scholarly journals Machine learning of stochastic gene network phenotypes

2019 ◽  
Author(s):  
Kyemyung Park ◽  
Thorsten Prüstel ◽  
Yong Lu ◽  
John S. Tsang
Keyword(s):  
Machine Learning ◽  
Biological Networks ◽  
Computationally Efficient ◽  
Stochastic Fluctuations ◽  
Large Numbers ◽  
Negative Feedbacks ◽  
Complex Circuits ◽  
Computational Resources ◽  
Parameter Values ◽  
Mechanistic Simulation

AbstractA recurrent challenge in biology is the development of predictive quantitative models because most molecular and cellular parameters have unknown values and realistic models are analytically intractable. While the dynamics of the system can be analyzed via computer simulations, substantial computational resources are often required given uncertain parameter values resulting in large numbers of parameter combinations, especially when realistic biological features are included. Simulation alone also often does not yield the kinds of intuitive insights from analytical solutions. Here we introduce a general framework combining stochastic/mechanistic simulation of reaction systems and machine learning of the simulation data to generate computationally efficient predictive models and interpretable parameter-phenotype maps. We applied our approach to investigate stochastic gene expression propagation in biological networks, which is a contemporary challenge in the quantitative modeling of single-cell heterogeneity. We found that accurate, predictive machine-learning models of stochastic simulation results can be constructed. Even in the simplest networks existing analytical schemes generated significantly less accurate predictions than our approach, which revealed interesting insights when applied to more complex circuits, including the extensive tunability of information propagation enabled by feedforward circuits and how even single negative feedbacks can utilize stochastic fluctuations to generate robust oscillations. Our approach is applicable beyond biology and opens up a new avenue for exploring complex dynamical systems.

Accurate Detection and Quantization of Leaf- Diseases through Soft Computing

2018 ◽  
Vol 1 (1) ◽  
pp. 236-247
Author(s):  
Divya Srivastava ◽  
Rajitha B. ◽  
Suneeta Agarwal
Keyword(s):  
Machine Learning ◽  
Image Processing ◽  
Agricultural Production ◽  
Bacterial Blight ◽  
Early Stage ◽  
Second Phase ◽  
Computationally Efficient ◽  
Stage Of Disease ◽  
Accurate Detection ◽  
Two Phases

Diseases in leaves can cause the significant reduction in both quality and quantity of agricultural production. If early and accurate detection of disease/diseases in leaves can be automated, then the proper remedy can be taken timely. A simple and computationally efficient approach is presented in this paper for disease/diseases detection on leaves. Only detecting the disease is not beneficial without knowing the stage of disease thus the paper also determine the stage of disease/diseases by quantizing the affected of the leaves by using digital image processing and machine learning. Though there exists a variety of diseases on leaves, but the bacterial and fungal spots (Early Scorch, Late Scorch, and Leaf Spot) are the most prominent diseases found on leaves. Keeping this in mind the paper deals with the detection of Bacterial Blight and Fungal Spot both at an early stage (Early Scorch) and late stage (Late Scorch) on the variety of leaves. The proposed approach is divided into two phases, in the first phase, it identifies one or more disease/diseases existing on leaves. In the second phase, amount of area affected by the disease/diseases is calculated. The experimental results obtained showed 97% accuracy using the proposed approach.

Using artificial neural network condensation to facilitate adaption of machine learning in medical settings by reducing computational burden (Preprint)

2020 ◽  
Author(s):  
Dianbo Liu
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Third World ◽  
Mortality Prediction ◽  
Neural Net ◽  
Medical Settings ◽  
Hidden Layer ◽  
Applications Of Machine Learning ◽  
Computational Resources ◽  
Developed Nations

BACKGROUND Applications of machine learning (ML) on health care can have a great impact on people’s lives. At the same time, medical data is usually big, requiring a significant amount of computational resources. Although it might not be a problem for wide-adoption of ML tools in developed nations, availability of computational resource can very well be limited in third-world nations and on mobile devices. This can prevent many people from benefiting of the advancement in ML applications for healthcare. OBJECTIVE In this paper we explored three methods to increase computational efficiency of either recurrent neural net-work(RNN) or feedforward (deep) neural network (DNN) while not compromising its accuracy. We used in-patient mortality prediction as our case analysis upon intensive care dataset. METHODS We reduced the size of RNN and DNN by applying pruning of “unused” neurons. Additionally, we modified the RNN structure by adding a hidden-layer to the RNN cell but reduce the total number of recurrent layers to accomplish a reduction of total parameters in the network. Finally, we implemented quantization on DNN—forcing the weights to be 8-bits instead of 32-bits. RESULTS We found that all methods increased implementation efficiency–including training speed, memory size and inference speed–without reducing the accuracy of mortality prediction. CONCLUSIONS This improvements allow the implementation of sophisticated NN algorithms on devices with lower computational resources.

