Literature DB >> 35353844

A feature transferring workflow between data-poor compounds in various tasks.

Xiaofei Sun1,2, Jingyuan Zhu3, Bin Chen2,4, Hengzhi You3, Huiqing Xu5.   

Abstract

Compound screening by in silico approaches has advantages in identifying high-activity leading compounds and can predict the safety of the drug. A key challenge is that the number of observations of drug activity and toxicity accumulation varies by target in different datasets, some of which are more understudied than others. Owing to an overall insufficiency and imbalance of drug data, it is hard to accurately predict drug activity and toxicity of multiple tasks by the existing models. To solve this problem, this paper proposed a two-stage transfer learning workflow to develop a novel prediction model, which can accurately predict drug activity and toxicity of the targets with insufficient observations. We built a balanced dataset based on the Tox21 dataset and developed a drug activity and toxicity prediction model based on Siamese networks and graph convolution to produce multitasking output. We also took advantage of transfer learning from data-rich targets to data-poor targets. We showed greater accuracy in predicting the activity and toxicity of compounds to targets with rich data and poor data. In Tox21, a relatively rich dataset, the prediction model accuracy for classification tasks was 0.877 AUROC. In the other five unbalanced datasets, we also found that transfer learning strategies brought the accuracy of models to a higher level in understudied targets. Our models can overcome the imbalance in target data and predict the compound activity and toxicity of understudied targets to help prioritize upcoming biological experiments.

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Year:  2022        PMID: 35353844      PMCID: PMC8967016          DOI: 10.1371/journal.pone.0266088

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


Introduction

Determining the intricate meanings of the information in chemical molecular systems from chemical structures is important for finding chemicals with favorable pharmacological, toxicological, and pharmacokinetic properties [1-5]. Existing studies show that screening potential drugs by predicting activity and toxicity in leading compounds can be of great help [6-11]. A considerable number of drug activity prediction methods based on machine learning have been investigated, including naive Bayes [6, 12, 13], logistic regression [7, 8], k-nearest neighbors [9], support vector machines [10, 11, 14–16], random forests [11, 17, 18], and artificial neural networks [16]. These methods have contributed significantly to the development of drug activity and toxicity prediction, but the problem of scarcity and imbalance of target data has not received sufficient attention. Recently, the advent of deep learning approaches has shown a significant impact on this traditional cheminformatics task due to their enormous capacity to learn the structure and properties of compounds [19-27]. These studies used descriptor-based or graph-based methods to predict the activity and toxicity of compounds to targets on publicly available datasets. The emergence of these latest approaches has further enhanced the effectiveness of drug activity and toxicity prediction, but the scarcity and imbalance of target data remain a challenge. A key challenge in the development of generalizable drug virtual screening models is the imbalance in target/task data, wherein the accumulated number of drug activities varies from target to target and the number of positive drugs is very rare [28]. In the Tox21 dataset [29], for example, targets such as GPCRs (G protein-coupled receptors), nuclear receptors, ion channels, and kinases have rich data on drug toxicity, while other targets have less data. Surprisingly, the imbalance in target data is more pronounced in many other datasets (Fig 1). Existing methods use original target and drug data without balancing or augmentation due to an ‘activity cliff’, which is a pair of compounds with high structural similarity but unexpectedly high activity differences [6-26]. In this work, we attempt to address the challenge of data imbalance and data scarcity to accurately predict drug activity and toxicity.
Fig 1

Summary of the Siamese graph convolutional network-based transfer learning workflow (SGT).

