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scFSNN: a feature selection method based on neural network for singlecell RNAseq data
BMC Genomics volumeÂ 25, ArticleÂ number:Â 264 (2024)
Abstract
While singlecell RNA sequencing (scRNAseq) allows researchers to analyze gene expression in individual cells, its unique characteristics like overdispersion, zeroinflation, high genegene correlation, and large data volume with many features pose challenges for most existing feature selection methods. In this paper, we present a feature selection method based on neural network (scFSNN) to solve classification problem for the scRNAseq data. scFSNN is an embedded method that can automatically select features (genes) during model training, control the false discovery rate of selected features and adaptively determine the number of features to be eliminated. Extensive simulation and real data studies demonstrate its excellent feature selection ability and predictive performance.
Introduction
Singlecell RNA sequencing (scRNAseq) can reveal heterogeneity and diversity across tissues, organs, and systems at single cell level and has helped researchers improve their understanding of complex biological questions [1, 2]. However, the analysis of scRNAseq data is challenging. First, scRNAseq data are overdispersion. The heterogeneity of gene expression levels in a cell population results in higher variability for scRNAseq data compared to bulk RNAseq data [3]. Second, scRNAseq data are zeroinflated, i.e., excess zeros are observed in typical scRNAseq data. There are two types of zeros in scRNAseq data: biological zeros (due to the high heterogeneity between cells, expression levels of some genes are genuinely zero in some cells) and technical zeros (referred to as dropout, some transcripts are missed during the RNAseq procedure, such as reverse transcription or cDNA amplification steps). Third, features (genes) in scRNAseq data may be highly correlated [4]. Fourth, with the rapid development of highthroughput sequencing technologies, the sample size of scRNAseq data increases dramatically [5, 6]. Fifth, scRNAseq data contains a vast number of features, each representing a gene in the sample cell. As is wellknown, the human genome comprises approximately 30,000 genes, and there is typically a small subset of features that genuinely correlates with the response. Together, these characteristics make classification a particularly challenging task for scRNAseq data.
Currently, there is a large number of approaches that can possibly be applied to classify cells from different conditions in scRNAseq data. For example, generic classifiers, such as support vector machines and random forest, are potential candidates [7, 8]. And there are some approaches that are specifically designed for RNAseq data. These approaches mainly rely on the assumption that expression level of each gene follows the zeroinflated negative binomial (ZINB) distribution. The Poisson, the zeroinflated Poisson (ZIP), and the negative binomial (NB) distributions are three special cases of the ZINB distribution. For example, PLDA assumes Poisson distribution for the discrete count data of RNAseq data [9] and ZIPLDA uses ZIP distribution for RNAseq data with excess zeros [10]. These two methods apply different techniques to deal with the different aspects of challenges of RNAseq data. Specifically, PLDA addresses the challenge of overdispersion through a power transformation, while ZIPLDA models the gene count with ZIP to consider the excess zeros in RNAseq data and uses the ratio of the sum of squares between groups to that of within groups to select the genes to reduce the dimension. SINC [7], on the other hand, performs classification based on deep neural network. To reduce the dimension of data, SINC conducts an Ftest on each gene to test whether means of different classes are significantly different and selects top 1500 genes after ranking the pvalues in increasing order.
Deep neural network (DNN) is a highly flexible machinelearning technique and has demonstrated superior performance in various scientific problems. Since DNN enables the capturing of complexity and nonlinearity in scRNAseq data and is highly scalable, it has the potential to overcome the first four challenges of scRNAseq data, namely, overdispersion, zeroinflation, high genegene correlation and large sample size [7, 11, 12]. To further boost predictive accuracy and interpretability, employing feature selection within a DNN framework is crucial. Although there are thousands of genes in scRNAseq data, most of genes are irrelevant to the output and useful information is concentrated in a small number of genes. The main goal of feature selection is to find a subset of the input features that explains the output well. This not only reduces computational resources, but also reduces noise and improves the model generalization on unseen data [13]. Feature selection can also reduce experimental costs since researchers can collect the expression levels of small set of features when making prediction [14]. Additionally, feature selection can enhance interpretability by selecting a subset of features with significant predictive power on the output [11].