scholarly journals OutlierNets: Highly Compact Deep Autoencoder Network Architectures for On-Device Acoustic Anomaly Detection

Sensors ◽  
2021 ◽  
Vol 21 (14) ◽  
pp. 4805
Author(s):  
Saad Abbasi ◽  
Mahmoud Famouri ◽  
Mohammad Javad Shafiee ◽  
Alexander Wong
Keyword(s):  
Machine Learning ◽  
Anomaly Detection ◽  
Detection Methods ◽  
Detection Accuracy ◽  
Network Architectures ◽  
Design Exploration ◽  
Convolutional Autoencoder ◽  
Acoustic Anomaly ◽  
Human Operators ◽  
Computational Resources

Human operators often diagnose industrial machinery via anomalous sounds. Given the new advances in the field of machine learning, automated acoustic anomaly detection can lead to reliable maintenance of machinery. However, deep learning-driven anomaly detection methods often require an extensive amount of computational resources prohibiting their deployment in factories. Here we explore a machine-driven design exploration strategy to create OutlierNets, a family of highly compact deep convolutional autoencoder network architectures featuring as few as 686 parameters, model sizes as small as 2.7 KB, and as low as 2.8 million FLOPs, with a detection accuracy matching or exceeding published architectures with as many as 4 million parameters. The architectures are deployed on an Intel Core i5 as well as a ARM Cortex A72 to assess performance on hardware that is likely to be used in industry. Experimental results on the model’s latency show that the OutlierNet architectures can achieve as much as 30x lower latency than published networks.

scholarly journals Towards Generative Design of Computationally Efficient Mathematical Models with Evolutionary Learning

Entropy ◽  
2020 ◽  
Vol 23 (1) ◽  
pp. 28
Author(s):  
Anna V. Kalyuzhnaya ◽  
Nikolay O. Nikitin ◽  
Alexander Hvatov ◽  
Mikhail Maslyaev ◽  
Mikhail Yachmenkov ◽  
...  
Keyword(s):  
Mathematical Models ◽  
Learning Approach ◽  
Model Structure ◽  
Evolutionary Learning ◽  
Learning Models ◽  
Computationally Efficient ◽  
Performance Models ◽  
Generative Design ◽  
Computational Resources ◽  
Machine Learning Models

In this paper, we describe the concept of generative design approach applied to the automated evolutionary learning of mathematical models in a computationally efficient way. To formalize the problems of models’ design and co-design, the generalized formulation of the modeling workflow is proposed. A parallelized evolutionary learning approach for the identification of model structure is described for the equation-based model and composite machine learning models. Moreover, the involvement of the performance models in the design process is analyzed. A set of experiments with various models and computational resources is conducted to verify different aspects of the proposed approach.

scholarly journals You Only Look Once, But Compute Twice: Service Function Chaining for Low-Latency Object Detection in Softwarized Networks

2021 ◽  
Vol 11 (5) ◽  
pp. 2177
Author(s):  
Zuo Xiang ◽  
Patrick Seeling ◽  
Frank H. P. Fitzek
Keyword(s):  
Machine Learning ◽  
Object Detection ◽  
Low Latency ◽  
Connected Vehicles ◽  
Network Nodes ◽  
Machine Learning Model ◽  
Fold Reduction ◽  
Broad Variety ◽  
Computational Resources ◽  
Service Latency

With increasing numbers of computer vision and object detection application scenarios, those requiring ultra-low service latency times have become increasingly prominent; e.g., those for autonomous and connected vehicles or smart city applications. The incorporation of machine learning through the applications of trained models in these scenarios can pose a computational challenge. The softwarization of networks provides opportunities to incorporate computing into the network, increasing flexibility by distributing workloads through offloading from client and edge nodes over in-network nodes to servers. In this article, we present an example for splitting the inference component of the YOLOv2 trained machine learning model between client, network, and service side processing to reduce the overall service latency. Assuming a client has 20% of the server computational resources, we observe a more than 12-fold reduction of service latency when incorporating our service split compared to on-client processing and and an increase in speed of more than 25% compared to performing everything on the server. Our approach is not only applicable to object detection, but can also be applied in a broad variety of machine learning-based applications and services.

scholarly journals Machine Learning for Statistical Modeling

2021 ◽  
Vol 26 (3) ◽  
pp. 1-17
Author(s):  
Urmimala Roy ◽  
Tanmoy Pramanik ◽  
Subhendu Roy ◽  
Avhishek Chatterjee ◽  
Leonard F. Register ◽  
...  
Keyword(s):  
Machine Learning ◽  
Time Distribution ◽  
Switching Time ◽  
A Priori ◽  
Random Access ◽  
Spin Transfer Torque ◽  
Support Vector ◽  
Micromagnetic Simulations ◽  
Physical Systems ◽  
Computational Resources

