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PLOS One logoLink to PLOS One
. 2021 Jul 23;16(7):e0254179. doi: 10.1371/journal.pone.0254179

Pollution index of waterfowl farm assessment and prediction based on temporal convoluted network

Jiande Huang 1,2,3,4,5,6, Shuangyin Liu 1,2,3,4,5,6,*,#, Shahbaz Gul Hassan 1,2,3,4,5,6,*,#, Longqin Xu 1,2,3,4,5,6
Editor: Chi-Hua Chen7
PMCID: PMC8301615  PMID: 34297737

Abstract

Environmental quality is a major factor that directly impacts waterfowl productivity. Accurate prediction of pollution index (PI) is the key to improving environmental management and pollution control. This study applied a new neural network model called temporal convolutional network and a denoising algorithm called wavelet transform (WT) for predicting future 12-, 24-, and 48-hour PI values at a waterfowl farm in Shanwei, China. The temporal convoluted network (TCN) model performance was compared with that of recurrent architectures with the same capacity, long-short time memory neural network (LSTM), and gated recurrent unit (GRU). Denoised environmental data, including ammonia, temperature, relative humidity, carbon dioxide (CO2), and total suspended particles (TSP), were used to construct the forecasting model. The simulation results showed that the TCN model in general produced a more precise PI prediction and provided the highest prediction accuracy for all phases (MAE = 0.0842, 0.0859, and 0.1115; RMSE = 0.0154, 0.0167, and 0.0273; R2 = 0.9789, 0.9791, and 0.9635). The PI assessment prediction model based on TCN exhibited the best prediction accuracy and general performance compared with other parallel forecasting models and is a suitable and useful tool for predicting PI in waterfowl farms.

Introduction

In response to the growing global demand for food, the Chinese waterfowl industry has grown to be a leader in both goose meat and goose egg production [1]. To meet this demand,

one mechanism to increase production is to increase housing and manage more geese. However, as the scale of intensive culture increases, there is a growing concern in China that waterfowl should be raised under conditions that promote animal welfare since productivity is related to environmental conditions in which the waterfowl are raised [1]. For example, the organic matter present in excreta and/or litter resulting in pollutant production, such as CO2, ammonia, and TSP, will not only impair geese and staff health but also have important consequences for society once the pollutants are out in the atmosphere [24]. According to this, to maintain and control optimal conditions for survival and good goose growth, establishing a habitat that is closer to a standard ecosystem is justified [4].

Labor shortages and increasing biosecurity practices will make it more difficult for producers to monitor and manage the production, health, and welfare status of all of their birds. Employing modern poultry management technology is necessary to increase production [5]. An example of how modern management technology can be used to monitor and control the poultry house environment is exemplified by humidity regulation via ventilation rate changes mediated by relative humidity sensors, as relative humidity is one of the more important environmental aspects of a poultry house [5]. In addition, more advanced systems are being researched. Bustamante et al. used a multisensor system to effectively assess barn ventilation system function by tracking temperature, air velocity and differential pressure in broiler houses [6]. Hanif et al. proposed an internet of things technology-based protection and monitoring of the environment of a poultry house to monitor the environment-related parameters such as air temperature, air humidity, CO2 level of concentration and ammonia concentration, which has been implemented successfully, leading to a safe environment and profit for the poultry industry [7]. The techniques mentioned above are both solutions for real-time environmental monitoring and control; however, relying on hardware monitoring in real time cannot capture the trend of environmental changes [8], and it is easy to miss the best time for adjustment, which leads to waterfowl health damage and property loss.

Cultivation environment forecasting has been studied for many years and has made some achievements in aquaculture and livestock breeding [910]. The technique estimates or predicts the future changes in target variables that cannot be obtained directly. For example, Jackman et al. generated a prediction model by using sensor inputs of relative humidity, CO2, temperature, and ammonia for environmental parameter and crop yield prediction [11]. In waterfowl production, a system such as this would allow for actions to be taken sooner by farmers if the environment is projected to be bad. However, few studies have applied prediction in waterfowl breeding. Therefore, it is necessary to apply environmental prediction technology to waterfowl production to fill this gap.

