scholarly journals Generalizable Machine Learning in Neuroscience Using Graph Neural Networks

2021 ◽  
Vol 4 ◽  
Author(s):  
Paul Y. Wang ◽  
Sandalika Sapra ◽  
Vivek Kurien George ◽  
Gabriel A. Silva
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Neural Systems ◽  
Graph Structure ◽  
Imaging Data ◽  
C Elegans ◽  
State Classification ◽  
Graph Neural Networks ◽  
Emergent Behaviors

Although a number of studies have explored deep learning in neuroscience, the application of these algorithms to neural systems on a microscopic scale, i.e. parameters relevant to lower scales of organization, remains relatively novel. Motivated by advances in whole-brain imaging, we examined the performance of deep learning models on microscopic neural dynamics and resulting emergent behaviors using calcium imaging data from the nematode C. elegans. As one of the only species for which neuron-level dynamics can be recorded, C. elegans serves as the ideal organism for designing and testing models bridging recent advances in deep learning and established concepts in neuroscience. We show that neural networks perform remarkably well on both neuron-level dynamics prediction and behavioral state classification. In addition, we compared the performance of structure agnostic neural networks and graph neural networks to investigate if graph structure can be exploited as a favourable inductive bias. To perform this experiment, we designed a graph neural network which explicitly infers relations between neurons from neural activity and leverages the inferred graph structure during computations. In our experiments, we found that graph neural networks generally outperformed structure agnostic models and excel in generalization on unseen organisms, implying a potential path to generalizable machine learning in neuroscience.

scholarly journals Representing Deep Neural Networks Latent Space Geometries with Graphs

Algorithms ◽  
2021 ◽  
Vol 14 (2) ◽  
pp. 39
Author(s):  
Carlos Lassance ◽  
Vincent Gripon ◽  
Antonio Ortega
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Objective Function ◽  
Learning Process ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
The Core ◽  
Learning Tasks ◽  
Latent Space

Deep Learning (DL) has attracted a lot of attention for its ability to reach state-of-the-art performance in many machine learning tasks. The core principle of DL methods consists of training composite architectures in an end-to-end fashion, where inputs are associated with outputs trained to optimize an objective function. Because of their compositional nature, DL architectures naturally exhibit several intermediate representations of the inputs, which belong to so-called latent spaces. When treated individually, these intermediate representations are most of the time unconstrained during the learning process, as it is unclear which properties should be favored. However, when processing a batch of inputs concurrently, the corresponding set of intermediate representations exhibit relations (what we call a geometry) on which desired properties can be sought. In this work, we show that it is possible to introduce constraints on these latent geometries to address various problems. In more detail, we propose to represent geometries by constructing similarity graphs from the intermediate representations obtained when processing a batch of inputs. By constraining these Latent Geometry Graphs (LGGs), we address the three following problems: (i) reproducing the behavior of a teacher architecture is achieved by mimicking its geometry, (ii) designing efficient embeddings for classification is achieved by targeting specific geometries, and (iii) robustness to deviations on inputs is achieved via enforcing smooth variation of geometry between consecutive latent spaces. Using standard vision benchmarks, we demonstrate the ability of the proposed geometry-based methods in solving the considered problems.

Graph-based knowledge tracing: Modeling student proficiency using graph neural networks

2021 ◽  
pp. 1-16
Author(s):  
Hiromi Nakagawa ◽  
Yusuke Iwasawa ◽  
Yutaka Matsuo
Keyword(s):  
Neural Networks ◽  
Student Performance ◽  
Classification Problem ◽  
Computer Assisted ◽  
Graph Structure ◽  
Inductive Bias ◽  
Additional Information ◽  
Knowledge Tracing ◽  
Open Datasets ◽  
Graph Neural Networks

