scholarly journals Meta-Learning Initializations for Low-Resource Drug Discovery

2020 ◽  
Author(s):  
Cuong Q. Nguyen ◽  
Constantine Kreatsoulas ◽  
Kim M. Branson
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
State Of The Art ◽  
Chemical Properties ◽  
Fine Tuning ◽  
Learning Performance ◽  
Low Resource ◽  
Average Improvement ◽  
Meta Learning ◽  
In Silico Models

Building in silico models to predict chemical properties and activities is a crucial step in drug discovery. However, drug discovery projects are often characterized by limited labeled data, hindering the applications of deep learning in this setting. Meanwhile advances in meta-learning have enabled state-of-the-art performances in few-shot learning benchmarks, naturally prompting the question: Can meta-learning improve deep learning performance in low-resource drug discovery projects? In this work, we assess the efficiency of the Model-Agnostic Meta-Learning (MAML) algorithm – along with its variants FO-MAML and ANIL – at learning to predict chemical properties and activities. Using the ChEMBL20 dataset to emulate low-resource settings, our benchmark shows that meta-initializations perform comparably to or outperform multi-task pre-training baselines on 16 out of 20 in-distribution tasks and on all out-of-distribution tasks, providing an average improvement in AUPRC of 7.2% and 14.9% respectively. Finally, we observe that meta-initializations consistently result in the best performing models across fine-tuning sets with k ∈ {16, 32, 64, 128, 256} instances.<br>

scholarly journals Meta-Learning Initializations for Low-Resource Drug Discovery

2020 ◽  
Author(s):  
Cuong Q. Nguyen ◽  
Constantine Kreatsoulas ◽  
Kim M. Branson
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
State Of The Art ◽  
Chemical Properties ◽  
Fine Tuning ◽  
Learning Performance ◽  
Low Resource ◽  
Average Improvement ◽  
Meta Learning ◽  
In Silico Models

Building in silico models to predict chemical properties and activities is a crucial step in drug discovery. However, drug discovery projects are often characterized by limited labeled data, hindering the applications of deep learning in this setting. Meanwhile advances in meta-learning have enabled state-of-the-art performances in few-shot learning benchmarks, naturally prompting the question: Can meta-learning improve deep learning performance in low-resource drug discovery projects? In this work, we assess the efficiency of the Model-Agnostic Meta-Learning (MAML) algorithm – along with its variants FO-MAML and ANIL – at learning to predict chemical properties and activities. Using the ChEMBL20 dataset to emulate low-resource settings, our benchmark shows that meta-initializations perform comparably to or outperform multi-task pre-training baselines on 16 out of 20 in-distribution tasks and on all out-of-distribution tasks, providing an average improvement in AUPRC of 7.2% and 14.9% respectively. Finally, we observe that meta-initializations consistently result in the best performing models across fine-tuning sets with k ∈ {16, 32, 64, 128, 256} instances.<br>

Review of the Applications of Deep Learning in Bioinformatics

2021 ◽  
Vol 15 (8) ◽  
pp. 898-911
Author(s):  
Yongqing Zhang ◽  
Jianrong Yan ◽  
Siyu Chen ◽  
Meiqin Gong ◽  
Dongrui Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
Biomedical Imaging ◽  
State Of The Art ◽  
Black Box ◽  
Medical Data ◽  
Biological Data ◽  
High Dimensional ◽  
Biological Research ◽  
Process Data

Rapid advances in biological research over recent years have significantly enriched biological and medical data resources. Deep learning-based techniques have been successfully utilized to process data in this field, and they have exhibited state-of-the-art performances even on high-dimensional, nonstructural, and black-box biological data. The aim of the current study is to provide an overview of the deep learning-based techniques used in biology and medicine and their state-of-the-art applications. In particular, we introduce the fundamentals of deep learning and then review the success of applying such methods to bioinformatics, biomedical imaging, biomedicine, and drug discovery. We also discuss the challenges and limitations of this field, and outline possible directions for further research.

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

Ensemble-based deep meta learning for medical image segmentation

2021 ◽  
pp. 1-7
Author(s):  
Usman Ahmed ◽  
Jerry Chun-Wei Lin ◽  
Gautam Srivastava
Keyword(s):  
Image Segmentation ◽  
Deep Learning ◽  
Learning Algorithm ◽  
State Of The Art ◽  
Medical Image Segmentation ◽  
The State ◽  
Data Set ◽  
Deep Learning Algorithm ◽  
Meta Learning ◽  
Small Set

Deep learning methods have led to a state of the art medical applications, such as image classification and segmentation. The data-driven deep learning application can help stakeholders to collaborate. However, limited labelled data set limits the deep learning algorithm to generalize for one domain into another. To handle the problem, meta-learning helps to learn from a small set of data. We proposed a meta learning-based image segmentation model that combines the learning of the state-of-the-art model and then used it to achieve domain adoption and high accuracy. Also, we proposed a prepossessing algorithm to increase the usability of the segments part and remove noise from the new test image. The proposed model can achieve 0.94 precision and 0.92 recall. The ability to increase 3.3% among the state-of-the-art algorithms.