The PI is a simple and easy assessment method for assessing environmental quality, and precise environmental quality assessment and prediction allow better environmental management practices and contribute to a more sustainable environmental management approach [1217]. In recent years, many studies on pollution models have been carried out to evaluate the quality of the environment based on the PI method, such as river quality status assessment and prediction [12, 1416], air quality status assessment and prediction [1719], and soil pollution assessment and prediction [20, 21]. Forecasting the concentration of water, air, and soil pollutants is an effective method for protecting public health, productivity, and travel by providing early warnings of harmful pollutants. Likewise, it is also important to assess and predict PI in advance for waterfowl farms so that, if necessary, the producer can intervene more quickly by using management practices to ensure a healthy context.

In general, PI formulations include lengthy computations and thus require considerable time and effort. Additionally, waterfowl environment pollutant data are dynamic, complex, and have high temporal and spatial variability [22, 23], and traditional forecasting methods such as multiple linear regression and autoregressive integrated moving average models have poor performance. Hence, a method to calculate PI in an efficient and precise way is required. Such approaches may benefit farmers when assessing and managing environmental quality.

Over the past few decades, artificial intelligence has been increasingly applied to solve various environmental engineering problems, including water quality modeling [24, 25] and air quality modeling [26]. Among them, STM is a class of neural networks that can only use the current input information and historical information. Compared with other AI-based models, LSTM is powerful for modeling sequence data such as time series or natural language [2729]. However, recursive neural networks such as LSTM and GRU process input sequences in parallel, so the cost of model training will increase with increasing length of input sequences. Moreover, distant historical memory will be forgotten, and they have a weak ability for temporal and spatial feature extraction [30]. Therefore, convolutional neural networks have attracted increasing attention in temporal and spatial sequence modeling. TCN [31], a model with a simple convolutional network architecture, is proposed to be applied to language modeling and music modeling and has demonstrated better performance than recurrent neural networks, especially in a long sequence. TCN has been proven to perform well in long sequence time series modeling. However, TCNs have not yet been applied in PI prediction. Therefore, a better TCN prediction architecture is explored to promote the predicted precision of PI in this study.

Waterfowl house environment data usually contain many sources of noise. To eliminate noise interference, extract essential feature information, and obtain high-quality data sets, experts have proposed many methods, such as WT, independent component analysis, and empirical mode decomposition [3234]. WT can decompose time series with different resolutions and distinguish between noise and useful signals. It has been successfully applied to pattern recognition and noise elimination. Liu et al. proposed a hybrid wavelet analysis and least squares support vector regression with a Cauchy partial swarm optimization algorithm model for dissolved oxygen prediction [9]. Kumar et al. obtained better-quality denoised electrocardiogram signals by a denoising technique using a stationary WT compared with empirical mode decomposition, the Fourier decomposition method, and discrete WTs [35]. To effectively improve the GPR image resolution, Zhang et al. combined WT and F-K filtering [36]. Samuel et al. conducted a comparative analysis of a set of machine learning models, and the results showed that the best combination for predicting the streamflow into the Sobradinho Reservoir was the bootstrap, WT and neural network [37].

Based on the above studies, this paper proposes a new waterfowl house environmental quality assessment and prediction model combining WT and a temporal convolutional network. The WT can reduce the noise of original environmental data and obtain high-quality data, and the temporal convolutional network can extract the temporal and spatial features of processed data, output precise environmental quality assessment, and predict results.

Materials and methods

Study area and data source

The waterfowl culture farm in Haifeng County (23°05’N, 115°19’E) in Shanwei City, China was investigated in the present study. With an area of approximately 53.3 hm2, the farm is a multifunctional integrated aquacultural base integrating waterfowl breeding, seeding breeding and intensive aquaculture.

