Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Flow-based Generative Models for Learning Manifold to Manifold Mappings.

ABSTRACT: Many measurements or observations in computer vision and machine learning manifest as non-Euclidean data. While recent proposals (like spherical CNN) have extended a number of deep neural network architectures to manifold-valued data, and this has often provided strong improvements in performance, the literature on generative models for manifold data is quite sparse. Partly due to this gap, there are also no modality transfer/translation models for manifold-valued data whereas numerous such methods based on generative models are available for natural images. This paper addresses this gap, motivated by a need in brain imaging - in doing so, we expand the operating range of certain generative models (as well as generative models for modality transfer) from natural images to images with manifold-valued measurements. Our main result is the design of a two-stream version of GLOW (flow-based invertible generative models) that can synthesize information of a field of one type of manifold-valued measurements given another. On the theoretical side, we introduce three kinds of invertible layers for manifold-valued data, which are not only analogous to their functionality in flow-based generative models (e.g., GLOW) but also preserve the key benefits (determinants of the Jacobian are easy to calculate). For experiments, on a large dataset from the Human Connectome Project (HCP), we show promising results where we can reliably and accurately reconstruct brain images of a field of orientation distribution functions (ODF) from diffusion tensor images (DTI), where the latter has a 5 × faster acquisition time but at the expense of worse angular resolution.

SUBMITTER: Zhen X

PROVIDER: S-EPMC8394699 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A quantum machine learning algorithm based on generative models.

Project description:Quantum computing and artificial intelligence, combined together, may revolutionize future technologies. A significant school of thought regarding artificial intelligence is based on generative models. Here, we propose a general quantum algorithm for machine learning based on a quantum generative model. We prove that our proposed model is more capable of representing probability distributions compared with classical generative models and has exponential speedup in learning and inference at least for some instances if a quantum computer cannot be efficiently simulated classically. Our result opens a new direction for quantum machine learning and offers a remarkable example where a quantum algorithm shows exponential improvement over classical algorithms in an important application field.

| S-EPMC6286170 | biostudies-literature

The neural coding framework for learning generative models.

Project description:Neural generative models can be used to learn complex probability distributions from data, to sample from them, and to produce probability density estimates. We propose a computational framework for developing neural generative models inspired by the theory of predictive processing in the brain. According to predictive processing theory, the neurons in the brain form a hierarchy in which neurons in one level form expectations about sensory inputs from another level. These neurons update their local models based on differences between their expectations and the observed signals. In a similar way, artificial neurons in our generative models predict what neighboring neurons will do, and adjust their parameters based on how well the predictions matched reality. In this work, we show that the neural generative models learned within our framework perform well in practice across several benchmark datasets and metrics and either remain competitive with or significantly outperform other generative models with similar functionality (such as the variational auto-encoder).

| S-EPMC9018730 | biostudies-literature

Learning Generative Models of Tissue Organization with Supervised GANs.

Project description:A key step in understanding the spatial organization of cells and tissues is the ability to construct generative models that accurately reflect that organization. In this paper, we focus on building generative models of electron microscope (EM) images in which the positions of cell membranes and mitochondria have been densely annotated, and propose a two-stage procedure that produces realistic images using Generative Adversarial Networks (or GANs) in a supervised way. In the first stage, we synthesize a label "image" given a noise "image" as input, which then provides supervision for EM image synthesis in the second stage. The full model naturally generates label-image pairs. We show that accurate synthetic EM images are produced using assessment via (1) shape features and global statistics, (2) segmentation accuracies, and (3) user studies. We also demonstrate further improvements by enforcing a reconstruction loss on intermediate synthetic labels and thus unifying the two stages into one single end-to-end framework.

| S-EPMC6119234 | biostudies-literature

Exploring generative deep learning for omics data using log-linear models.

Project description:MotivationFollowing many successful applications to image data, deep learning is now also increasingly considered for omics data. In particular, generative deep learning not only provides competitive prediction performance, but also allows for uncovering structure by generating synthetic samples. However, exploration and visualization is not as straightforward as with image applications.ResultsWe demonstrate how log-linear models, fitted to the generated, synthetic data can be used to extract patterns from omics data, learned by deep generative techniques. Specifically, interactions between latent representations learned by the approaches and generated synthetic data are used to determine sets of joint patterns. Distances of patterns with respect to the distribution of latent representations are then visualized in low-dimensional coordinate systems, e.g. for monitoring training progress. This is illustrated with simulated data and subsequently with cortical single-cell gene expression data. Using different kinds of deep generative techniques, specifically variational autoencoders and deep Boltzmann machines, the proposed approach highlights how the techniques uncover underlying structure. It facilitates the real-world use of such generative deep learning techniques to gain biological insights from omics data.Availability and implementationThe code for the approach as well as an accompanying Jupyter notebook, which illustrates the application of our approach, is available via the GitHub repository: https://github.com/ssehztirom/Exploring-generative-deep-learning-for-omics-data-by-using-log-linear-models.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC7755415 | biostudies-literature

Causal Learning via Manifold Regularization.

Project description:This paper frames causal structure estimation as a machine learning task. The idea is to treat indicators of causal relationships between variables as 'labels' and to exploit available data on the variables of interest to provide features for the labelling task. Background scientific knowledge or any available interventional data provide labels on some causal relationships and the remainder are treated as unlabelled. To illustrate the key ideas, we develop a distance-based approach (based on bivariate histograms) within a manifold regularization framework. We present empirical results on three different biological data sets (including examples where causal effects can be verified by experimental intervention), that together demonstrate the efficacy and general nature of the approach as well as its simplicity from a user's point of view.

| S-EPMC6986916 | biostudies-literature

Manifold learning for parameter reduction.