The feature selection methods are usually classified into three categories: filter, wrapper and embedded methods [15]. Filter methods select features based on certain criteria which measures the relevance between the features and output, and the selection procedure does not involve the model training. This makes filter methods overlook the interactions among features. On the other hand, wrapper and embedded methods attempt to select features that optimize the performance of a specific learning algorithm. Specifically, wrapper methods evaluate subsets of features based on learning algorithmsâ€™ predictive power, while embedded methods select features during the training of the learning algorithm. One type of widely used embedded method involves the regularization of parameters of learning algorithms [16, 17]. For example, spare group Lasso is used to penalize the set of outgoing weights from the same input node in neural networks to impose grouplevel sparsity on the networkâ€™s connections [18, 19]. Another line of research, which is relevant, uses backward elimination procedure to eliminate one or several least irrelevant features among all remaining features. For example, SurvNet, based on newly proposed measure of feature importance and an elimination procedure with FDR control, can adaptively eliminate features and estimate the false discovery rate at each step [11].
In this paper, we propose a feature selection method based on framework of deep neural network for scRNAseq data. Our method is an embedded method that selects features during model training. The procedure starts with all input features, and sequentially deletes features that have least impact on the fit. Features with the smallest importance scores are candidates for removal. At each step, false discovery rate is estimated to control the quality of remaining features. Due to the inherent advantages of DNN, scFSNN does not impose an assumption of specific statistical distributions for gene expression levels and enables the capturing of the complexity and nonlinearity in scRNAseq data. Furthermore, the implementation of scFSNN procedure that is based on popular deep learning framework, PyTorch, is highly scalable and can be applied to large data sets.
Methods
Let \(\varvec{X}^{'}=x^{'}_{ij}\) denote an \(n\times p\) count matrix of scRNAseq data with n cells and p genes, where \(x^{'}_{ij}\) is the expression level for gene j in cell i, \(i=1,\ldots ,n\) and \(j=1,\ldots ,p\). Let \(y_i\) denote the output, \(y_i\) can be onedimensional or multidimensional. The tuple \((\varvec{x}^{'}_{i.}, y_i)\) represents the ith sample. We first normalize \(\varvec{X}^{'}\) with total counts for each cell. To train the neural network more efficiently and stably, we also take the logarithm and standardize the normalized data. Let \(\varvec{X}=(x_{ij})_{i=1,\ldots ,n; j=1,\ldots ,p}\) be the normalized, logtransformed and standardized data, that is,
where \(d_0\) is the median of total numbers of counts, \(d_i\) is the total counts of ith cell, \(i=1,\ldots , n\), \(m_j\) and \(s_j\) are the mean and standard deviation of each gene for normalized and logtransformed data.
An overview of scFSNN is shown in Fig. 1. The architecture of deep neural network of scFSNN is given below:
where B, E and O represent the first hidden, second hidden and output layers. The two hidden layers have 256 and 128 nodes, and all layers are fully connected. Additionally, we use batch normalization [20] and dropout method [21] on each hidden layer, with a dropout rate set to 0.5. The loss function L is cross entropy, and an Adam optimizer with a learning rate 0.001 is used for training the model. The batch size is set to 32.
To select truly relevant features with the output, scFSNN starts with all input features and deletes features that have the smallest importance scores at each step. Additionally, we introduce a number of surrogate features known to be irrelevant to the output to estimate the false discovery rate. Similar to SurvNet [11], we define the importance score of jth feature as the average of absolute values of \(\frac{\partial L(y_i, O_i)}{\partial x_{ij}}\)
where \(O_i\) is the output of the network for the ith sample. The term \(\frac{\partial L(y_i, O_i)}{\partial x_{ij}}\) describes how the loss changes with jth feature in the ith sample, thus \(S_j\) measures the average of loss changes with respect to jth feature. Therefore, a larger \(S_j\) indicates a larger impact of jth feature on the loss function.
In order to determine when we should stop the feature selection procedure and how many features to discard at each step, we need to estimate false discovery rate (FDR) after each training step. Assume that in the original data there are p features among which there are \(p_0\) irrelevant (null) ones. We introduce q known null features to the original data by random sampling from the original data matrix without replacement. Therefore, scFSNN starts with \(p+q\) features, at each step, it deletes a number of features with the smallest important scores, which may be original features or surrogate features. Suppose, after several training steps, there are r features retained in the neural network, among which there are \(r_0\) surrogate features. Thus, the proportion of surrogate features that have not been deleted is \(r_0/q\). If we assume the distributions of importance scores for null features from original data and the surrogate features are similar, then the number of null features from original data that still retain in the network is \(\frac{r_0}{q}\times p_0\). The estimate of FDR of \(rr_0\) original features is given by
In practice, \(p_0\) is usually unknown, and in order to estimate FDR, we need to first estimate \(p_0\).
