Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric analysis (IGA) have been used for modeling the material transport process via solving partial differential equations (PDEs), they require long computation time and huge computation resources to ensure accurate geometry representation and solution, thus limit their biomedical application. Here we present a graph neural network (GNN)-based deep learning model to learn the IGA-based material transport simulation and provide fast material concentration prediction within neurite networks of any topology. Given input boundary conditions and geometry configurations, the well-trained model can predict the dynamical concentration change during the transport process with an average error less than 10% and 120∼330 times faster compared to IGA simulations. The effectiveness of the proposed model is demonstrated within several complex neurite networks.
more »
« less
Reaction diffusion system prediction based on convolutional neural network
The reaction-diffusion system is naturally used in chemistry to represent substances reacting and diffusing over the spatial domain. Its solution illustrates the underlying process of a chemical reaction and displays diverse spatial patterns of the substances. Numerical methods like finite element method (FEM) are widely used to derive the approximate solution for the reaction-diffusion system. However, these methods require long computation time and huge computation resources when the system becomes complex. In this paper, we study the physics of a two-dimensional one-component reaction-diffusion system by using machine learning. An encoder-decoder based convolutional neural network (CNN) is designed and trained to directly predict the concentration distribution, bypassing the expensive FEM calculation process. Different simulation parameters, boundary conditions, geometry configurations and time are considered as the input features of the proposed learning model. In particular, the trained CNN model manages to learn the time-dependent behaviour of the reaction-diffusion system through the input time feature. Thus, the model is capable of providing concentration prediction at certain time directly with high test accuracy (mean relative error <3.04%) and 300 times faster than the traditional FEM. Our CNN-based learning model provides a rapid and accurate tool for predicting the concentration distribution of the reaction-diffusion system.
more » « less- Award ID(s):
- 1804929
- NSF-PAR ID:
- 10154064
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Reports
- Volume:
- 10
- Issue:
- 1
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
null (Ed.)Abstract Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric analysis (IGA) have been used for modeling the material transport process via solving partial differential equations (PDEs), they require long computation time and huge computation resources to ensure accurate geometry representation and solution, thus limit their biomedical application. Here we present a graph neural network (GNN)-based deep learning model to learn the IGA-based material transport simulation and provide fast material concentration prediction within neurite networks of any topology. Given input boundary conditions and geometry configurations, the well-trained model can predict the dynamical concentration change during the transport process with an average error less than 10% and $$120 \sim 330$$ 120 ∼ 330 times faster compared to IGA simulations. The effectiveness of the proposed model is demonstrated within several complex neurite networks.more » « less
-
more » « less
Abstract Machine learning (ML) tools are able to learn relationships between the inputs and outputs of large complex systems directly from data. However, for time-varying systems, the predictive capabilities of ML tools degrade if the systems are no longer accurately represented by the data with which the ML models were trained. For complex systems, re-training is only possible if the changes are slow relative to the rate at which large numbers of new input-output training data can be non-invasively recorded. In this work, we present an approach to deep learning for time-varying systems that does not require re-training, but uses instead an adaptive feedback in the architecture of deep convolutional neural networks (CNN). The feedback is based only on available system output measurements and is applied in the encoded low-dimensional dense layers of the encoder-decoder CNNs. First, we develop an inverse model of a complex accelerator system to map output beam measurements to input beam distributions, while both the accelerator components and the unknown input beam distribution vary rapidly with time. We then demonstrate our method on experimental measurements of the input and output beam distributions of the HiRES ultra-fast electron diffraction (UED) beam line at Lawrence Berkeley National Laboratory, and showcase its ability for automatic tracking of the time varying photocathode quantum efficiency map. Our method can be successfully used to aid both physics and ML-based surrogate online models to provide non-invasive beam diagnostics.
-
Purpose To develop a method of biologically guided deep learning for post-radiation 18 FDG-PET image outcome prediction based on pre-radiation images and radiotherapy dose information. Methods Based on the classic reaction–diffusion mechanism, a novel biological model was proposed using a partial differential equation that incorporates spatial radiation dose distribution as a patient-specific treatment information variable. A 7-layer encoder–decoder-based convolutional neural network (CNN) was designed and trained to learn the proposed biological model. As such, the model could generate post-radiation 18 FDG-PET image outcome predictions with breakdown biological components for enhanced explainability. The proposed method was developed using 64 oropharyngeal patients with paired 18 FDG-PET studies before and after 20-Gy delivery (2 Gy/day fraction) by intensity-modulated radiotherapy (IMRT). In a two-branch deep learning execution, the proposed CNN learns specific terms in the biological model from paired 18 FDG-PET images and spatial dose distribution in one branch, and the biological model generates post-20-Gy 18 FDG-PET image prediction in the other branch. As in 2D execution, 718/233/230 axial slices from 38/13/13 patients were used for training/validation/independent test. The prediction image results in test cases were compared with the ground-truth results quantitatively. Results The proposed method successfully generated post-20-Gy 18 FDG-PET image outcome prediction with breakdown illustrations of biological model components. Standardized uptake value (SUV) mean values in 18 FDG high-uptake regions of predicted images (2.45 ± 0.25) were similar to ground-truth results (2.51 ± 0.33). In 2D-based Gamma analysis, the median/mean Gamma Index (<1) passing rate of test images was 96.5%/92.8% using the 5%/5 mm criterion; such result was improved to 99.9%/99.6% when 10%/10 mm was adopted. Conclusion The developed biologically guided deep learning method achieved post-20-Gy 18 FDG-PET image outcome predictions in good agreement with ground-truth results. With the breakdown biological modeling components, the outcome image predictions could be used in adaptive radiotherapy decision-making to optimize personalized plans for the best outcome in the future.more » « less
-
The widespread use of distributed energy sources (DERs) raises significant challenges for power system design, planning, and operation, leading to wide adaptation of tools on hosting capacity analysis (HCA). Traditional HCA methods conduct extensive power flow analysis. Due to the computation burden, these time-consuming methods fail to provide online hosting capacity (HC) in large distribution systems. To solve the problem, we first propose a deep learning-based problem formulation for HCA, which conducts offline training and determines HC in real time. The used learning model, long short-term memory (LSTM), implements historical time-series data to capture periodical patterns in distribution systems. However, directly applying LSTMs suffers from low accuracy due to the lack of consideration on spatial information, where location information like feeder topology is critical in nodal HCA. Therefore, we modify the forget gate function to dual forget gates, to capture the spatial correlation within the grid. Such a design turns the LSTM into the Spatial-Temporal LSTM (ST-LSTM). Moreover, as voltage violations are the most vital constraints in HCA, we design a voltage sensitivity gate to increase accuracy further. The results of LSTMs and ST-LSTMs on feeders, such as IEEE 34-, 123-bus feeders, and utility feeders, validate our designs.more » « less