Project description:Large scale dynamical systems (e.g. many nonlinear coupled differential equations) can often be summarized in terms of only a few state variables (a few equations), a trait that reduces complexity and facilitates exploration of behavioral aspects of otherwise intractable models. High model dimensionality and complexity makes symbolic, pen-and-paper model reduction tedious and impractical, a difficulty addressed by recently developed frameworks that computerize reduction. Symbolic work has the benefit, however, of identifying both reduced state variables and parameter combinations that matter most (effective parameters, "inputs"); whereas current computational reduction schemes leave the parameter reduction aspect mostly unaddressed. As the interest in mapping out and optimizing complex input-output relations keeps growing, it becomes clear that combating the curse of dimensionality also requires efficient schemes for input space exploration and reduction. Here, we explore systematic, data-driven parameter reduction by means of effective parameter identification, starting from current nonlinear manifoldlearning techniques enabling state space reduction. Our approach aspires to extend the data-driven determination of effective state variables with the data-driven discovery of effective model parameters, and thus to accelerate the exploration of high-dimensional parameter spaces associated with complex models.

| S-EPMC6528681 | biostudies-literature

Cross-Situational Learning with Bayesian Generative Models for Multimodal Category and Word Learning in Robots.

Project description:In this paper, we propose a Bayesian generative model that can form multiple categories based on each sensory-channel and can associate words with any of the four sensory-channels (action, position, object, and color). This paper focuses on cross-situational learning using the co-occurrence between words and information of sensory-channels in complex situations rather than conventional situations of cross-situational learning. We conducted a learning scenario using a simulator and a real humanoid iCub robot. In the scenario, a human tutor provided a sentence that describes an object of visual attention and an accompanying action to the robot. The scenario was set as follows: the number of words per sensory-channel was three or four, and the number of trials for learning was 20 and 40 for the simulator and 25 and 40 for the real robot. The experimental results showed that the proposed method was able to estimate the multiple categorizations and to learn the relationships between multiple sensory-channels and words accurately. In addition, we conducted an action generation task and an action description task based on word meanings learned in the cross-situational learning scenario. The experimental results showed that the robot could successfully use the word meanings learned by using the proposed method.

| S-EPMC5742219 | biostudies-literature

Learning and inference using complex generative models in a spatial localization task.

Project description:A large body of research has established that, under relatively simple task conditions, human observers integrate uncertain sensory information with learned prior knowledge in an approximately Bayes-optimal manner. However, in many natural tasks, observers must perform this sensory-plus-prior integration when the underlying generative model of the environment consists of multiple causes. Here we ask if the Bayes-optimal integration seen with simple tasks also applies to such natural tasks when the generative model is more complex, or whether observers rely instead on a less efficient set of heuristics that approximate ideal performance. Participants localized a "hidden" target whose position on a touch screen was sampled from a location-contingent bimodal generative model with different variances around each mode. Over repeated exposure to this task, participants learned the a priori locations of the target (i.e., the bimodal generative model), and integrated this learned knowledge with uncertain sensory information on a trial-by-trial basis in a manner consistent with the predictions of Bayes-optimal behavior. In particular, participants rapidly learned the locations of the two modes of the generative model, but the relative variances of the modes were learned much more slowly. Taken together, our results suggest that human performance in a more complex localization task, which requires the integration of sensory information with learned knowledge of a bimodal generative model, is consistent with the predictions of Bayes-optimal behavior, but involves a much longer time-course than in simpler tasks.

| S-EPMC4790422 | biostudies-literature

Learning to encode cellular responses to systematic perturbations with deep generative models.

Project description:Cellular signaling systems play a vital role in maintaining homeostasis when a cell is exposed to different perturbations. Components of the systems are organized as hierarchical networks, and perturbing different components often leads to transcriptomic profiles that exhibit compositional statistical patterns. Mining such patterns to investigate how cellular signals are encoded is an important problem in systems biology, where artificial intelligence techniques can be of great assistance. Here, we investigated the capability of deep generative models (DGMs) to modeling signaling systems and learn representations of cellular states underlying transcriptomic responses to diverse perturbations. Specifically, we show that the variational autoencoder and the supervised vector-quantized variational autoencoder can accurately regenerate gene expression data in response to perturbagen treatments. The models can learn representations that reveal the relationships between different classes of perturbagens and enable mappings between drugs and their target genes. In summary, DGMs can adequately learn and depict how cellular signals are encoded. The resulting representations have broad applications, demonstrating the power of artificial intelligence in systems biology and precision medicine.

| S-EPMC7648057 | biostudies-literature

Discovering generative models from event logs: data-driven simulation vs deep learning.

Project description:A generative model is a statistical model capable of generating new data instances from previously observed ones. In the context of business processes, a generative model creates new execution traces from a set of historical traces, also known as an event log. Two types of generative business process models have been developed in previous work: data-driven simulation models and deep learning models. Until now, these two approaches have evolved independently, and their relative performance has not been studied. This paper fills this gap by empirically comparing a data-driven simulation approach with multiple deep learning approaches for building generative business process models. The study sheds light on the relative strengths of these two approaches and raises the prospect of developing hybrid approaches that combine these strengths.

| S-EPMC8293933 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data