Recent advancements in computer-assisted learning systems have caused an increase in the research in knowledge tracing, wherein student performance is predicted over time. Student coursework can potentially be structured as a graph. Incorporating this graph-structured nature into a knowledge tracing model as a relational inductive bias can improve its performance; however, previous methods, such as deep knowledge tracing, did not consider such a latent graph structure. Inspired by the recent successes of graph neural networks (GNNs), we herein propose a GNN-based knowledge tracing method, i.e., graph-based knowledge tracing. Casting the knowledge structure as a graph enabled us to reformulate the knowledge tracing task as a time-series node-level classification problem in the GNN. As the knowledge graph structure is not explicitly provided in most cases, we propose various implementations of the graph structure. Empirical validations on two open datasets indicated that our method could potentially improve the prediction of student performance and demonstrated more interpretable predictions compared to those of the previous methods, without the requirement of any additional information.

scholarly journals Image classification using Deep learning

2018 ◽  
Vol 7 (2.7) ◽  
pp. 614 ◽  
Author(s):  
M Manoj krishna ◽  
M Neelima ◽  
M Harshali ◽  
M Venu Gopala Rao
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Image Processing ◽  
Computer Vision ◽  
Deep Learning ◽  
Image Classification ◽  
Convolutional Neural Networks ◽  
Classical Problem

The image classification is a classical problem of image processing, computer vision and machine learning fields. In this paper we study the image classification using deep learning. We use AlexNet architecture with convolutional neural networks for this purpose. Four test images are selected from the ImageNet database for the classification purpose. We cropped the images for various portion areas and conducted experiments. The results show the effectiveness of deep learning based image classification using AlexNet.  

scholarly journals A primer on deep learning and convolutional neural networks for clinicians

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lara Lloret Iglesias ◽  
Pablo Sanz Bellón ◽  
Amaia Pérez del Barrio ◽  
Pablo Menéndez Fernández-Miranda ◽  
David Rodríguez González ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Learning Capabilities ◽  
Computer Vision Applications ◽  
Fully Connected ◽  
Imaging Perspective ◽  
Adaptive Momentum

AbstractDeep learning is nowadays at the forefront of artificial intelligence. More precisely, the use of convolutional neural networks has drastically improved the learning capabilities of computer vision applications, being able to directly consider raw data without any prior feature extraction. Advanced methods in the machine learning field, such as adaptive momentum algorithms or dropout regularization, have dramatically improved the convolutional neural networks predicting ability, outperforming that of conventional fully connected neural networks. This work summarizes, in an intended didactic way, the main aspects of these cutting-edge techniques from a medical imaging perspective.

scholarly journals Deep Learning Strategies for ProtoDUNE Raw Data Denoising

2022 ◽  
Vol 6 (1) ◽  
Author(s):  
Marco Rossi ◽  
Sofia Vallecorsa
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Learning Strategies ◽  
Simulation Data ◽  
Raw Data ◽  
Digital Detector ◽  
Speed Up ◽  
Neural Network Hardware ◽  
Graph Neural Networks ◽  
High Level

AbstractIn this work, we investigate different machine learning-based strategies for denoising raw simulation data from the ProtoDUNE experiment. The ProtoDUNE detector is hosted by CERN and it aims to test and calibrate the technologies for DUNE, a forthcoming experiment in neutrino physics. The reconstruction workchain consists of converting digital detector signals into physical high-level quantities. We address the first step in reconstruction, namely raw data denoising, leveraging deep learning algorithms. We design two architectures based on graph neural networks, aiming to enhance the receptive field of basic convolutional neural networks. We benchmark this approach against traditional algorithms implemented by the DUNE collaboration. We test the capabilities of graph neural network hardware accelerator setups to speed up training and inference processes.

scholarly journals Convolutional Neural Network for Iris Recognition

2021 ◽  
Author(s):  
Wael Alnahari
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Iris Recognition ◽  
Recognition System ◽  
High Accuracy ◽  
Accuracy Rate

Abstract In this paper, I proposed an iris recognition system by using deep learning via neural networks (CNN). Although CNN is used for machine learning, the recognition is achieved by building a non-trained CNN network with multiple layers. The main objective of the code the test pictures’ category (aka person name) with a high accuracy rate after having extracted enough features from training pictures of the same category which are obtained from a that I added to the code. I used IITD iris which included 10 iris pictures for 223 people.

