scholarly journals Aerial hyperspectral imagery and deep neural networks for high-throughput yield phenotyping in wheat

2020 ◽  
Vol 172 ◽  
pp. 105299 ◽  
Author(s):  
Ali Moghimi ◽  
Ce Yang ◽  
James A. Anderson
Keyword(s):  
Neural Networks ◽  
High Throughput ◽  
Deep Neural Networks ◽  
Hyperspectral Imagery

scholarly journals Reconfigurable Binary Neural Network Accelerator with Adaptive Parallelism Scheme

Electronics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 230
Author(s):  
Jaechan Cho ◽  
Yongchul Jung ◽  
Seongjoo Lee ◽  
Yunho Jung
Keyword(s):  
Neural Networks ◽  
High Throughput ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Throughput Performance ◽  
Adaptive Parallelism ◽  
Sensor Applications ◽  
Binary Neural Network ◽  
Target Layer ◽  
Network Topologies

Binary neural networks (BNNs) have attracted significant interest for the implementation of deep neural networks (DNNs) on resource-constrained edge devices, and various BNN accelerator architectures have been proposed to achieve higher efficiency. BNN accelerators can be divided into two categories: streaming and layer accelerators. Although streaming accelerators designed for a specific BNN network topology provide high throughput, they are infeasible for various sensor applications in edge AI because of their complexity and inflexibility. In contrast, layer accelerators with reasonable resources can support various network topologies, but they operate with the same parallelism for all the layers of the BNN, which degrades throughput performance at certain layers. To overcome this problem, we propose a BNN accelerator with adaptive parallelism that offers high throughput performance in all layers. The proposed accelerator analyzes target layer parameters and operates with optimal parallelism using reasonable resources. In addition, this architecture is able to fully compute all types of BNN layers thanks to its reconfigurability, and it can achieve a higher area–speed efficiency than existing accelerators. In performance evaluation using state-of-the-art BNN topologies, the designed BNN accelerator achieved an area–speed efficiency 9.69 times higher than previous FPGA implementations and 24% higher than existing VLSI implementations for BNNs.

scholarly journals Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification

2021 ◽  
Vol 17 (3) ◽  
pp. e1008864
Author(s):  
Daniel R. Ripoll ◽  
Sidhartha Chaudhury ◽  
Anders Wallqvist
Keyword(s):  
Neural Networks ◽  
B Cell ◽  
High Throughput ◽  
Large Scale ◽  
Deep Neural Networks ◽  
Viral Infections ◽  
Adaptive Immune Response ◽  
Sequence Information ◽  
Data Generation ◽  
Binding Interface

High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in these large datasets, in particular the identification of therapeutic antibodies (Abs) or those associated with disease exposure and protection. Here, we describe our efforts to use artificial intelligence (AI)-based image-analyses for prospective classification of Abs based solely on sequence information. We hypothesized that Abs recognizing the same part of an antigen share a limited set of features at the binding interface, and that the binding site regions of these Abs share share common structure and physicochemical property patterns that can serve as a “fingerprint” to recognize uncharacterized Abs. We combined large-scale sequence-based protein-structure predictions to generate ensembles of 3-D Ab models, reduced the Ab binding interface to a 2-D image (fingerprint), used pre-trained convolutional neural networks to extract features, and trained deep neural networks (DNNs) to classify Abs. We evaluated this approach using Ab sequences derived from human HIV and Ebola viral infections to differentiate between two Abs, Abs belonging to specific B-cell family lineages, and Abs with different epitope preferences. In addition, we explored a different type of DNN method to detect one class of Abs from a larger pool of Abs. Testing on Ab sets that had been kept aside during model training, we achieved average prediction accuracies ranging from 71–96% depending on the complexity of the classification task. The high level of accuracies reached during these classification tests suggests that the DNN models were able to learn a series of structural patterns shared by Abs belonging to the same class. The developed methodology provides a means to apply AI-based image recognition techniques to analyze high-throughput B-cell sequencing datasets (repertoires) for Ab classification.

scholarly journals DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i634-i642
Author(s):  
Maor Asif ◽  
Yaron Orenstein
Keyword(s):  
Neural Networks ◽  
Dna Binding ◽  
High Throughput ◽  
Dna Sequences ◽  
Deep Neural Networks ◽  
High Throughput Sequencing ◽  
Supplementary Information ◽  
Computational Technique ◽  
Model Parameters ◽  
Binding Prediction

