Unsupervised feature learning for electrocardiogram data using the convolutional variational autoencoder.
Ontology highlight
ABSTRACT:
SUBMITTER: Jang JH
PROVIDER: S-EPMC8635334 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:High-resolution manometry (HRM) is the primary method for diagnosing esophageal motility disorders and its interpretation and classification are based on variables (features) from data of each swallow. Modeling and learning the semantics directly from raw swallow data could not only help automate the feature extraction, but also alleviate the bias from pre-defined features. With more than 32-thousand raw swallow data, a generative model using the approach of variational auto-encoder (VAE) was developed, which, to our knowledge, is the first deep-learning-based unsupervised model on raw esophageal manometry data. The VAE model was reformulated to include different types of loss motivated by domain knowledge and tuned with different hyper-parameters. Training of the VAE model was found sensitive on the learning rate and hence the evidence lower bound objective (ELBO) was further scaled by the data dimension. Case studies showed that the dimensionality of latent space have a big impact on the learned semantics. In particular, cases with 4-dimensional latent variables were found to encode various physiologically meaningful contraction patterns, including strength, propagation pattern as well as sphincter relaxation. Cases with so-called hybrid L2 loss seemed to better capture the coherence of contraction/relaxation transition. Discriminating capability was further evaluated using simple linear discriminative analysis (LDA) on predicting swallow type and swallow pressurization, which yields clustering patterns consistent with clinical impression. The current work on modeling and understanding swallow-level data will guide the development of study-level models for automatic diagnosis as the next stage.
| S-EPMC7901248 | biostudies-literature
Project description:Recent resting-state fMRI studies have shown that brain activity exhibits temporal variations in functional connectivity by using various approaches including sliding window correlation, co-activation patterns, independent component analysis, quasi-periodic patterns, and hidden Markov models. These methods often model the brain activity as a discretized hopping among several brain states that are defined by the spatial configurations of network activity. However, the discretized states are merely a simplification of what is likely to be a continuous process, where each network evolves over time following its unique path. To model these characteristic spatiotemporal trajectories, we trained a variational autoencoder using rs-fMRI data and evaluated the spatiotemporal features of the latent variables obtained from the trained networks. Our results suggest that there are a relatively small number of approximately orthogonal whole-brain spatiotemporal patterns that capture the most prominent features of rs-fMRI data, which can serve as the building blocks to construct all possible spatiotemporal dynamics in resting state fMRI. These spatiotemporal patterns provide insight into how activity flows across the brain in concordance with known network structures and functional connectivity gradients.
| S-EPMC8637345 | biostudies-literature
Project description:Deep learning approaches are widely used to search molecular structures for a candidate drug/material. The basic approach in drug/material candidate structure discovery is to embed a relationship that holds between a molecular structure and the physical property into a low-dimensional vector space (chemical space) and search for a candidate molecular structure in that space based on a desired physical property value. Deep learning simplifies the structure search by efficiently modeling the structure of the chemical space with greater detail and lower dimensions than the original input space. In our research, we propose an effective method for molecular embedding learning that combines variational autoencoders (VAEs) and metric learning using any physical property. Our method enables molecular structures and physical properties to be embedded locally and continuously into VAEs' latent space while maintaining the consistency of the relationship between the structural features and the physical properties of molecules to yield better predictions.
| S-EPMC7900996 | biostudies-literature
Project description:In this paper, a reinforcement learning model is proposed that can maximize the predicted binding affinity between a generated molecule and target proteins. The model used to generate molecules in the proposed model was the Stacked Conditional Variation AutoEncoder (Stack-CVAE), which acts as an agent in reinforcement learning so that the resulting chemical formulas have the desired chemical properties and show high binding affinity with specific target proteins. We generated 1000 chemical formulas using the chemical properties of sorafenib and the three target kinases of sorafenib. Then, we confirmed that Stack-CVAE generates more of the valid and unique chemical compounds that have the desired chemical properties and predicted binding affinity better than other generative models. More detailed analysis for 100 of the top scoring molecules show that they are novel ones not found in existing chemical databases. Moreover, they reveal significantly higher predicted binding affinity score for Raf kinases than for other kinases. Furthermore, they are highly druggable and synthesizable.
