A novel molecular representation with BiGRU neural networks for learning atom

2019 ◽  
Vol 21 (6) ◽  
pp. 2099-2111 ◽  
Author(s):  
Xuan Lin ◽  
Zhe Quan ◽  
Zhi-Jie Wang ◽  
Huang Huang ◽  
Xiangxiang Zeng
Keyword(s):  
Neural Networks ◽  
Drug Discovery ◽  
Related Problem ◽  
State Of The Art ◽  
Binary Classification ◽  
Classification Problems ◽  
Novel Method ◽  
Low Dimensional ◽  
Vector Representations ◽  
Gated Recurrent Unit

Abstract Molecular representations play critical roles in researching drug design and properties, and effective methods are beneficial to assisting in the calculation of molecules and solving related problem in drug discovery. In previous years, most of the traditional molecular representations are based on hand-crafted features and rely heavily on biological experimentations, which are often costly and time consuming. However, recent researches achieve promising results using machine learning on various domains. In this article, we present a novel method named Smi2Vec-BiGRU that is designed for learning atoms and solving the single- and multitask binary classification problems in the field of drug discovery, which are the basic and also key problems in this field. Specifically, our approach transforms the molecule data in the SMILES format into a set of sample vectors and then feeds them into the bidirectional gated recurrent unit neural networks for training, which learns low-dimensional vector representations for molecular drug. We conduct extensive experiments on several widely used benchmarks including Tox21, SIDER and ClinTox. The experimental results show that our approach can achieve state-of-the-art performance on these benchmarking datasets, demonstrating the feasibility and competitiveness of our proposed approach.

AutoLinker: Automatic Fragment Linking with Deep Conditional Transformer Neural Networks

2020 ◽  
Author(s):  
Yuyao Yang ◽  
Shuangjia Zheng ◽  
Shimin Su ◽  
Jun Xu ◽  
Hongming Chen
Keyword(s):  
Neural Networks ◽  
Drug Discovery ◽  
Drug Design ◽  
State Of The Art ◽  
The State ◽  
Generative Model ◽  
Lead Optimization ◽  
Scaffold Hopping ◽  
Reference Models ◽  
Lead Generation

Fragment based drug design represents a promising drug discovery paradigm complimentary to the traditional HTS based lead generation strategy. How to link fragment structures to increase compound affinity is remaining a challenge task in this paradigm. Hereby a novel deep generative model (AutoLinker) for linking fragments is developed with the potential for applying in the fragment-based lead generation scenario. The state-of-the-art transformer architecture was employed to learn the linker grammar and generate novel linker. Our results show that, given starting fragments and user customized linker constraints, our AutoLinker model can design abundant drug-like molecules fulfilling these constraints and its performance was superior to other reference models. Moreover, several examples were showcased that AutoLinker can be useful tools for carrying out drug design tasks such as fragment linking, lead optimization and scaffold hopping.

scholarly journals Improving Land Cover Classification Using Genetic Programming for Feature Construction

2021 ◽  
Vol 13 (9) ◽  
pp. 1623
Author(s):  
João E. Batista ◽  
Ana I. R. Cabral ◽  
Maria J. P. Vasconcelos ◽  
Leonardo Vanneschi ◽  
Sara Silva
Keyword(s):  
Land Cover ◽  
Genetic Programming ◽  
Satellite Images ◽  
State Of The Art ◽  
Binary Classification ◽  
Feature Construction ◽  
Classification Problems ◽  
Construction Methods ◽  
Box Models

Genetic programming (GP) is a powerful machine learning (ML) algorithm that can produce readable white-box models. Although successfully used for solving an array of problems in different scientific areas, GP is still not well known in the field of remote sensing. The M3GP algorithm, a variant of the standard GP algorithm, performs feature construction by evolving hyperfeatures from the original ones. In this work, we use the M3GP algorithm on several sets of satellite images over different countries to create hyperfeatures from satellite bands to improve the classification of land cover types. We add the evolved hyperfeatures to the reference datasets and observe a significant improvement of the performance of three state-of-the-art ML algorithms (decision trees, random forests, and XGBoost) on multiclass classifications and no significant effect on the binary classifications. We show that adding the M3GP hyperfeatures to the reference datasets brings better results than adding the well-known spectral indices NDVI, NDWI, and NBR. We also compare the performance of the M3GP hyperfeatures in the binary classification problems with those created by other feature construction methods such as FFX and EFS.