Abstract Motivation Transcription factor (TF) DNA-binding is a central mechanism in gene regulation. Biologists would like to know where and when these factors bind DNA. Hence, they require accurate DNA-binding models to enable binding prediction to any DNA sequence. Recent technological advancements measure the binding of a single TF to thousands of DNA sequences. One of the prevailing techniques, high-throughput SELEX, measures protein–DNA binding by high-throughput sequencing over several cycles of enrichment. Unfortunately, current computational methods to infer the binding preferences from high-throughput SELEX data do not exploit the richness of these data, and are under-using the most advanced computational technique, deep neural networks. Results To better characterize the binding preferences of TFs from these experimental data, we developed DeepSELEX, a new algorithm to infer intrinsic DNA-binding preferences using deep neural networks. DeepSELEX takes advantage of the richness of high-throughput sequencing data and learns the DNA-binding preferences by observing the changes in DNA sequences through the experimental cycles. DeepSELEX outperforms extant methods for the task of DNA-binding inference from high-throughput SELEX data in binding prediction in vitro and is on par with the state of the art in in vivo binding prediction. Analysis of model parameters reveals it learns biologically relevant features that shed light on TFs’ binding mechanism. Availability and implementation DeepSELEX is available through github.com/OrensteinLab/DeepSELEX/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Multiterminal Pathfinding in Practical VLSI Systems with Deep Neural Networks

2022 ◽  
Author(s):  
Dmitry Utyamishev ◽  
Inna Partin-Vaisband
Keyword(s):  
Neural Networks ◽  
High Throughput ◽  
Deep Neural Networks ◽  
Task Complexity ◽  
State Of The Art ◽  
Synthetic Dataset ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Deep Image ◽  
Magnitude Improvement

Abstract A multiterminal obstacle-avoiding pathfinding approach is proposed. The approach is inspired by deep image learning. The key idea is based on training a conditional generative adversarial network (cGAN) to interpret a pathfinding task as a graphical bitmap and consequently map a pathfinding task onto a pathfinding solution represented by another bitmap. To enable the proposed cGAN pathfinding, a methodology for generating synthetic dataset is also proposed. The cGAN model is implemented in Python/Keras, trained on synthetically generated data, evaluated on practical VLSI benchmarks, and compared with state-of-the-art. Due to effective parallelization on GPU hardware, the proposed approach yields a state-of-the-art like wirelength and a better runtime and throughput for moderately complex pathfinding tasks. However, the runtime and throughput with the proposed approach remain constant with an increasing task complexity, promising orders of magnitude improvement over state-of-the-art in complex pathfinding tasks. The cGAN pathfinder can be exploited in numerous high throughput applications, such as, navigation, tracking, and routing in complex VLSI systems. The last is of particular interest to this work.

scholarly journals Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology

2021 ◽  
Vol 17 (7) ◽  
pp. e1009135
Author(s):  
Adrian J. Green ◽  
Martin J. Mohlenkamp ◽  
Jhuma Das ◽  
Meenal Chaudhari ◽  
Lisa Truong ◽  
...  
Keyword(s):  
Neural Networks ◽  
High Throughput ◽  
Environmental Protection Agency ◽  
High Throughput Screening ◽  
Deep Neural Networks ◽  
Generative Adversarial Networks ◽  
Support Vector ◽  
Large Set ◽  
Toxicity Data

There are currently 85,000 chemicals registered with the Environmental Protection Agency (EPA) under the Toxic Substances Control Act, but only a small fraction have measured toxicological data. To address this gap, high-throughput screening (HTS) and computational methods are vital. As part of one such HTS effort, embryonic zebrafish were used to examine a suite of morphological and mortality endpoints at six concentrations from over 1,000 unique chemicals found in the ToxCast library (phase 1 and 2). We hypothesized that by using a conditional generative adversarial network (cGAN) or deep neural networks (DNN), and leveraging this large set of toxicity data we could efficiently predict toxic outcomes of untested chemicals. Utilizing a novel method in this space, we converted the 3D structural information into a weighted set of points while retaining all information about the structure. In vivo toxicity and chemical data were used to train two neural network generators. The first was a DNN (Go-ZT) while the second utilized cGAN architecture (GAN-ZT) to train generators to produce toxicity data. Our results showed that Go-ZT significantly outperformed the cGAN, support vector machine, random forest and multilayer perceptron models in cross-validation, and when tested against an external test dataset. By combining both Go-ZT and GAN-ZT, our consensus model improved the SE, SP, PPV, and Kappa, to 71.4%, 95.9%, 71.4% and 0.673, respectively, resulting in an area under the receiver operating characteristic (AUROC) of 0.837. Considering their potential use as prescreening tools, these models could provide in vivo toxicity predictions and insight into the hundreds of thousands of untested chemicals to prioritize compounds for HT testing.

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