There are a large number of understudied targets in clinical and scientific research (Fig 1), such as ADRB2, OPRK1, and PPARRG. Many obstacles hinder drug activity and toxicity studies at these targets. For example, due to the difficulty of obtaining tumor tissue fragments of bone metastasis, the scarcity of sarcomatous-type tumors, and the difficulty in culturing bone tissue into cell lines, the number of cell models is insufficient [30, 31]. Due to the shortage of these cell line models, corresponding high-throughput screening is difficult to carry out, and target studies are also greatly restricted. Therefore, there is an urgent need to develop a generalizable drug activity and toxicity prediction tool to promote the understanding of understudied targets. We are trying to develop a generalizable drug activity and toxicity prediction model to address the challenge of data scarcity for understudied targets. The training data for understudied targets were insufficient: in addition to the small total number of their experimental observations, the positive rate of drug activity was also very low. The potential solution to this data scarcity problem is to take advantage of information from data-rich targets to data-poor targets. Because these different targets have biological commonality, the drugs have similar activity and toxicity to them to some extent [31-33]. Therefore, we proposed utilizing the drug activity and toxicity of data-rich targets through transfer learning to help improve the performance of the model on data-poor targets. Transfer learning is the recognition of knowledge and skills learned from previous domains/tasks and their application to new domains/tasks. To learn about the generalizable expression of drug activity and toxicity to targets, we selected Tox21, which is relatively data-rich (high number of experimental observations and high drug-positive rates), to produce a balanced dataset. We used the drugs and targets in our balanced Tox21 dataset to train the Siamese graph convolutional neural network model and verified our model in five datasets: ToxCast, HIV, MUV, PCBA, and FreeSolv after transfer learning (Fig 1).

Materials

A balanced dataset

Our balanced dataset is based on the Tox21 dataset, which is designed to help scientists understand the potential of the chemicals and compounds being tested through the Toxicology in the 21st Century initiative to disrupt biological pathways in ways that may result in toxic effects [2, 7–9, 14, 19–24, 29]. The numbers of targets and unique compounds were 12 and 7831, respectively. There were a total of 93972 compound toxicity experimental observations (i.e., a pair of compounds and targets), of which the number of drugs and the positive rate of drugs varied from target to target. For a target in the Tox21 dataset, we first took a pair of positive compounds, then a pair of negative compounds, and then a positive compound and a negative compound. We repeatedly obtained pairs of data until a new balanced dataset for the Siamese network was built. The dataset contains 23,493 toxicity experimental data. We compared the model using this balanced dataset with the baseline study using Tox21 [34]. We used five other datasets for verification (Fig 2): (i) ToxCast: another dataset from the same initiative as Tox21 that uses virtual high-throughput screening to provide toxicology data. It contains qualitative results from more than 600 experiments on 8615 compounds [29]. (ii) MUV: a dataset designed for virtual screening technology that contains approximately 90,000 compounds involving 17 tasks, and the positive compounds in this dataset are structurally distinct from each other [34, 35]. (iii) PCBA: PubChem BioAssay [35-38] is a dataset of small-molecule biological activity produced by high-throughput screening. We used a subset of PubChem in MoleculeNet containing 400,000 compounds and 128 biological assays. (iv) HIV: The HIV dataset [34, 37], an AIDS antiviral screening dataset introduced by the Drug Treatment Program (DTP), tested the ability of 41,913 compounds to suppress HIV. (v) FreeSolv: The Free Solvation Database [35], used in the SAMCL Blind Prediction Challenge, contains the hydration free energy of 643 compound molecules.
Fig 2

Data distribution of the drug datasets.

The first graph in the first row is an overview of the proportions of positive drug samples of the targets in datasets a Tox21, b MUV, c PCBA, and d Toxcast, and other graphs show in detail the distribution of positive samples in each dataset.

Data distribution of the drug datasets.

The first graph in the first row is an overview of the proportions of positive drug samples of the targets in datasets a Tox21, b MUV, c PCBA, and d Toxcast, and other graphs show in detail the distribution of positive samples in each dataset.

Compound features

SMILES is a linear representation of molecular structures that uniquely describes a molecule with an ASCII string. SMILES uses atomic symbols to represent the atoms themselves and special characters to represent the relationships between atoms. We used Rdkit (http://www.rdkit.org) to process SMILES into rich atomic features such as degree, implicit valence, formal charge, number of radical electrons, and adjacency list and then input these features into the compound encoder. The molecular features of the compound were extracted by the compound encoder detailed in a later section.

