that the best model was DQN without LSTM, obtaining classification and recognition accuracies of up to 90.37%±10.7% and 82.52%±10.9%, respectively. The results obtained in this work demonstrate that RL methods such as DQN and Double-DQN can obtain promising results for classification and recognition problems based on EMG signals.
| S-EPMC10144727 | biostudies-literature
Project description:MotivationAntibiotic resistance constitutes a major public health crisis, and finding new sources of antimicrobial drugs is crucial to solving it. Bacteriocins, which are bacterially produced antimicrobial peptide products, are candidates for broadening the available choices of antimicrobials. However, the discovery of new bacteriocins by genomic mining is hampered by their sequences' low complexity and high variance, which frustrates sequence similarity-based searches.ResultsHere we use word embeddings of protein sequences to represent bacteriocins, and apply a word embedding method that accounts for amino acid order in protein sequences, to predict novel bacteriocins from protein sequences without using sequence similarity. Our method predicts, with a high probability, six yet unknown putative bacteriocins in Lactobacillus. Generalized, the representation of sequences with word embeddings preserving sequence order information can be applied to peptide and protein classification problems for which sequence similarity cannot be used.Availability and implementationData and source code for this project are freely available at: https://github.com/nafizh/NeuBI.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC6581433 | biostudies-literature
Project description:The many successes of deep neural networks (DNNs) over the past decade have largely been driven by computational scale rather than insights from biological intelligence. Here, we explore if these trends have also carried concomitant improvements in explaining the visual strategies humans rely on for object recognition. We do this by comparing two related but distinct properties of visual strategies in humans and DNNs: where they believe important visual features are in images and how they use those features to categorize objects. Across 84 different DNNs trained on ImageNet and three independent datasets measuring the where and the how of human visual strategies for object recognition on those images, we find a systematic trade-off between DNN categorization accuracy and alignment with human visual strategies for object recognition. State-of-the-art DNNs are progressively becoming less aligned with humans as their accuracy improves. We rectify this growing issue with our neural harmonizer: a general-purpose training routine that both aligns DNN and human visual strategies and improves categorization accuracy. Our work represents the first demonstration that the scaling laws [1-3] that are guiding the design of DNNs today have also produced worse models of human vision. We release our code and data at https://serre-lab.github.io/Harmonization to help the field build more human-like DNNs.
| S-EPMC10353762 | biostudies-literature