The environmental data were collected by the waterfowl culture internet of thing (IoT) online monitoring terminal system, and its architecture is shown in Fig 1. The system is equipped with a temperature sensor, ammonia concentration sensor, humidity sensor, etc. The environmental information is uploaded to the cloud, and users can obtain on-site information by accessing the web server through mobile phones or personal computers.

Fig 1. Schematic diagram of the waterfowl farm monitoring system based on the internet of things.

Fig 1

According to the importance of the environment and expert research, we selected 5 environmental factors, as shown in Table 1. Among them, ammonia is a toxic gas and the greatest concern of environmental pollution in waterfowl production, adversely affecting the ecosystem, environment, and health of birds and people. Less than 10 ppm is the ideal limit [38]. Relative humidity can impact bird health, and high relative humidity may worsen broiler geese performance; the ideal value is 70% [39]. Heat stress is a major concern in waterfowl production; high and low temperatures will reduce the growth performance and survivability of waterfowl, and temperatures less than 27°C and more than 10°C are ideal [40]. TSP is from the birds themselves as well as from the feed, litter, and building materials and may serve as a pathogen disseminator and bring about lung damage; less than 10 mg/m3 is the ideal limit [38]. Additionally, the levels of relative humidity, ammonia, CO2, temperature and TSP are known to be correlated with each other [5]. These factors are important for waterfowl production and can be monitored and optimized.

Table 1. The selected environmental parameters for PI prediction.

Environmental factor Unit Limit Influences
Ammonia ppm 10 Ammonia is a toxic gas impairing animal performance and bird and staff health [4142].
Relative humidity % 70 High relative humidity may worsen broiler geese performance [39].
Temperature °C 10~27 Influences poultry welfare and food intake, as well as increases susceptibility to disease and flock mortality rate [40].
CO2 ppm 1500 A decrease in production and bird health can occur [41].
TSP mg/m3 8 A higher incidence of lung damage [38].

Data sets

In this report, environmental data, including ammonia, relative humidity, temperature, CO2 and TSP, were collected from July 1st to September 28th, 2019, at intervals of 20 minutes. There were 72 sets of data collected per day with a total yield of 6480 observed samples. For model generation, the first 4536 sets of data were used for model training, and the remaining 1944 sets were used as the testing data to estimate the prediction performance of the constructed model.

Pollution index

The PI in this study was formulated within the criteria for evaluating the environmental quality of livestock and waterfowl farms by the Quality and Technology Supervision Bureau of China. The single PI can be calculated as:

I=CiCsi (1)

where Ci is the measured concentration of environmental pollutants and Csi is the standard concentration limit of pollutants. The composite PI of waterfowl house environment quality can be described as follows:

Pi={Imax1/nIi}12 (2)

where Imax is the maximum single PI among all pollutants, n is the number of pollutants, and Ii is the single PI of pollutant i.

Wavelet transform

Continuous WTs for a given waterfowl environment signal s(k) can be described as follows:

WTs(a,b)=1as(k)(ψ(tba))¯dx (3)

where ()¯ denotes the complex conjugate, ψ(x) is the wavelet function, a is the time scale dilation and b is the time translation. By controlling the values of parameters a and b, signal time-frequency positioning can be achieved. The WT can decompose signals into multiple resolutions. However, the symbols in realization communication are discrete data, so the continuous WT needs to be discretized. Suppose a=a0j,b=kb0a0j,j,kZ, when a0 = 2,b0 = 1:

ψj,k(n)=2j2ψ(2jnk) (4)

The discrete waterfowl environment signal s(n) can be transformed as:

D(j,k)=ks(n)ψj,k¯(n) (5)

The Mallat algorithm can quickly calculate the orthogonal WT coefficients and realize signal decomposition and reconstruction [43]. The approximation coefficients sj+1(n) and detail coefficients dj+1(n) can be recurrently related by the Mallat algorithm as follows:

sj+1(k)=nh0(n2k)sj(n) (6)
dj+1(k)=nh1(n2k)sj(n) (7)

where h0 and h1 are the high-pass filter and low-pass filter, respectively. The reconstruction is the inverse process of decomposition:

sj(k)=nsj+1(n)h0(k2n)+ndj+1(n)h1(k2n) (8)