Methods

Method overview

Our transfer learning method for enhancing drug activity and toxicity prediction with scarce data is to transfer parameters of models pretrained using a balanced training set to a prediction model for the specific targets. We first trained the toxicity prediction model of data-rich targets from a balanced dataset containing the drug toxicity of 12 different targets. The Siamese network facilitates the integration of two network structures in a parameter-sharing manner, benefiting the learning of data-poor targets, so we used the Siamese network in pretraining the model. In addition, the graph convolutional neural network has obvious advantages in obtaining molecular representation, which we took as a feature extractor in the Siamese network. We initialized the prediction model of data-poor targets using the parameters of the pretrained model and retrained it with the corresponding data. Our Siamese graph convolutional neural network (Fig 3a) determines whether a pair of compounds belongs to the same class by the distance between them and produces a corresponding probability distribution through the decision layer. We formulated this prediction problem. Given an input block x ≔ {C, C} of compound C and compound C, the prediction model f is a function such that where y is the similarity score of two compounds. We used two compound encoders that share parameters to form a Siamese network and trained it on a balanced dataset to generate a pretrained Siamese graph model that can be used for subsequent transfer learning.
Fig 3

A graphical representation of the network described in this article.

a Siamese graph convolutional neural network with shared weights, b graph convolution operation, c graph pooling operation, and d graph gathering operation in the network.

A graphical representation of the network described in this article.

a Siamese graph convolutional neural network with shared weights, b graph convolution operation, c graph pooling operation, and d graph gathering operation in the network.

Compound encoder

We used graph convolutional networks (Fig 3b) to encode SMILES sequences because the latest studies [35-38] suggest that graph convolutional networks have an advantage in processing molecular structures. The compound encoder learns the molecular representation of each compound. Considering that the number of atoms in a molecule changes widely and the value of degree is relatively limited, the compound encoder stores and calculates atoms by degree. Each atomic feature, such as implicit valence, is first represented as a one-hot vector, and then the one-hot vectors of all atomic features are combined and fed into the compound encoder. A compound could be considered a graph, its nodes representing atoms, and the edges that connect them together are bonds. In graph convolution [36], for a node, we feed its features and neighbors into two dense layers and then add the output of the dense layers as the new features of the node. The calculations of the new features of nodes with the same degree share weights. In a compound, if an atom a has a total of n neighbors, its new features after graph convolution can be formulated as where W is the weight of node a; W is the weight of the neighboring nodes; b is bias, and σ is the activation function ReLU. The yellow arrows represent the dense layers of atomic a and its neighbors, with weights of W and W, respectively. Similar to the convolutional neural network, the graph pooling layer (Fig 3c) is used in the compound encoder. Graph pooling is the operation of returning the largest or average feature among an atom and its neighbors. Graph pooling increases the receptive field without adding additional parameters: In graph convolution and graph pooling, each atom has a descriptor vector. However, to make a final prediction, a fixed-size vector descriptor for the entire graph will be required. The graph gather layer (Fig 3d) sums all the feature vectors of all atoms in the compound molecule to obtain the molecular feature vector:

Tox21 prediction model

Our goal is to predict the activity and toxicity of unobserved compounds at a given target and to prioritize compounds that can be used in experiments. To achieve this, we used transfer learning in addition to Siamese graph convolutional neural networks and data balancing. We transferred the parameters of the drug encoder in the Siamese graph model to a new prediction model, which we call the Tox21 prediction model, and retrained it using the Tox21 dataset. Our Tox21 prediction model consists of a drug encoder and a decision network (Fig 4) for toxicity prediction in an end-to-end manner.
Fig 4

The transfer learning workflow for data-poor targets.

Two stages are used to transfer model parameters from data-rich targets to data-poor targets in specific datasets.

The transfer learning workflow for data-poor targets.

Two stages are used to transfer model parameters from data-rich targets to data-poor targets in specific datasets.