| S-EPMC9733204 | biostudies-literature
Project description:Resting state functional magnetic resonance imaging (rsfMRI) data exhibits complex but structured patterns. However, the underlying origins are unclear and entangled in rsfMRI data. Here we establish a variational auto-encoder, as a generative model trainable with unsupervised learning, to disentangle the unknown sources of rsfMRI activity. After being trained with large data from the Human Connectome Project, the model has learned to represent and generate patterns of cortical activity and connectivity using latent variables. The latent representation and its trajectory represent the spatiotemporal characteristics of rsfMRI activity. The latent variables reflect the principal gradients of the latent trajectory and drive activity changes in cortical networks. Representational geometry captured as covariance or correlation between latent variables, rather than cortical connectivity, can be used as a more reliable feature to accurately identify subjects from a large group, even if only a short period of data is available in each subject. Our results demonstrate that VAE is a valuable addition to existing tools, particularly suited for unsupervised representation learning of resting state fMRI activity.
| S-EPMC8485214 | biostudies-literature
Project description:Goal-driven and feedforward-only convolutional neural networks (CNN) have been shown to be able to predict and decode cortical responses to natural images or videos. Here, we explored an alternative deep neural network, variational auto-encoder (VAE), as a computational model of the visual cortex. We trained a VAE with a five-layer encoder and a five-layer decoder to learn visual representations from a diverse set of unlabeled images. Using the trained VAE, we predicted and decoded cortical activity observed with functional magnetic resonance imaging (fMRI) from three human subjects passively watching natural videos. Compared to CNN, VAE could predict the video-evoked cortical responses with comparable accuracy in early visual areas, but relatively lower accuracy in higher-order visual areas. The distinction between CNN and VAE in terms of encoding performance was primarily attributed to their different learning objectives, rather than their different model architecture or number of parameters. Despite lower encoding accuracies, VAE offered a more convenient strategy for decoding the fMRI activity to reconstruct the video input, by first converting the fMRI activity to the VAE's latent variables, and then converting the latent variables to the reconstructed video frames through the VAE's decoder. This strategy was more advantageous than alternative decoding methods, e.g. partial least squares regression, for being able to reconstruct both the spatial structure and color of the visual input. Such findings highlight VAE as an unsupervised model for learning visual representation, as well as its potential and limitations for explaining cortical responses and reconstructing naturalistic and diverse visual experiences.
| S-EPMC6592726 | biostudies-literature
Project description:BackgroundMultiple studies have shown the utility of transcriptome-wide RNA-seq profiles as features for machine learning-based prediction of response to chemotherapy in cancer. While tumor transcriptome profiles are publicly available for thousands of tumors for many cancer types, a relatively modest number of tumor profiles are clinically annotated for response to chemotherapy. The paucity of labeled examples and the high dimension of the feature data limit performance for predicting therapeutic response using fully-supervised classification methods. Recently, multiple studies have established the utility of a deep neural network approach, the variational autoencoder (VAE), for generating meaningful latent features from original data. Here, we report the first study of a semi-supervised approach using VAE-encoded tumor transcriptome features and regularized gradient boosted decision trees (XGBoost) to predict chemotherapy drug response for five cancer types: colon, pancreatic, bladder, breast, and sarcoma.ResultsWe found: (1) VAE-encoding of the tumor transcriptome preserves the cancer type identity of the tumor, suggesting preservation of biologically relevant information; and (2) as a feature-set for supervised classification to predict response-to-chemotherapy, the unsupervised VAE encoding of the tumor's gene expression profile leads to better area under the receiver operating characteristic curve and area under the precision-recall curve classification performance than the original gene expression profile or the PCA principal components or the ICA components of the gene expression profile, in four out of five cancer types that we tested.ConclusionsGiven high-dimensional "omics" data, the VAE is a powerful tool for obtaining a nonlinear low-dimensional embedding; it yields features that retain biological patterns that distinguish between different types of cancer and that enable more accurate tumor transcriptome-based prediction of response to chemotherapy than would be possible using the original data or their principal components.
| S-EPMC8456615 | biostudies-literature
Project description:Predicting future brain topography can give insight into neural correlates of aging and neurodegeneration. Due to variability in the aging process, it has been challenging to precisely estimate brain topographical change according to aging. Here, we predict age-related brain metabolic change by generating future brain 18F-Fluorodeoxyglucose PET. A cross-sectional PET dataset of cognitively normal subjects with different age was used to develop a generative model. The model generated PET images using age information and characteristic individual features. Predicted regional metabolic changes were correlated with the real changes obtained by follow-up data. This model was applied to produce a brain metabolism aging movie by generating PET at different ages. Normal population distribution of brain metabolic topography at each age was estimated as well. In addition, a generative model using APOE4 status as well as age as inputs revealed a significant effect of APOE4 status on age-related metabolic changes particularly in the calcarine, lingual cortex, hippocampus, and amygdala. It suggested APOE4 could be a factor affecting individual variability in age-related metabolic degeneration in normal elderly. This predictive model may not only be extended to understanding the cognitive aging process, but apply to the development of a preclinical biomarker for various brain disorders.