Different environmental factors may contain different kinds of noise. To achieve the best effect of the denoising process and obtain quality data, we adopt four wavelet functions, Db4, Haar, Coif, and Sym10, to process each environmental dataset. The signal-noise ratio (SNR) and normalized cross correlation (NCC) were used to evaluate the denoised effect, which can be described as:

SNR=I12(I2I1)2 (9)
NCC=(I1mean(I1))(I2mean(I2))(I1mean(I1))2×(I2mean(I2))2 (10)

where I1 is the denoised signal and I2 is the original signal; theoretically, the larger the SNR and NCC are, the better the noise reduction effect.

Support vector machine

SVM has good generalization ability in solving nonlinear, small sample, and high-dimensional pattern recognition, and the optimal solution obtained is global, which solves the local optimal problem that cannot be avoided in other algorithms. The prediction process of the SVM includes support vector determination, kernel function selection, kernel parameter determination, and solution.

Random forest

RF is a nonlinear ensemble model that establishes and averages a large number of random distribution decision trees for regression or classification tasks [44]. A decision tree or classification and regression tree that constructs the RF is a nonparametric model. According to the complexity of the input data, the tree grows in the process of learning. Decision nodes and leaf nodes are the main components of the decision tree. Each input sample is estimated by a test function of decision nodes and passed to different branches according to the features of the sample. After all trees are trained, each tree can predict the test sample set according to the node threshold, and the results of each tree are combined to vote to determine the final result of the entire random forest.

Long short-term memory neural network

The LSTM neural network is a special kind of recurrent neural network. It was first proposed by Ho-chreiter and Schmidhuber [45]. Its appearance effectively solved the gradient explosion problem of traditional recurrent neural networks. At the same time, the LSTM neural network has long-term memory to handle long-term sequence data.

Gated recurrent unit

A GRU is a type of recurrent neural network (RNN). Similar to a long short-term memory neural network (LSTM), it is also proposed to solve long-term and gradient backpropagation problems. LSTM and GRU have similar performances, but compared with LSTM, GRU is computationally cheaper.

Temporal convoluted network

TCN, like LSTM, is a novel neural network architecture that can be used for time series prediction. The outstanding advantage of TCNs is that they not only have much longer memory but also have higher computational efficiency than LSTM and other recurrent neural networks [46].

In general, a nature sequence modeling task is any function f:XT+1YT+1 that produces the mapping:

y0,y1,...,yT=f(x0,x1,...,xt) (11)

The goal of the sequence model is to fit this function f to minimize the expected loss. It satisfies the causal constraint that yt depends only on x0,x1,…,xt and not on future inputs xt+1 and that the output has the same length as the input.

As shown in Fig 2, to satisfy the causal constraint, TCN uses a 1D fully convolutional network architecture [47], which is different from the traditional convoluted neural network in that the value at time t only depends on the value at time t and before in the previous layer. In addition, zero padding of length (kernel size—1) is added to keep subsequent layers the same length as previous layers.

Fig 2. Causal convolution construction.

Fig 2

One of the goals of TCNs is a long effective history size, which means an extremely deep network or very large filters. However, more convolution layers or larger filters bring about the problems of disappearing gradients, complex training, and poor fitting effects. To solve the problems above, dilated convolutions [31] were employed in the TCN. Specifically, given a sequence input Xn+1 = {x0,x1,…,xn} and convolution function f:{0,1,,k1}, the dilated convolution operation was defined as follows:

F(s)=i=0k1f(i)xsid (12)

where k is the kernel size, d is the dilated factor, and sid accounts for the direction of the past. When d = 1, a dilated convolution is equal to a regular convolution. As shown in Fig 3, as the number of layers increases, the dilated factor d grows, and the top layer can represent a wider range of inputs. On the other hand, choosing a larger kernel size k of the filter can also effectively expand the receptive field of a ConvNet.