Fine-tuning to data-poor targets

We focused on transfer learning from data-rich targets in a balanced dataset to targets whose data are scarce in other unbalanced datasets (Fig 4). In the transfer learning experiments, we selected the ToxCast, HIV, MUV, PCBA, and FreeSolv datasets (Fig 2) because most of their targets had fewer observations and low positive rates, but the total number of observations was sufficient to build a prediction model for comparative experiments. The drug toxicity prediction model in the first stage, which is pretrained with data-rich Tox21 targets, learns the underlying mechanism between compounds and targets, and then the prediction model for specific data-insufficient targets transfers the pretrained model parameters from the Tox21 model and fine-tunes the parameters. Optional fine-tuning strategies include (i) retraining all parameters, (ii) fixing the compound encoder, retraining the decision layer, and (iii) not retraining at all. By comparing the performance of these three different strategies in unbalanced datasets, the first strategy was found to be optimal, so we used the first fine-tuning strategy in subsequent experiments.

Training loss

Our Siamese graph convolutional neural network learns multiple tasks on a balanced dataset, and the training loss is the contrastive loss: where Y is the label of whether two compounds are the same class; m is the threshold, and D represents the Euclidean distance of the two compound features and : The training loss for the Tox21 model and fine-tuning were similarly defined: where S is a softmax function: We first minimized L loss with all training batches in the balanced dataset and then switched to L in fine-tuning for training. Optimizer was Adam in TensorFlow 1.6.0.

Evaluation

Training and test set

We evaluated the prediction models with external validation on unbalanced datasets with data-poor targets. For datasets with scarce target data such as ToxCast, HIV, MUV, PCBA, and FreeSolv, we set aside some of the data as independent test sets (20%) and the rest as training sets (80%). The drugs in the test set do not overlap with the training set. Each data-poor target had a small number of distinct drugs, and different targets sometimes shared drugs. Note that each training or test set of the Siamese graph convolutional network was a tuple {d, d} of drug pairs for certain targets, while each training or test set in fine-tuning was a drug.

Accuracy measures

We used different criteria to measure the accuracy of regression and classification tasks. The classification accuracy measure was the area under the ROC curve (AUC); the regression accuracy measures were R2, RMSE, and MAE.

Baselines

We compared the accuracy of our classification tasks with five baseline methods: (i) Attentive FP, which is a new graph neural network architecture for molecular representation and uses graph attention mechanisms to learn from a drug discovery dataset [37]. (ii) Neural FP is a kind of circular fingerprint that can be generated differentiably by a neural network, which allows end-to-end learning of molecules of any size and shape [37]. (iii) GraphConv directly uses the molecular connectivity graph as input and provides a learnable featurization process that extracts meaningful representations of molecules [34, 39]. (iv) ECFP+LR that utilizes linear regression using molecular extended-connectivity fingerprints (ECFPs) on specific tasks [34]. (v) SVM that maps input vectors to a high-dimensional feature space through nonlinear mapping, where an optimal separating hyperplane is constructed to separate the samples [34]. The benchmark accuracy values of various methods (including Attentive FP, Neural FP, GraphConv, ECFP-LR, and SVM) are listed in the referenced papers [34, 37].

Results

Prediction accuracy of data-rich targets

We used three split methods, index, random, and scaffold, to split the dataset into a training set, validation set, and test set. We first evaluated the accuracy of the model trained and tested using data-rich targets in Tox21 (Fig 5a). We achieved better performance on these datasets than the baseline approaches. On the test sets generated using these three split methods, we achieved AUROCs of 0.833, 0.877, and 0.761, while Neural FP, Attentive FP, and ECFP-LR achieved AUROCs of 0.829, 0.858, and 0.755 on the test set generated using the random method. We found that our Siamese graph convolutional neural network has significant AUROC improvements over GraphConv in the training, validation, and test sets. This proves the advantages of data balancing and Siamese graph convolutional neural networks.
Fig 5

Performance comparison between our model and the baseline model in multitask classification and regression tasks.

The area under the curve (AUC) of the ROC curve of various models in the a Tox21 and b Freesolv datasets.

Performance comparison between our model and the baseline model in multitask classification and regression tasks.