In scFSNN, we initially train the neural network with all features for 30 epochs, and \(p_0\) is estimated as
where \(S_m\) is the median importance score of surrogate features. If we assume the distributions of importance scores for null features from original data and the surrogate features are similar, the features from original data with importance scores less than \(S_m\) are most likely to be null ones and the number of null features from original data is twice of \(\#\{S_j<S_m\}\).
Finally, we can estimate the FDR as
In practice, it is also a common strategy to replace \(p_0\) by p [11, 22]. However, this strategy is too conservative if \(p_0\) is much less than p, which may be a common situation for scRNAseq data. Our estimate of \(p_0\) can make the estimate of FDR more accurate.
In order to improve the efficiency of the procedure, we delete \(\left\lceil \varepsilon \times \left(1\frac{\eta ^{*}}{\hat{\eta }} \right) \times r_0 \right\rceil\) features each time as [11], where \(\varepsilon\) is a constant between 0 and 1, \(\eta ^{*}\) is a userdefined threshold. In all experiments in this paper, we set \(q=\left\lfloor \frac{p}{2}\right\rfloor\), \(\eta ^{*}=0.1\) and \(\varepsilon =0.1\). In numerical experiments, we randomly divided the cells in each dataset without replacement into three sets. The first set, containing \(64\%\) of the cells, was used for training the deep learning model. The second set, comprising \(16\%\) of the cells, served as the validation set for calculating the importance scores and subsequently estimating the FDR. The remaining \(20\%\) of cells formed the test set, untouched until the feature selection procedure and parameter estimation were completed.
Though the sample size of scRNAseq data is often high, certain situations present limitations in obtaining sufficient samples due to factors like limited bioresources, prohibitive costs, or ethical considerations [23]. To further improve predictive performance in small datasets, we augment data based on convex pseudodata (CPD) [24, 25]. Typically, a prediction algorithm performs better if given a large enough sample from the underlying distribution. Data augmentation, which artificially generates additional data from the existing data is a commonly used technique in DNN, especially in computer vision. CPD is a relatively simple and nonparametric data augmentation method and depends only on a single parameter, \(d, 0<d<1\). The additional sample is generated in steps as follows.

1.
Randomly select two samples \((\varvec{x}_{i.}, y_i)\) and \((\varvec{x}_{j.}, y_j)\) from the original data.

2.
Select a random number \(\alpha\) from a uniform distribution on the interval (0,Â d).

3.
The new generated sample is \((x^{*}, y^{*})\), where \(x^{*}=(1\alpha )\varvec{x}_{i.}+\alpha \varvec{x}_{j.}\) and \(y^{*}=y_i\).
In the preprocessing stage, we use the CPD procedure to randomly generate new data \(\varvec{X}^{*}\) and use samples from both \(\varvec{X}\) and \(\varvec{X}^{*}\) to train the model. In all experiments, we set \(d=0.2\).
Results
Simulation evaluation of scFSNN
To evaluate the feature selection performance of scFSNN in classification analysis of scRNAseq, we designed the following simulations under extensive settings approximating different biological scenarios. Specifically, we applied the R package Splatter [26] to simulate scRNAseq read count data. We simulated datasets with two classes, each dataset contains 10000 genes. Here, we consider two studies. In Study 1, we fix the proportion of DE genes as 0.05, and vary the number of cells from 1000 to 5000. In Study 2, we fix the number of cells as 2000, and vary the proportion of DE genes from 0.02 to 0.3. We compared scFSNN with five other classifiers, including SurvNet and four variants of penalized methods. Four variants of penalized methods penalize first hidden layersâ€™ parameters of neural networks by \(\textrm{L}_1\), \(\textrm{L}_2\), \(\textrm{GL}\) (group Lasso) and \(\textrm{SGL}\) (sparse group Lasso) [18]. We ran the penalized methods by setting \(\lambda\) in the exponential range \(10^{j}\), with j going from 1 to 5 on eight real datasets (Supplementary Figs. S1, S2). We can see that from \(10^{3}\) onwards, their accuracies are basically indistinguishable as shown in [18]. Hence, in all numerical experiments, we report the results for penalized methods with fixed tuning parameter \(10^{3.5}\) to reduce the computational complexity.