Fig 3. Dilated convolution construction.

Fig 3

Residual connections proved to be an effective method for deep network training to converge quickly and reduce the risk of overfitting [48]. As shown in Fig 4, the residual block used in the TCN has two branches from input to output. The first branch contains a series convolution layer, parameter regularization, rectified linear unit, and dropout layer in order. This was a flexible architecture that allows the layer to modify parameters such as the activation function and dropout rate. The second branch ensures that the output sequence length is equal to the length of the input: if the lengths of the input sequence and output sequence are equal, the output layer is connected to the input layer through identity mapping; otherwise, the output layer is connected to the input layer through a 1×1 convolution.

Fig 4. An example of residual connection in a TCN.

Fig 4

Performance criteria

In this paper, the mean absolute error (MAE), root mean square error (RMSE) and coefficient of determination (R2) were selected to measure the prediction accuracy and operation efficiency, and MAE, RMSE and R2 are defined as follows:

MAE=1Ni=1N|yiyi| (13)
RMSE=1Ni=1N(yiyi)2 (14)
R2=(i=1N(yiy¯)(yiy¯))2i=1N(yiy¯)2i=1N(yiy¯)2 (15)

where N is the total number of actual points in the data, yi is the observed value of period i, yi is the prediction value of period i, y is the average of observed values, and yt is the average of prediction values.

The waterfowl house environment quality assessment and prediction model

The algorithms used in this paper were implemented in Python 3.7 programming language. The equipment used in this work has an Intel Core i5-5200u processor, CPU @2.20 GHz and 8.0 GB of random access memory installed.

Both WT and TCN have the unique advantage of being able to capture data characteristics in time series. Thus, this paper uses WT-TCN to construct a model to assess and forecast the PI of waterfowl houses. The implementation process for our model is shown in Fig 5. In this study, we first reduce or eliminate the noise of environmental data by WT. Then, the denoised data and PI data were used as the input to train the TCN, and finally, the waterfowl house environment quality assessment and prediction model was obtained.

Fig 5. Construction process of the PI prediction model.

Fig 5

Results and discussion

Simulation results and discussion

As shown in Table 2, wavelet function Db4 was suitable for ammonia data (SNR = 9.4318, NCC = 0.9485), Sym10 was suitable for temperature data (SNR = 7.4635, NCC = 0.9221), relative humidity data (SNR = 4.0809, NCC = 0.8630), and CO2 data (SNR = 1.7785, NCC = 0.7793), and Coif was suitable for TSP data (SNR = 13.1443, NCC = 0.9771). The best denoised results of each environmental dataset are shown in Fig 6.

Table 2. Denoised performance of five parameters.

Target Performance criteria Wavelet function
Db4 Haar Coif Sym10
Ammonia SNR/(dB) 9.4318 8.8287 9.3769 9.3602
NCC 0.9485 0.9432 0.9484 0.9474
Temperature SNR/(dB) 7.2491 6.5372 7.0205 7.4635
NCC 0.9192 0.9061 0.9149 0.9221
Relative humidity SNR/(dB) 3.9422 3.6395 3.8920 4.0809
NCC 0.8600 0.8559 0.8596 0.8630
CO2 SNR/(dB) 1.7064 1.3855 1.4991 1.7785
NCC 0.7764 0.7642 0.7689 0.7793
TSP SNR/(dB) 12.8848 12.6578 13.1443 13.1142
NCC 0.9756 0.9745 0.9771 0.9769

Fig 6. Results of noise reduction of five parameters by WT.

Fig 6

(a) Ammonia sequence. (b) Temperature sequence. (c) Relative humidity sequence. (d) CO2 sequence. (e) TSP sequence.

In this study, we tested the TCN’s memory and feature extraction capability for environment data sequences of different lengths. Fig 7 shows that TCN consistently converges to approximately 0.01 MSE for all sequence lengths, whereas GRU and LSTM degenerate quickly as the sequence lengths grow. These results suggest that TCN is better at long sequence memory and feature extraction than its recurrent counterparts.