We propose a methodology to perform process variation-aware device and circuit design using fully physics-based simulations within limited computational resources, without developing a compact model. Machine learning (ML), specifically a support vector regression (SVR) model, has been used. The SVR model has been trained using a dataset of devices simulated a priori, and the accuracy of prediction by the trained SVR model has been demonstrated. To produce a switching time distribution from the trained ML model, we only had to generate the dataset to train and validate the model, which needed ∼500 hours of computation. On the other hand, if 10 6 samples were to be simulated using the same computation resources to generate a switching time distribution from micromagnetic simulations, it would have taken ∼250 days. Spin-transfer-torque random access memory (STTRAM) has been used to demonstrate the method. However, different physical systems may be considered, different ML models can be used for different physical systems and/or different device parameter sets, and similar ends could be achieved by training the ML model using measured device data.

Geometrical design of a crystal growth system guided by a machine learning algorithm

CrystEngComm ◽  
2021 ◽  
Author(s):  
Wancheng Yu ◽  
Can Zhu ◽  
Yosuke Tsunooka ◽  
Wei Huang ◽  
Yifan Dang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Crystal Growth ◽  
High Speed ◽  
Learning Algorithm ◽  
Computational Techniques ◽  
Machine Learning Algorithm ◽  
Geometrical Design ◽  
Large Numbers ◽  
Growth System ◽  
Speed Method

This study proposes a new high-speed method for designing crystal growth systems. It is capable of optimizing large numbers of parameters simultaneously which is difficult for traditional experimental and computational techniques.

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes

2021 ◽  
pp. gr.275777.121
Author(s):  
George W Armstrong ◽  
Kalen Cantrell ◽  
Shi Huang ◽  
Daniel McDonald ◽  
Niina Haiminen ◽  
...  
Keyword(s):  
Carbon Footprint ◽  
Phylogenetic Diversity ◽  
Alpha Diversity ◽  
Previous Method ◽  
Metagenomic Data ◽  
Efficient Computation ◽  
Computationally Efficient ◽  
Dataset Size ◽  
Computational Resources ◽  
Older Populations

The number of publicly available microbiome samples is continually growing. As dataset size increases, bottlenecks arise in standard analytical pipelines. Faith’s phylogenetic diversity is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's Phylogenetic Diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.

scholarly journals Encoding Health Records into Pathway Representations for Deep Learning

2021 ◽  
Author(s):  
Marco Luca Sbodio ◽  
Natasha Mulligan ◽  
Stefanie Speichert ◽  
Vanessa Lopez ◽  
Joao Bettencourt-Silva
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Source Code ◽  
Training Dataset ◽  
Health Records ◽  
Learning Tasks ◽  
Patient Pathways ◽  
Computational Resources ◽  
The Impact

There is a growing trend in building deep learning patient representations from health records to obtain a comprehensive view of a patient’s data for machine learning tasks. This paper proposes a reproducible approach to generate patient pathways from health records and to transform them into a machine-processable image-like structure useful for deep learning tasks. Based on this approach, we generated over a million pathways from FAIR synthetic health records and used them to train a convolutional neural network. Our initial experiments show the accuracy of the CNN on a prediction task is comparable or better than other autoencoders trained on the same data, while requiring significantly less computational resources for training. We also assess the impact of the size of the training dataset on autoencoders performances. The source code for generating pathways from health records is provided as open source.

scholarly journals Random Forests for Genetic Association Studies

2011 ◽  
Vol 10 (1) ◽  
Author(s):  
Benjamin A Goldstein ◽  
Eric C Polley ◽  
Farren B. S. Briggs
Keyword(s):  
Machine Learning ◽  
Genetic Association ◽  
Random Forests ◽  
Learning Algorithm ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Machine Learning Algorithms ◽  
Computationally Efficient ◽  
Genetic Studies ◽  
Variable Importance Measures

The Random Forests (RF) algorithm has become a commonly used machine learning algorithm for genetic association studies. It is well suited for genetic applications since it is both computationally efficient and models genetic causal mechanisms well. With its growing ubiquity, there has been inconsistent and less than optimal use of RF in the literature. The purpose of this review is to breakdown the theoretical and statistical basis of RF so that practitioners are able to apply it in their work. An emphasis is placed on showing how the various components contribute to bias and variance, as well as discussing variable importance measures. Applications specific to genetic studies are highlighted. To provide context, RF is compared to other commonly used machine learning algorithms.

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