Since the predictive accuracy of all methods is close to 1 in these relatively simple binary classification settings, here we mainly use FDR to evaluate the feature selection ability of scFSNN. We repeat the simulation 20 times for each setting. Study 1 examines the effect of sample sizes on the classification. It is shown that the FDRs of scFSNN and SurvNet are less than the prespecified threshold in all settings with different sample sizes, and the FDRs of \(\textrm{L}_1\) and SGL decrease with an increasing number of sample sizes (Table 1). This indicates that scFSNN and SurvNet perform significantly better than penalized methods, even when the sample size is small. Study 2 explores the effect of the number of differentially expressed genes on the binary classification. It is shown that the FDR of all methods decreases with the increasing number of differentially expressed genes (Table 2). scFSNN also demonstrates its superiority over the other methods in Study 2.
Application to real data
We apply scFSNN and several other classifiers to eight scRNAseq datasets generated by different experimental protocols (Dropseq, SmartSeq2, CELSeq, inDrop and 10xgenomics). An overview of these datasets is given in Table 3. We filter out genes that have zero counts in more than \(80\%\) of cells. The numbers of remaining genes are shown in Table 3. Here, we use the last name of the publicationâ€™s first author to denote each dataset. Adam [27] applied the cold protease scRNAseq procedure to the newborn postnatal day 1 (P1) mouse kidney and clustered the isolated cells into nine classes(Cap Mesenchyme, Distal Tubule, Endothelial, Loop of Henle, Nephron Progenitor, Podocytes, Proximal Tubule, Stromal and Ureteric Bud). We use all nine cell types with a sample size of 4853 in the dataset. Dong [28] conducted scRNAseq analysis of 1916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos. Here, we select 332 liver cells with three classes(E9.5, E10.5, E11.5) in our dataset. Bacher [29] investigated the lowavidity CD4+ T cell responses to SARSCoV2 in both unexposed individuals and patients with COVID19. The cells, derived from 6 unexposed individuals and 14 COVID19 patients, were classified as healthy, nonhospitalized, mildmoderate, or severe based on the donorâ€™s health status and disease severity. We randomly selected 15,957 cells from these four categories for our classification task. Enge [30] contains 2282 pancreas cells from eight donors spanning six decades of life and comprising six categories: A cells, acinar cells, D cells, B cells, duct cells, and stellate cells. To identify rare cell types, Grun [31] sequenced the transcriptome of hundreds of randomly selected cells from mouse intestinal organoids. We use the count data from 1547 cells across 3 classes, including Reg4positive cells, YFPpositive cells and Lgr5positive cell, for classification analysis. Baron [32] unveiled the pancreas population structure with the transcriptomes of over 12000 pancreatic cells from four human donors and two mice. The dataset Baron includes all major cell groups from the human donors, excluding those with less than 200 cells. The cell types in Baron are acinar, activated stellate, alpha, beta, delta, ductal, endothelial and gamma. Chen [33] profiled transcriptomes of more than 14000 single cells and identified 45 transcriptionally distinct cell subtypes in the adult mouse hypothalamus. Based on the expression of the pan neuronal makers Snap25 and Syt1, the 45 cell clusters were divided into 34 neuronal(Snap25/Syt1high) and 11 nonneuronal clusters(Snap25/Syt1negative or low). We selected 7930 cells with 6 clusters (Astro, Tany, MO, OPC, Micro and Macro) out of the 11 nonneuronal clusters for the classification task. Alzheimerâ€™s disease (AD) is the most common form of dementia but has no effective treatment. Lau [34] performed singlenucleus transcriptome analysis on 179392 nuclei from prefrontal cortical samples of twelve Alzheimerâ€™s disease (AD) patients and nine normal control (NC) subjects. The data are categorized into AD group and NC groups based on disease status. For this dataset, we filtered out genes with zero counts in over \(90\%\) of cells, resulting in 6569 genes for analysis. Due to the large dataset size, data augmentation was not utilized.