Fig 7. Performance of three models in sequences of different lengths.

Fig 7

Then, TCNs were used to predict PI at different time intervals, including 12 hours, 24 hours, and 48 hours (predicting 12 hours, 24 hours and 48 hours in the future every 20 minutes). Table 3 shows that TCN has the best performance in all simulation results compared with the other models. We noted that as the prediction time interval increased, the prediction effect decreased. This can be expected because a long prediction time interval needs a much longer effective history, which is a challenge for time series models. The performance of TCN fluctuates when the prediction time interval changes from 12 hours to 24 hours, but the wave motion ranges in MAE, RMSE and R2 of TCN and GRU are less than 10%. However, the wave motion range in MAE, RMSE and R2 of LSTM reached 25% when the prediction time interval changed from 12 hours to 24 hours and reached 112% when the prediction time interval changed from 24 hours to 48 hours. Moreover, the traditional SVM and RF models had poor performance in this study, which may be caused by the lack of long-time series memory ability compared with the recurrent neural network. In addition, scatter plots, Taylor plots and box plots were also used here to visualize the predictive performance of various models.

Table 3. Comparison of model performance.

MAE RMSE R2
Hours 12 24 48 12 24 48 12 48 48
TCN 0.0842 0.0859 0.1115 0.0154 0.0167 0.0273 0.9789 0.9791 0.9635
GRU 0.1728 0.1810 0.1922 0.0759 0.0789 0.0789 0.8937 0.8903 0.8898
LSTM 0.1892 0.2523 0.4434 0.0824 0.1388 0.2953 0.8896 0.8082 0.6078
SVM 0.5919 0.7245 0.8991 0.3292 0.3537 0.8181 0.8512 0.7748 0.6617
RF 0.2744 0.5794 0.9571 0.3407 0.3555 0.7513 0.8809 0.8050 0.6799

The scatter plot in Fig 8 visualized the agreement between the predicted and observed values of PI. In Fig 8, the baseline is drawn as a reference, and the perfect agreement between the observed and predicted data is described. SVM and RF models are far away from the best line. All three TCN models showed outstanding prediction performance (points close to the best line). Additionally, in the three phases, TCN is slightly far from the best line when PI reaches 3.5 or more, but GRU and LSTM perform worse. The reason for this phenomenon may be the input data of the environmental parameter CO2; all were in the normal range and no data exceeded the standard value or were distributed near the border value (Fig 5(D)), leading to the trained models having low sensitivity for a high PI and prediction difficulty.

Fig 8. Agreement between the observed and predicted PI values for the model considered in this study.

Fig 8

(a) Future 12-hour prediction. (b) Future 24-hour prediction. (c) Future 48-hour prediction.

Furthermore, the models were also evaluated using Taylor plots for the three phases in Fig 9. In a Taylor figure correlation coefficient, normalized standard deviation and RMSE were drawn, and the distance between the point corresponding to the model with the best prediction performance and the "observation" point was the least. Again, Taylor plots showed that the TCN model has the best prediction performance.

Fig 9. Normalized Taylor diagrams.

Fig 9

(a) Future 12-hour prediction. (b) Future 24-hour prediction. (c) Future 48-hour prediction.

Finally, Fig 10 compares the observed and predicted PI value dispersion and indicates the median (M) in a box plot. The performance of the three models was very similar in phase one, with the median values being very close (Mobserved = 1.612, MTCN = 1.602, MGRU = 1.648, MLSTM = 1.719,MSVM = 1.569, and MRF = 1.854), but the box shape of TCN is closer to the box shape of the observed data, which also means that all prediction results of TCN were better than the others. In both phase two and phase three, the performances of LSTM and GRU obviously worsen as the prediction interval grows, while the TCN performance does not change much. Overall, TCN substantially outperforms generic recurrent architectures such as LSTM and GRU.

Fig 10. Box plot of observed and predicted PI values.