scholarly journals Label Distribution for Learning with Noisy Labels

2020 ◽  
Author(s):  
Yun-Peng Liu ◽  
Ning Xu ◽  
Yu Zhang ◽  
Xin Geng
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Learning Algorithm ◽  
State Of The Art ◽  
Confidence Estimation ◽  
Novel Method ◽  
Real World Datasets ◽  
Label Distribution ◽  
Noisy Labels

The performances of deep neural networks (DNNs) crucially rely on the quality of labeling. In some situations, labels are easily corrupted, and therefore some labels become noisy labels. Thus, designing algorithms that deal with noisy labels is of great importance for learning robust DNNs. However, it is difficult to distinguish between clean labels and noisy labels, which becomes the bottleneck of many methods. To address the problem, this paper proposes a novel method named Label Distribution based Confidence Estimation (LDCE). LDCE estimates the confidence of the observed labels based on label distribution. Then, the boundary between clean labels and noisy labels becomes clear according to confidence scores. To verify the effectiveness of the method, LDCE is combined with the existing learning algorithm to train robust DNNs. Experiments on both synthetic and real-world datasets substantiate the superiority of the proposed algorithm against state-of-the-art methods.

scholarly journals Improving Land Cover Classification Using Genetic Programming for Feature Construction

2020 ◽  
Author(s):  
João Batista ◽  
Ana Cabral ◽  
Maria Vasconcelos ◽  
Leonardo Vanneschi ◽  
Sara Silva
Keyword(s):  
Land Cover ◽  
Genetic Programming ◽  
Satellite Images ◽  
State Of The Art ◽  
Binary Classification ◽  
Feature Construction ◽  
Classification Problems ◽  
Construction Methods ◽  
Box Models

Genetic Programming (GP) is a powerful Machine Learning (ML) algorithm that can produce readable white-box models. Although successfully used for solving an array of problems in different scientific areas, GP is still not well known in Remote Sensing. The M3GP algorithm, a variant of the standard GP algorithm, performs Feature Construction by evolving hyper-features from the original ones. In this work, we use the M3GP algorithm on several sets of satellite images over different countries to create hyper-feature from satellite bands to improve the classification of land cover types. We add the evolved hyper-features to the reference datasets and observe a significant improvement of the performance of three state-of-the-art ML algorithms (Decision Trees, Random Forests and XGBoost) on multiclass classifications and no significant effect on the binary classifications. We show that adding the M3GP hyper-features to the reference datasets brings better results than adding the well-known spectral indices NDVI, NDWI and NBR. We also compare the performance of the M3GP hyper-features in the binary classification problems with those created by other Feature Construction methods like FFX and EFS.

scholarly journals Interpolation Consistency Training for Semi-supervised Learning

2019 ◽  
Author(s):  
Vikas Verma ◽  
Alex Lamb ◽  
Juho Kannala ◽  
Yoshua Bengio ◽  
David Lopez-Paz
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Supervised Learning ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Data Distribution ◽  
Network Architectures ◽  
Low Density ◽  
Decision Boundary ◽  
Classification Problems

We introduce Interpolation Consistency Training (ICT), a simple and computation efficient algorithm for training Deep Neural Networks in the semi-supervised learning paradigm. ICT encourages the prediction at an interpolation of unlabeled points to be consistent with the interpolation of the predictions at those points. In classification problems, ICT moves the decision boundary to low-density regions of the data distribution. Our experiments show that ICT achieves state-of-the-art performance when applied to standard neural network architectures on the CIFAR-10 and SVHN benchmark dataset.

scholarly journals Improving Land Cover Classification Using Genetic Programming for Feature Construction

2020 ◽  
Author(s):  
João E. Batista ◽  
Ana I. R. Cabral ◽  
Maria J. P. Vasconcelos ◽  
Leonardo Vanneschi ◽  
Sara Silva
Keyword(s):  
Land Cover ◽  
Genetic Programming ◽  
Satellite Images ◽  
State Of The Art ◽  
Binary Classification ◽  
Feature Construction ◽  
Classification Problems ◽  
Construction Methods ◽  
Box Models

Genetic Programming (GP) is a powerful Machine Learning (ML) algorithm that can produce readable white-box models. Although successfully used for solving an array of problems in different scientific areas, GP is still not well known in Remote Sensing. The M3GP algorithm, a variant of the standard GP algorithm, performs Feature Construction by evolving hyper-features from the original ones. In this work, we use the M3GP algorithm on several sets of satellite images over different countries to create hyper-feature from satellite bands to improve the classification of land cover types. We add the evolved hyper-features to the reference datasets and observe a significant improvement of the performance of three state-of-the-art ML algorithms (Decision Trees, Random Forests and XGBoost) on multiclass classifications and no significant effect on the binary classifications. We show that adding the M3GP hyper-features to the reference datasets brings better results than adding the well-known spectral indices NDVI, NDWI and NBR. We also compare the performance of the M3GP hyper-features in the binary classification problems with those created by other Feature Construction methods like FFX and EFS.