The area under the curve (AUC) of the ROC curve of various models in the a Tox21 and b Freesolv datasets.

Prediction accuracy of a specific model with transfer learning

We then experimented with poor data targets in the FreeSolv (Fig 5b), MUV, PCBA (Fig 6), and ToxCast, HIV (Fig 7) datasets. We found that proper transfer learning can improve the accuracy of drug activity and toxicity prediction at targets with poor data. In the classification tasks of the PCBA, MUV, ToxCast, and HIV datasets, we achieved AUROCs of 0.858, 0.715, 0.655, 0.804, 0.851, 0.747, 0.725, 0.715, 0.655, and 0.772, 0.856, 0.805 using the index, random, and scaffold split methods, respectively. In the regression task of FreeSolv datasets, we achieved 0.953 R2, 0.778 RMSE, 0.539 MAE, 0.936 R2, 0.899 RMSE, 0.585 MAE, and 0.755 R2, 1.85 RMSE, 1.519 MAE, respectively (Figs 5b and 8). This method can also make the prediction of each task consistent with the observed value, and improve the unbalanced performance of the model between tasks (Figs 9–11). The area under the ROC curve (AUC) of various models in the Tox21, ToxCast, MUV, and HIV datasets is shown in Table 1. In addition to R2, RMSE and MAE (kcal/mol) are also provided to perfectly reflect the performance of the models in FreeSolv data set (Table 2).
Fig 6

Performance comparison between our model and the baseline model in multitask classification tasks.

The area under the curve (AUC) of the ROC curve of various models in the a PCBA and b MUV datasets.

Fig 7

Performance comparison between our model and the baseline model in multitask classification tasks.

The area under the curve (AUC) of the ROC curve of various models in the a HIV and b Toxcast datasets.

Fig 8

Performance comparison between our model and the baseline model in the regression task.

a RMSE and b MAE (kcal/mol) are provided to perfectly reflect the performance of the models in the regression task of the Freesolv dataset.

Fig 9

The correlation between predictions and observations of our model on different tasks in tox21 data set (index split).

Fig 11

The correlation between predictions and observations of our model on different tasks in tox21 data set (scaffold split).

Table 1

The area under curve (AUC) of the ROC curve of various models in Tox21, ToxCast, MUV and HIV data sets.

Data SetModelSplit MethodTrainValidTest
Tox21ECFP+LRIndex0.9030.7040.738
Random0.9010.7420.755
Scaffold0.9050.6510.697
GraphConvIndex0.9450.8290.820
Random0.9380.8330.846
Scaffold0.9550.7780.752
Neural FPRandom--0.829
Attentive FPRandom--0.858
Our (general model)Index0.9780.8260.833
Random0.9720.8370.877
Scaffold0.9780.7800.761
ToxCastECFP+LRIndex0.7270.5780.464
Random0.7130.5380.557
Scaffold0.7170.4960.496
GraphConvIndex0.9040.7230.708
Random0.9010.7340.754
Scaffold0.9140.6620.640
Our (Transfer learning)Index0.9400.7310.725
Random0.9660.7350.715
Scaffold0.9460.6830.655
PCBAECFP+LRIndex0.8090.7760.781
Random0.8080.7720.773
Scaffold0.8110.7460.757
GraphConvIndex0.8950.8550.851
Random0.8960.8540.855
Scaffold0.9000.8290.829
Our (Transfer learning)Index0.9080.8520.858
Random0.9090.8550.861
Scaffold0.9020.8330.842
MUVECFP+LRIndex0.9600.7730.717
Random0.9540.7800.740
Scaffold0.9560.7020.712
GraphConvIndex0.9510.8160.792
Random0.9490.7870.836
Scaffold0.9790.7790.735
Attentive FPRandom--0.843
Our (Transfer learning)Index0.9790.8260.804
Random0.9880.7900.851
Scaffold0.9850.7860.747
HIVECFP+LRIndex0.8640.7390.741
Random0.8600.8060.809
Scaffold0.8580.7980.738
SVMScaffold--0.792
GraphConvIndex0.9450.7790.728
Random0.9390.8350.822
Scaffold0.9380.7950.769
Attentive FPScaffold--0.832
Our (Transfer learning)Index0.9650.8060.772
Random0.9740.8460.856
Scaffold0.9690.8070.805
Table 2

The Performances in FreeSolv data set.