Fig 10

(a) Future 12-hour prediction. (b) Future 24-hour prediction. (c) Future 48-hour prediction.

In summary, TCN combines best practices such as dilations and residual connections with the causal convolutions needed for autoregressive prediction. The experimental results indicate that for all prediction time interval phases, the TCN model provides high performance for PI forecasting, especially in the long prediction time interval problem. On the other hand, the LSTM model appears to be the ‘weakest’ model of all three models; furthermore, it also indicates that a simple convolutional architecture is more effective across time sequence modeling tasks than recurrent architectures such as LSTM. On the other hand, a new type of temporal convoluted neural network is more competitive in the PI time series prediction of waterfowl farms than the traditional machine learning model.

Conclusions and future research

To further promote waterfowl house environment monitoring and controlling technology, reduce labor and increase the production effect, this study analyses the shortcomings of existing methods and introduces a new way to guide waterfowl house environment management by learning from other fields.

The new method investigates the application of denoised WT and the performance of three neural network models and two mechanical learning models in predicting the PI of the waterfowl house environment using environmental quality parameters at different intervals. The results indicate that the TCN model has the best performance in predicting PI. The GRU model has similar performance but lower performance when the prediction time interval changed, and the LSTM model performed the worst among the three models, although it still provided fairly accurate PI predictions.

The models presented in this paper, in particular the TCN model, could provide accurate and long-interval PI predictions of waterfowl house environments and monitor them in real time. The simulation results show that this method can be applied in waterfowl house environment prediction. The future trend of the environment can be estimated and predicted compared with traditional real-time monitoring technology, which may allow better waterfowl house environment management practices, better culture plan design, and, in general, contribute to a more sustainable waterfowl house management approach.

The environmental parameters selected in the present study may also pose a limitation because of the lack of equipment. Future work may include the use of more environmental parameters to evaluate PI and apply the model in more waterfowl breeding sites to improve the production effect and further verify the model.

Supporting information

S1 Dataset

(XLSX)

Acknowledgments

The authors would like to thank native English experts Michele Genovese, Dr. Murtaza Hasan and AJE for revising the manuscript.

Data Availability

All relevant data are within the paper and its Supporting Information files.

Funding Statement

This work was supported in part by the National Natural Science Foundation of China under Grants 61871475, 61471133, and 61571444, awarded to Dr. Shuangyin Liu, in part by the special project of laboratory construction of Guangzhou Innovation Platform Construction Plan under Grant 201905010006 awarded to Dr. Shuangyin Liu, Guangzhou key research and development project under Grant 202103000033 awarded to Dr. Shuangyin Liu, Guangdong Science and Technology Plan of Project under Grant 2017B0101260016 awarded to Dr. Shuangyin Liu, National Key Technologies R & D Program of China under Grant 2016YFD0500510 awarded to Dr. Shuangyin Liu, Guangdong key research and development project under Grant 2020B0202080002 awarded to Dr. Shuangyin Liu, the foundation for High-level Talents in Higher Education of Guangdong Province under Grants 2017GCZX0014, 2016KZDXM0013, 2017KTSCX094, and 2018LM2168 awarded to Dr. Shuangyin Liu, and Beijing Natural Science Foundation under Grant 4182023 awarded to Dr. Shuangyin Liu. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Decision Letter 0

Chi-Hua Chen

23 Feb 2021

PONE-D-21-03161

Pollution index of poultry farm assessment and prediction based on temporal convoluted network

PLOS ONE

Dear Dr. Liu,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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We look forward to receiving your revised manuscript.

Kind regards,

Chi-Hua Chen, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Partly

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Reviewer #1: N/A

Reviewer #2: No

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Reviewer #1: No

Reviewer #2: No

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Reviewer #1: No

Reviewer #2: No

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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: This manuscript develops a method to apply AI to predict a pollution index for a poultry farm in China. While I think the methods have promise, the authors need to address the following major issues before it is suitable for publication.