To assess the predictive performance of scFSNN and other classifiers, we employ a twostep procedure for splitting the dataset into training, validation, and test subsets. We first split the dataset into two nonoverlapping portions: a training set for model training (\(80\%\)) and a test set (\(20\%\)) for performance evaluation. For methods that donâ€™t require a validation set, we directly train the model on the training set and assess its accuracy on the test set. For methods like ours that require a validation set, we further split the training set into separate training and validation sets using an 8:2 ratio. The training set, containing \(64\%\) of the cells, is used to update the deep learning modelâ€™s parameters, while the validation set,containing \(16\%\) of the cells, help calculate feature importance scores and estimate the false discovery rate (FDR). The random split is repeated 20 times for each dataset, and average test accuracies are reported.
We compared scFSNN with nine other classifiers, including SurvNet, four variants of penalized methods, two generic classifiers and two classifiers specifically designed for RNAseq dataset. The two generic classifiers are RF (Random Forest) and AllFeature (deep learning algorithm using all features in the datasets as input). In AllFeature network, the number of nodes in input layer is the number of genes and there are 256 and 128 nodes in two hidden layers, respectively. Batch normalization [20] and dropout [21] with a rate of 0.5 are used to accelerate deep network training and control overfitting. The loss function is cross entropy and Adam optimizer [35] with learning rate 0.001 is used to train the model.
The two classifiers designed for RNAseq data are ZIPLDA [10] and SINC [7]. ZIPLDA is based on zeroinflated Poisson distribution and designed for bulk RNAseq datasets. ZIPLDA ranks genes by the ratio of sum of squares between groups to within groups for each gene and selects first K genes. Here, we set \(K=1000\) as recommended [10]. SINC is also a deep learning based algorithm. In datapreprocessing, SINC conducts an Ftest on each gene to test whether different classes have significantly different mean expression levels and selects the top 1500 genes with smallest \(P\)values as the input for deep learning neural network.
The results are summarized in Fig. 2 and Supplementary Tables S3 and S4. Overall, we find that scFSNN gives the highest predictive accuracies on seven out of the eight datasets, and its predictive accuracies are very close to the best on the other dataset (0.9897 versus 0.9907 for SINC on Chen). We also note that both SINC and AllFeature perform quite well in terms of predictive accuracy, and these two methods consistently outperform nondeep learning based methods RF and ZIPLDA. This indicates that deep learning can capture more complicated relationship between input and target than other generic and modelbased classifiers.
To evaluate the sparsity of the model input, we also consider the number of selected features for scFSNN and five other classifiers which include feature selection in the procedures. In real datasets, we can not assess how many selected features are truly relevant to the target. In classification, our primary goals are twofold: first, to build a highly accurate model for predicting future observations, and second, to unveil the underlying relationships between features and the response variable, enriching our scientific understanding. In deep learning based methods, we do not expect to gain a concise relationship between each feature and the target. However, it is important to know which features are truly used in the model to make predictions. Therefore, we expect the final model to achieve high predictive accuracy with a small input size.
Figure 3, Supplementary Tables S3 and S5 show the number of selected features and predictive accuracy for six methods on the eight datasets. Note that we can not adaptively determine the number of features for SINC and ZIPLDA and fix them as 1500 and 1000, respectively. We can see that SINC achieves comparable predictive accuracy as scFSNN in many datasets, and it commonly uses many more features, except for Lau. SINCâ€™s predictive accuracy is \(82.3\%\) for the Lau dataset, indicating that it uses too few genes in the model. Notably, SurvNet selects smallest number of features in all datasets, but its predictive accuracy is also much smaller compared to scFSNN. This indicates that SurvNet may be too conservative and miss some important features. For the penalized methods, GL and SGL, they select a larger number of features than scFSNN, but the predictive accuracies are significantly smaller in all datasets.
To evaluate performance of scFSNN in terms of marker gene selection in a real dataset, we use the subdata of Baron dataset including cells from three healthy human donors with six types of cells (alpha, beta, gamma, delta, acinar and ductal). Baron dataset provides a list of 62 known marker genes for related cell types in pancreatic islets [32]. After filtering out genes with zero counts in more than \(80\%\) cells, there are 50 marker genes remain. Both scFSNN and SINC achieve the highest predictive accuracy (98.86%), but scFSNN selects more marker genes (42 vs 25) while retaining fewer features (624 vs 1500) than SINC (Table 4). SurvNet has a slightly smaller predictive accuracy with 26 selected marker genes out of 134 genes in the model.