R2, RMSE and MAE (kcal/mol) are provided to reflect the performance of the models.

ModelSplit MethodValidTest
R 2 RMSEMAE R 2 RMSEMAE
GraphConvIndex0.9350.9090.7030.9410.9630.738
Random0.9280.9820.6440.8951.2280.803
Scaffold0.8832.1151.5550.7092.0671.535
Our (Transfer learning)Index0.9520.7510.5790.9530.7780.539
Random0.9090.9000.7010.9360.8990.585
Scaffold0.9002.551.4600.7551.851.519

Performance comparison between our model and the baseline model in multitask classification tasks.

The area under the curve (AUC) of the ROC curve of various models in the a PCBA and b MUV datasets. The area under the curve (AUC) of the ROC curve of various models in the a HIV and b Toxcast datasets.

Performance comparison between our model and the baseline model in the regression task.

a RMSE and b MAE (kcal/mol) are provided to perfectly reflect the performance of the models in the regression task of the Freesolv dataset.

The Performances in FreeSolv data set.

R2, RMSE and MAE (kcal/mol) are provided to reflect the performance of the models.

Discussion

The purpose of this study was to develop drug activity and toxicity prediction models that can even be used for targets with poor data. To this end, we (i) created a balanced dataset from the Tox21 dataset, which is relatively data-rich for the targets, (ii) integrated the graph convolution and Siamese network and used it to train a model of the toxicity of compounds to targets using the physical and chemical features of compounds in the balanced dataset, and (iii) transferred the toxicity prediction model from data-rich targets to data-poor targets. Finally, the proposed models more accurately predicted the activity and toxicity of compounds in the other five datasets than existing methods using an appropriate transfer learning strategy. Our main contribution is that we approached understudied targets for drug activity and toxicity prediction. Balanced target data are the strongest support for estimating drug activity and toxicity but are only available when sufficient study is done. Inadequate research on these targets leads to an imbalance in the corresponding drug activity and toxicity data, which consequently becomes an obstacle to the development of drugs for these targets. Our drug activity and toxicity prediction models successfully address the lack and imbalance of target data while achieving competitive accuracy. Although our study focused on predicting the activity and toxicity of understudied targets, our models showed greater accuracy than baseline models, even in general data-rich targets. This improved accuracy is due to the use of data balancing and the Siamese graph network in the first stage of our transfer learning. We created a balanced dataset from the Tox21 dataset, which is relatively rich in target data, for a pretrained model that combines graph convolution and the Siamese network. Balanced data allow us to maximize the few-shot learning capabilities of Siamese graph networks. In addition, this model has a good ability to indicate the correlation between molecular substructure and toxicity or activity (Fig 12).
Fig 12

An example diagram showing the correlation between atomic and molecular toxicity using similarity maps.

Red represents a higher correlation, and green represents a lower correlation.

An example diagram showing the correlation between atomic and molecular toxicity using similarity maps.

Red represents a higher correlation, and green represents a lower correlation. The limitation of this study is that the model cannot achieve high accuracy (no more than 80%) in the ToxCast dataset. A possible explanation for this might be that the ToxCast dataset has the largest number of targets (617), the largest imbalance, and low drug positive rates (with positive rates ranging from 0–19% between targets), so the presence of a large number of understudied targets may result in discrepancies in model predictions and observations.