scholarly journals Prediction of Disease-related microRNAs through Integrating Attributes of microRNA Nodes and Multiple Kinds of Connecting Edges

Molecules ◽  
2019 ◽  
Vol 24 (17) ◽  
pp. 3099 ◽  
Author(s):  
Xuan ◽  
Li ◽  
Zhang ◽  
Zhang ◽  
Song
Keyword(s):  
State Of The Art ◽  
Dimensional Space ◽  
Nonnegative Matrix ◽  
Superior Performance ◽  
Pancreatic Cancers ◽  
Node Attribute ◽  
Disease Associations ◽  
Node Attributes ◽  
Novel Method ◽  
Low Dimensional

Identifying disease-associated microRNAs (disease miRNAs) contributes to the understanding of disease pathogenesis. Most previous computational biology studies focused on multiple kinds of connecting edges of miRNAs and diseases, including miRNA–miRNA similarities, disease–disease similarities, and miRNA–disease associations. Few methods exploited the node attribute information related to miRNA family and cluster. The previous methods do not completely consider the sparsity of node attributes. Additionally, it is challenging to deeply integrate the node attributes of miRNAs and the similarities and associations related to miRNAs and diseases. In the present study, we propose a novel method, known as MDAPred, based on nonnegative matrix factorization to predict candidate disease miRNAs. MDAPred integrates the node attributes of miRNAs and the related similarities and associations of miRNAs and diseases. Since a miRNA is typically subordinate to a family or a cluster, the node attributes of miRNAs are sparse. Similarly, the data for miRNA and disease similarities are sparse. Projecting the miRNA and disease similarities and miRNA node attributes into a common low-dimensional space contributes to estimating miRNA-disease associations. Simultaneously, the possibility that a miRNA is associated with a disease depends on the miRNA’s neighbour information. Therefore, MDAPred deeply integrates projections of multiple kinds of connecting edges, projections of miRNAs node attributes, and neighbour information of miRNAs. The cross-validation results showed that MDAPred achieved superior performance compared to other state-of-the-art methods for predicting disease-miRNA associations. MDAPred can also retrieve more actual miRNA-disease associations at the top of prediction results, which is very important for biologists. Additionally, case studies of breast, lung, and pancreatic cancers further confirmed the ability of MDAPred to discover potential miRNA–disease associations.

scholarly journals Evaluating semantometrics from computer science publications

2020 ◽  
Vol 125 (3) ◽  
pp. 2915-2954
Author(s):  
Christin Katharina Kreutz ◽  
Premtim Sahitaj ◽  
Ralf Schenkel
Keyword(s):  
State Of The Art ◽  
Binary Classification ◽  
Citation Network ◽  
Distance Measures ◽  
Semantic Features ◽  
Citation Networks ◽  
Current State ◽  
Publication Time ◽  
Citation Practices ◽  
Vector Representations

AbstractIdentification of important works and assessment of importance of publications in vast scientific corpora are challenging yet common tasks subjected by many research projects. While the influence of citations in finding seminal papers has been analysed thoroughly, citation-based approaches come with several problems. Their impracticality when confronted with new publications which did not yet receive any citations, area-dependent citation practices and different reasons for citing are only a few drawbacks of them. Methods relying on more than citations, for example semantic features such as words or topics contained in publications of citation networks, are regarded with less vigour while providing promising preliminary results. In this work we tackle the issue of classifying publications with their respective referenced and citing papers as either seminal, survey or uninfluential by utilising semantometrics. We use distance measures over words, semantics, topics and publication years of papers in their citation network to engineer features on which we predict the class of a publication. We present the SUSdblp dataset consisting of 1980 labelled entries to provide a means of evaluating this approach. A classification accuracy of up to .9247 was achieved when combining multiple types of features using semantometrics. This is +.1232 compared to the current state of the art (SOTA) which uses binary classification to identify papers from classes seminal and survey. The utilisation of one-vector representations for the ternary classification task resulted in an accuracy of .949 which is +.1475 compared to the binary SOTA. Classification based on information available at publication time derived with semantometrics resulted in an accuracy of .8152 while an accuracy of .9323 could be achieved when using one-vector representations.

Sign in / Sign up

Export Citation Format

Share Document