scholarly journals Benchmarking Graph Neural Networks for Materials Chemistry

2021 ◽  
Author(s):  
Victor Fung ◽  
Jiaxin Zhang ◽  
Eric Juarez ◽  
Bobby Sumpter
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Materials Chemistry ◽  
Learning Models ◽  
High Data ◽  
Hyperparameter Selection ◽  
Computational Materials ◽  
Conventional Models ◽  
Graph Neural Networks ◽  
Machine Learning Models

Graph neural networks (GNNs) have received intense interest as a rapidly expanding class of machine learning models remarkably well-suited for materials applications. To date, a number of successful GNNs have been proposed and demonstrated for systems ranging from crystal stability to electronic property prediction and to surface chemistry and heterogeneous catalysis. However, a consistent benchmark of these models remains lacking, hindering the development and consistent evaluation of new models in the materials field. Here, we present a workflow and testing platform, MatDeepLearn, for quickly and reproducibly assessing and comparing GNNs and other machine learning models. We use this platform to optimize and evaluate a selection of top performing GNNs on several representative datasets in computational materials chemistry. From our investigations we note the importance of hyperparameter selection and find roughly similar performances for the top models once optimized. We identify several strengths in GNNs over conventional models in cases with compositionally diverse datasets and in its overall flexibility with respect to inputs, due to learned rather than defined representations. Meanwhile several weaknesses of GNNs are also observed including high data requirements, and suggestions for further improvement for applications in materials chemistry are proposed.

Train Deep Learning Models using subsurface geological images datasets

2021 ◽  
Author(s):  
Ramy Abdallah ◽  
Clare E. Bond ◽  
Robert W.H. Butler
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Learning Models ◽  
Structural Interpretation ◽  
Performance Accuracy ◽  
Learning Techniques ◽  
Machine Learning Models

<p>Machine learning is being presented as a new solution for a wide range of geoscience problems. Primarily machine learning has been used for 3D seismic data processing, seismic facies analysis and well log data correlation. The rapid development in technology with open-source artificial intelligence libraries and the accessibility of affordable computer graphics processing units (GPU) makes the application of machine learning in geosciences increasingly tractable. However, the application of artificial intelligence in structural interpretation workflows of subsurface datasets is still ambiguous. This study aims to use machine learning techniques to classify images of folds and fold-thrust structures. Here we show that convolutional neural networks (CNNs) as supervised deep learning techniques provide excellent algorithms to discriminate between geological image datasets. Four different datasets of images have been used to train and test the machine learning models. These four datasets are a seismic character dataset with five classes (faults, folds, salt, flat layers and basement), folds types with three classes (buckle, chevron and conjugate), fault types with three classes (normal, reverse and thrust) and fold-thrust geometries with three classes (fault bend fold, fault propagation fold and detachment fold). These image datasets are used to investigate three machine learning models. One Feedforward linear neural network model and two convolutional neural networks models (Convolution 2d layer transforms sequential model and Residual block model (ResNet with 9, 34, and 50 layers)). Validation and testing datasets forms a critical part of testing the model’s performance accuracy. The ResNet model records the highest performance accuracy score, of the machine learning models tested. Our CNN image classification model analysis provides a framework for applying machine learning to increase structural interpretation efficiency, and shows that CNN classification models can be applied effectively to geoscience problems. The study provides a starting point to apply unsupervised machine learning approaches to sub-surface structural interpretation workflows.</p>

Deep Learning and Biomedical Engineering

Biotechnology ◽  
2019 ◽  
pp. 562-575
Author(s):  
Suraj Sawant
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Deep Learning ◽  
Real World ◽  
Biomedical Engineering ◽  
Input Data ◽  
Reference Source ◽  
Data Input ◽  
Essential Information

Deep learning (DL) is a method of machine learning, as running over artificial neural networks, which has a structure above the standards to deal with large amounts of data. That is generally because of the increasing amount of data, input data sizes, and of course, greater complexity of objective real-world problems. Performed research studies in the associated literature show that the DL currently has a good performance among considered problems and it seems to be a strong solution for more advanced problems of the future. In this context, this chapter aims to provide some essential information about DL and its applications within the field of biomedical engineering. The chapter is organized as a reference source for enabling readers to have an idea about the relation between DL and biomedical engineering.

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