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

scholarly journals Deep learning for plankton and coral classification

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Alessandra Lumini ◽  
Loris Nanni ◽  
Gianluca Maguolo
Keyword(s):  
Deep Learning ◽  
Performance Improvement ◽  
State Of The Art ◽  
Source Code ◽  
Fine Tuning ◽  
Automated System ◽  
Training Procedure ◽  
Single Model ◽  
Training Models ◽  
Heterogeneous Ensemble

In this paper, we present a study about an automated system for monitoring underwater ecosystems. The system here proposed is based on the fusion of different deep learning methods. We study how to create an ensemble based of different Convolutional Neural Network (CNN) models, fine-tuned on several datasets with the aim of exploiting their diversity. The aim of our study is to experiment the possibility of fine-tuning CNNs for underwater imagery analysis, the opportunity of using different datasets for pre-training models, the possibility to design an ensemble using the same architecture with small variations in the training procedure.Our experiments, performed on 5 well-known datasets (3 plankton and 2 coral datasets) show that the combination of such different CNN models in a heterogeneous ensemble grants a substantial performance improvement with respect to other state-of-the-art approaches in all the tested problems. One of the main contributions of this work is a wide experimental evaluation of famous CNN architectures to report the performance of both the single CNN and the ensemble of CNNs in different problems. Moreover, we show how to create an ensemble which improves the performance of the best single model. The MATLAB source code is freely link provided in title page.

scholarly journals A merged molecular representation learning for molecular properties prediction with a web-based service

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hyunseob Kim ◽  
Jeongcheol Lee ◽  
Sunil Ahn ◽  
Jongsuk Ruth Lee
Keyword(s):  
Deep Learning ◽  
Quantitative Estimation ◽  
Chemical Properties ◽  
Representation Learning ◽  
Fine Tuning ◽  
Learning Models ◽  
Web Based ◽  
Property Prediction ◽  
Matrix Embedding ◽  
Molecular Properties Prediction

AbstractDeep learning has brought a dramatic development in molecular property prediction that is crucial in the field of drug discovery using various representations such as fingerprints, SMILES, and graphs. In particular, SMILES is used in various deep learning models via character-based approaches. However, SMILES has a limitation in that it is hard to reflect chemical properties. In this paper, we propose a new self-supervised method to learn SMILES and chemical contexts of molecules simultaneously in pre-training the Transformer. The key of our model is learning structures with adjacency matrix embedding and learning logics that can infer descriptors via Quantitative Estimation of Drug-likeness prediction in pre-training. As a result, our method improves the generalization of the data and achieves the best average performance by benchmarking downstream tasks. Moreover, we develop a web-based fine-tuning service to utilize our model on various tasks.

scholarly journals Tri-net for Semi-Supervised Deep Learning

2018 ◽  
Author(s):  
Dong-Dong Chen ◽  
Wei Wang ◽  
Wei Gao ◽  
Zhi-Hua Zhou
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Error Rate ◽  
Deep Neural Network ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Fine Tuning ◽  
Learning Methods ◽  
Model Initialization

Deep neural networks have witnessed great successes in various real applications, but it requires a large number of labeled data for training. In this paper, we propose tri-net, a deep neural network which is able to use massive unlabeled data to help learning with limited labeled data. We consider model initialization, diversity augmentation and pseudo-label editing simultaneously. In our work, we utilize output smearing to initialize modules, use fine-tuning on labeled data to augment diversity and eliminate unstable pseudo-labels to alleviate the influence of suspicious pseudo-labeled data. Experiments show that our method achieves the best performance in comparison with state-of-the-art semi-supervised deep learning methods. In particular, it achieves 8.30% error rate on CIFAR-10 by using only 4000 labeled examples.

Deep Learning Techniques and COVID-19 Drug Discovery: Fundamentals, State-of-the-Art and Future Directions

2021 ◽  
pp. 9-31 ◽  
Author(s):  
Mohammad Behdad Jamshidi ◽  
Ali Lalbakhsh ◽  
Jakub Talla ◽  
Zdeněk Peroutka ◽  
Sobhan Roshani ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Discovery ◽  
State Of The Art ◽  
Future Directions ◽  
Learning Techniques

scholarly journals ManyModalQA: Modality Disambiguation and QA over Diverse Inputs

2020 ◽  
Vol 34 (05) ◽  
pp. 7879-7886
Author(s):  
Darryl Hannan ◽  
Akshay Jain ◽  
Mohit Bansal
Keyword(s):  
Transfer Learning ◽  
Human Performance ◽  
Question Answering ◽  
State Of The Art ◽  
Fine Tuning ◽  
Low Resource ◽  
Lower Accuracy ◽  
End To End ◽  
Text Images ◽  
Training Sets

We present a new multimodal question answering challenge, ManyModalQA, in which an agent must answer a question by considering three distinct modalities: text, images, and tables. We collect our data by scraping Wikipedia and then utilize crowdsourcing to collect question-answer pairs. Our questions are ambiguous, in that the modality that contains the answer is not easily determined based solely upon the question. To demonstrate this ambiguity, we construct a modality selector (or disambiguator) network, and this model gets substantially lower accuracy on our challenge set, compared to existing datasets, indicating that our questions are more ambiguous. By analyzing this model, we investigate which words in the question are indicative of the modality. Next, we construct a simple baseline ManyModalQA model, which, based on the prediction from the modality selector, fires a corresponding pre-trained state-of-the-art unimodal QA model. We focus on providing the community with a new manymodal evaluation set and only provide a fine-tuning set, with the expectation that existing datasets and approaches will be transferred for most of the training, to encourage low-resource generalization without large, monolithic training sets for each new task. There is a significant gap between our baseline models and human performance; therefore, we hope that this challenge encourages research in end-to-end modality disambiguation and multimodal QA models, as well as transfer learning.

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