| S-EPMC6052253 | biostudies-literature
Project description:An accurate personality model is crucial to many research fields. Most personality models have been constructed using linear factor analysis (LFA). In this paper, we investigate if an effective deep learning tool for factor extraction, the Variational Autoencoder (VAE), can be applied to explore the factor structure of a set of personality variables. To compare VAE with LFA, we applied VAE to an International Personality Item Pool (IPIP) Big 5 dataset and an IPIP HEXACO (Humility-Honesty, Emotionality, Extroversion, Agreeableness, Conscientiousness, Openness) dataset. We found that LFA tends to break factors into ever smaller, yet still significant fractions, when the number of assumed latent factors increases, leading to the need to organize personality variables at the factor level and then the facet level. On the other hand, the factor structure returned by VAE is very stable and VAE only adds noise-like factors after significant factors are found as the number of assumed latent factors increases. VAE reported more stable factors by elevating some facets in the HEXACO scale to the factor level. Since this is a data-driven process that exhausts all stable and significant factors that can be found, it is not necessary to further conduct facet level analysis and it is anticipated that VAE will have broad applications in exploratory factor analysis in personality research.
| S-EPMC9388855 | biostudies-literature
Project description:Objective:To create an system to aid in the analysis of art history by classifying and grouping digitized paintings based on stylistic features automatically learned without prior knowledge. Material and Methods:6,776 digitized paintings from 8 different artistic styles (Art Nouveau, Baroque, Expressionism, Impressionism, Realism, Romanticism, Renaissance, and Post-Impressionism) were utilized to classify (predict) and cluster (group) paintings according to style. The method of unsupervised feature learning with K-means (UFLK), inspired by deep learning, was utilized to extract features from the paintings. These features were then used in: (1) a support vector machine algorithm to classify the style of new test paintings based on a training set of paintings having known style labels; and (2) a spectral clustering algorithm to group the paintings into distinct style groups (anonymously, without employing any known style labels). Classification performance was determined by accuracy and F-score. Clustering performance was determined by: 1) the ability to recover the original stylistic groupings (using a cost analysis of all possible combinations of 8 group label assignments); 2) F-score; and 3) a reliability analysis. The latter analysis used two novel ways to determine the distribution of the null-hypothesis: (a) a uniform distribution projected onto the principal components of the original data; and (b) a randomized, weighted adjacency matrix. The ability to gain insights into art was tested by a semantic analysis of the clustering results. For this purpose, we represented the featural characteristics of each painting by an N-dimensional feature vector, and plotted the distance between vector endpoints (i.e., similarity between paintings). Then, we color-coded the endpoints with the assigned lowest-cost style labels. The scatterplot was visually inspected for separation of the paintings, where the amount of separation between color clusters provides semantic information on the interrelatedness between styles. Results:The UFLK-extracted features resembled the edges/lines/colors in the paintings. For feature-based classification of paintings, the macro-averaged F-score was 0.469. Classification accuracy and F-score were similar/higher compared to other classification methods using more complex feature learning models (e.g., convolutional neural networks, a supervised algorithm). The clustering via UFLK-extracted features yielded 8 unlabeled style groupings. In 6 of 8 clusters, the most common true painting style matched the cluster style assigned by cost analysis. The clustering had an F-score of 0.212. (There are no comparison methods for clustering paintings.) For the semantic analysis, the featural characteristics of Baroque and Art Nouveau were found to be similar, indicating a relationship between these styles. Discussion/Conclusion:The UFLK method can extract features from digitized paintings. We were able to extract characteristics of art without any prior information about the nature of the features or the stylistic designation of the paintings. The methods herein may provide art researchers with the latest computational techniques for the documentation, interpretation, and forensics of art. The tools could assist the preservation of culturally sensitive works of art for future generations, and provide new insights into works of art and the artists who created them.
| S-EPMC6051702 | biostudies-literature