Conclusion

In summary, our model is an end-to-end prediction model of drug activity and toxicity, learning the interaction between drugs and targets. Based on the fact that similar gene expression is shared by different target tissues and therefore drugs exhibit activity and toxicity to the targets in a similar manner, we used a siamese graph convolutional neural network and transfer learning from data-rich targets to data-poor targets to enable prediction models to play a role in data-poor targets. For future work, our drug activity and toxicity prediction models can reveal the underlying mechanisms of interaction between other potential targets and drugs and provide new methods for efficient and low-cost drug discovery. In order to make the model proposed in this paper can be used in common situation, it is essential to establish massive multi-task datasets for pretraining, which is also an interesting attempt for our future research work. 9 Feb 2022
PONE-D-22-00703
A feature transferring workflow between data-poor compounds in various tasks
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Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: In the results required comparison table for exiting terms and proposed idea with all the parameters. The Abstract is clear and implementation, conclusion meet the requirement. The manuscript has been written in standard English. Reviewer #2: The authors have developed drug activity and toxicity prediction based on Siamese networks and graph convolution to produce multitasking output for understudied targets to overcome the scarcity of drug data. The problem solved in the article is significant and relevant to the venue. The scientific novelty and contributions of this paper are good enough for publication. However, I have a few suggestions worth including to represent the article better. Positive aspects of the paper: This paper is well motivated and easy to follow. Experiments are well designed, and the proposed algorithm works well compared to baseline algorithms. Suggestion/comments: The authors should highlight the novelty and motivation of their proposed method. Further, they should highlight the challenges or limitations of the proposed work. I suggest adding some statistical analysis tests to validate the results. The paper needs proofreading to eliminate any typos errors, for example, on page 2, line 21. ********** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: Anandhan K Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.
3 Mar 2022 Dear academic editor and reviewers, I am very appreciated for your comments and suggestions. I have revised this manuscript and especially paid much attention to your comments and suggestions. The details of the revision are as follows: Replies to the academic editor: 1. The style of the manuscript has been modified in the latex file to comply with the requirements of the template. 2. The completeness and style of the reference list have been reviewed, and the retracted articles are not cited. 3. The statement “There was no additional external funding received for this study.” has been included in our updated Funding Statement. 4.“The funder provided support in the form of salaries for authors [XS, JZ, BC, HY and HX], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.” has been included in our updated Funding Statement. 5. "This does not alter our adherence to PLOS ONE policies on sharing data and materials.” has been included within our Competing Interests Statement. 6. An updated Funding Statement and Competing Interests Statement have been included in our cover letter. Replies to Reviewer #1: 1. The comparison tables (Tables 1 and 2) for exiting terms and proposed idea with all the parameters has been added in the results. Replies to Reviewer #2: 1. The novelty and motivation of the proposed method have been highlighted in the abstract as: Owing to an overall insufficiency and imbalance of drug data, it is hard to accurately predict drug activity and toxicity of multiple tasks by the existing models. To solve this problem, this paper proposed a two-stage transfer learning workflow to develop a novel prediction model, which can accurately predict drug activity and toxicity of the targets with insufficient observations. 2. The challenges and limitations of the proposed work have been highlighted in the conclusion as: In order to make the model proposed in this paper can be used in common situation, it is essential to establish massive multi-task datasets for pretraining, which is also an interesting attempt for our future research work. 3. Some statistical analysis tests, as illustrated in Figures 9, 10 and 11, have been added to validate the results. 4. The manuscript has been proofread to eliminate typos errors. For example, line 21 on page 2 has been revised to read: For example, due to the difficulty of obtaining tumor tissue fragments of bone metastasis, the scarcity of sarcomatous-type tumors, and the difficulty in culturing bone tissue into cell lines, the number of cell models is insufficient. We thank you in advance for considering our manuscript for publication in PLOS ONE. Sincerely, Xiaofei Sun Submitted filename: Response to Reviewers.docx Click here for additional data file. 15 Mar 2022 A feature transferring workflow between data-poor compounds in various tasks PONE-D-22-00703R1 Dear Dr. Chen, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Sathishkumar V E Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ********** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: All the correction has been updated. The reviewer comments are updated in the new version article. ********** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: ANANDHAN K 21 Mar 2022 PONE-D-22-00703R1 A feature transferring workflow between data-poor compounds in various tasks Dear Dr. Chen: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Sathishkumar V E Academic Editor PLOS ONE
  35 in total