Effects of \(p_0\) and data augmentation
When estimating FDR, it is a common strategy to set \(p_0\) as p for simplicity [11]. When the number of truly relevant features is small, which means \(p_0\) is close to p, this strategy is reasonable. However, the number of truly relevant features may be nonnegligible in scRNAseq datasets. When this happens, \(\hat{\eta }\) is overestimated and the procedure is too conservative. To assess the impact of estimates of \(p_0\), we compare the proposed scFSNN with one that sets \(p_0\) as p. We perform the feature selection procedures 50 times for each case and report the predictive accuracies.
Data augmentation is a technique that artificially creates new training data from existing training data and is commonly used by DNN in computer vision. To assess its impact on scFSNNâ€™s performance, we compared the proposed scFSNN with a version without data augmentation. This experiment was repeated 50 times.
Figure 4 and Supplementary Table S6 show that setting the hyperparameter \(p_0\) to \(\textrm{min}(\#\{S_j<S_m\}\times 2, p)\) leads to statistically significant improvements in accuracy for three datasets and comparable accuracy in others for scFSNN. Furthermore, Fig. 5 and Supplementary Table S7 reveal that data augmentation significantly enhances performance on the two smallscale datasets, Dong and Grun. For the remaining dataset, scFSNN again exhibits comparable predictive accuracy.
For realworld applications of scFSNN, we recommend considering both \(p_0\) estimation and data augmentation as they have the potential to improve model performance.
Influence of the normalization method
We utilized the total counts normalization method (TCN), wherein each cellâ€™s counts are divided by its total counts and then multiplied by a scale factor (we set the scale factor as the median total counts across all cells). The resulting values are then naturallog transformed using log1p. This approach bears resemblance to Seuratâ€™s log normalization method [36] and is a widely adopted, straightforward option for normalizing scRNAseq data. To stabilize the training process, we further standardized the normalized data, making its mean and standard deviation become 0 and 1, respectively.
To illustrate the influence of the normalization method throughout the procedure, we assessed the performance of feature selection methods across three datasets, employing three different normalization methods: TCN, TMM [37], and SCTransform [38]. As shown in the Table 5, all three normalization methods perform similarly on all datasets.
Conclusions
Fast and accurate feature selection is critical for largescale classification analysis in scRNAseq datasets. Finding informative gene sets from numerous candidates can greatly enhance explanatory ability, improve predictive accuracy, and reduce the labor and cost of applying scRNAseq to clinical tests, therapeutic discovery and genetic screens. In this paper, we have proposed an embedded algorithm for the classification of samples based on the DNN framework, scFSNN, that incorporate a fast and simple backward feature selection procedure. scFSNN can adaptively choose the number of genes to be deleted at each step, thus accelerating the feature selection procedure. scFSNN controls the FDR by generating a set of null genes to estimate the null distribution, avoiding the use of methods that have highly computational burden, such as crossvalidation. Furthermore, by using data augmentation, scFSNN can achieve high generalization predictive abilities. Our experimental results demonstrate that our scFSNN algorithm achieve higher predictive accuracy with substantially informative genes than other algorithms for scRNAseq datasets. Based on these results, we believe that scFSNN can be fruitfully applied to many scRNAseq datasets.
Availability of data and materials
The code developed for the study of scFSNN is publicly available at the Github repository https://github.com/linbingqing/scFSNN. All scRNAseq data used in this paper are available publicly in Gene Expression Omnibus under accession number GSE94333 (Adam [27]), GSE87038 (Dong [28]), GSE62270 (Grun [31]), GSE81547 (Enge [30]), GSE84133 (Baron [32]) and GSE87544 (Chen [33]), GSE157827 (Lau [34]).
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Bingqing Linâ€™s research was supported by the National Natural Science Foundation of China (NSFC) (Grant No. 11701386). Yan Zhouâ€™s research was supported by the National Natural Science Foundation of China (Grant No. 12071305, 12371295) and the Natural Science Foundation of Guangdong Province of China (2023A1515011399).
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BQL (SZU) conceived the idea. MJP, BQL, BQL (SZU) condtributed to the design of the study. MJP, BQL (SZU), JZ and YZ processed the data and conducted simulation and real dataset experiments. MJP and BQL (SZU) wrote the manuscript. All authors read and approved the final manuscript.
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Peng, M., Lin, B., Zhang, J. et al. scFSNN: a feature selection method based on neural network for singlecell RNAseq data. BMC Genomics 25, 264 (2024). https://doi.org/10.1186/s12864024101601
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DOI: https://doi.org/10.1186/s12864024101601