1.  Random forest prediction of mutagenicity from empirical physicochemical descriptors.

Authors:  Qing-You Zhang; João Aires-de-Sousa
Journal:  J Chem Inf Model       Date:  2007 Jan-Feb       Impact factor: 4.956

2.  Anticancer drug synergy prediction in understudied tissues using transfer learning.

Authors:  Yejin Kim; Shuyu Zheng; Jing Tang; Wenjin Jim Zheng; Zhao Li; Xiaoqian Jiang
Journal:  J Am Med Inform Assoc       Date:  2021-01-15       Impact factor: 4.497

3.  Deep Learning for Drug-Induced Liver Injury.

Authors:  Youjun Xu; Ziwei Dai; Fangjin Chen; Shuaishi Gao; Jianfeng Pei; Luhua Lai
Journal:  J Chem Inf Model       Date:  2015-10-13       Impact factor: 4.956

Review 4.  From machine learning to deep learning: progress in machine intelligence for rational drug discovery.

Authors:  Lu Zhang; Jianjun Tan; Dan Han; Hao Zhu
Journal:  Drug Discov Today       Date:  2017-09-04       Impact factor: 7.851

5.  Prediction of Human Cytochrome P450 Inhibition Using a Multitask Deep Autoencoder Neural Network.

Authors:  Xiang Li; Youjun Xu; Luhua Lai; Jianfeng Pei
Journal:  Mol Pharm       Date:  2018-05-30       Impact factor: 4.939

6.  The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.

Authors:  Jordi Barretina; Giordano Caponigro; Nicolas Stransky; Kavitha Venkatesan; Adam A Margolin; Sungjoon Kim; Christopher J Wilson; Joseph Lehár; Gregory V Kryukov; Dmitriy Sonkin; Anupama Reddy; Manway Liu; Lauren Murray; Michael F Berger; John E Monahan; Paula Morais; Jodi Meltzer; Adam Korejwa; Judit Jané-Valbuena; Felipa A Mapa; Joseph Thibault; Eva Bric-Furlong; Pichai Raman; Aaron Shipway; Ingo H Engels; Jill Cheng; Guoying K Yu; Jianjun Yu; Peter Aspesi; Melanie de Silva; Kalpana Jagtap; Michael D Jones; Li Wang; Charles Hatton; Emanuele Palescandolo; Supriya Gupta; Scott Mahan; Carrie Sougnez; Robert C Onofrio; Ted Liefeld; Laura MacConaill; Wendy Winckler; Michael Reich; Nanxin Li; Jill P Mesirov; Stacey B Gabriel; Gad Getz; Kristin Ardlie; Vivien Chan; Vic E Myer; Barbara L Weber; Jeff Porter; Markus Warmuth; Peter Finan; Jennifer L Harris; Matthew Meyerson; Todd R Golub; Michael P Morrissey; William R Sellers; Robert Schlegel; Levi A Garraway
Journal:  Nature       Date:  2012-03-28       Impact factor: 49.962

7.  Large-scale ligand-based predictive modelling using support vector machines.

Authors:  Jonathan Alvarsson; Samuel Lampa; Wesley Schaal; Claes Andersson; Jarl E S Wikberg; Ola Spjuth
Journal:  J Cheminform       Date:  2016-08-10       Impact factor: 5.514

8.  New Advances in the Study of Bone Tumors: A Lesson From the 3D Environment.

Authors:  Margherita Cortini; Nicola Baldini; Sofia Avnet
Journal:  Front Physiol       Date:  2019-06-26       Impact factor: 4.566

9.  Machine learning methods in chemoinformatics.

Authors:  John B O Mitchell
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2014-09-01

10.  Application of transfer learning for cancer drug sensitivity prediction.

Authors:  Saugato Rahman Dhruba; Raziur Rahman; Kevin Matlock; Souparno Ghosh; Ranadip Pal
Journal:  BMC Bioinformatics       Date:  2018-12-28       Impact factor: 3.169

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