Major:

> The English and grammar are fair to poor throughout. I have included in the minor comments below some instances in just the abstract and first couple of paragraphs but I do not have time to edit the entire manuscript. This needs to be addressed as it made it difficult to follow along.

> The motivation for the paper is lacking. Why do we need such a robust prediction method? Can the facilities actually use it to make changes? If so, does the interval required to make adjustments align with the model's ability to predict (Figure 8). For example L 58-59 is the only place you mention that it would benefit farmers, but would it? In what way? How could it be used?

> At its most basic premise, this paper is quite simple. Calculate a very simple pollution index from a few variables and see if you can predict with ML methods. It would benefit by comparing these computationally intensive methods to simpler prediction methods...does it even warrant the use of ML? What about other pollution indices? Or individual variables? Another example is you state that (L 56-58) traditional methods have bad performance. So why not show that with your data to really make the case for your work??

> L73-74: You state that TCN can better solve the modeling problem associated with PI, but you have yet to establish what those problems are. Is it just the noise which you discuss in the next paragraph? If so, why not compare the traditional methods with denoised data as well to see if the denoising was the most helpful thing or the ML approach?

> L92-95: no need to outline the paper. Delete these lines.

> Section 2.1 --you need a LOT more information on the study area. Include a map of where Shanwei is. L 99-101 describe the system but a schematic would be helpful including where the sampling is occurring. I'm also confused about what kind of animal is in the farm. A couple of times the paper mentions chicken but here it says waterfowl. So, what kind of animal is in the farm and how many are there typically? What kind of structure is the facility? Are their air ventilation systems, etc. that can help to control the parameters being measured? The data source section is missing a lot of information. I cannot tell what most of the things in Figure 1 are. It needs a narrative or more details. What kinds of sensors were there? What methods were they using to detect? What is the time frame of collection? What season did you collect data?

> Section 2.4 you need to include descriptions of all of the methods you used, not just TCN (eg LSTM, GRU)

> You have SO MANY methods in the results. All of sections 4.1, 4.2, 4.3, then lines 251-255 of section 4.4 are methods and need to be in the methods section.

> It's not clear from your methods how you split up to test the prediction of future time intervals. What time intervals were used for training? For example were your training sets 12 hour intervals trying to predict future 12, 24, and 48? It's unclear

> There is a severe lack of discussion here. What does it mean that you can predict reasonably well the future 12 hours? How does the fact that your data come from a very short time period in one year affect your results? Why do all of your predictions fail in the higher levels of pollution indices? It would be helpful to provide plots (even if in SI) of the individual data that went into the PI predictions. When the PI was high and difficult to predict, which variables were responsible, and how could this help improve future predictions? There is a lot of information hiding behind the PI calculation that would be useful to readers and for you to dive into.

> Your last line 329-330 leaves me wondering what international guidelines you are referring to and would your study have been better if you used them, so why didn't you use them and what are they?

Figures:

1 - very confusing and not enough detail. Again you need to describe the equipment used to obtain the data and the methods on board.

5 - I don't think this is quite right. Shouldn't environmental data that has been wavelet transformed have an arrow going into the pollution index, and not into the TCN? And didn't you calculate GRU and LTSM as well so where are they?

Figure 6 - units for data? what kind of range do these data have? What is the x-axis?

Minor (only for abstract and first paragraph):

> L 20-21: The first sentence is very strong, do you have anything to back up this claim? If not, reword.

> L21-22: Sounds like you invented TCN and WT, which I don't think is the case so reword. I think what you mean is your study uses/applied these methods.

> L23: the poultry to a poultry

> L23: Shanwei may not mean anything to people outside of China so suggest saying China or in Shanwei, China

> L24: is to was

> L26: Probably better to use "environmental" than "environment" when referring to the data you used throughout.

> L27: Co2 should be CO2 (with the 2 as a subscript)

> L27: I've never heard it called "total particulate suspended". Do you mean total suspended particles?

> L27: con-structing is just constructing

> L27: is to are

> L28: "the" in front of TCN

> L29: prediction

> L29: phases

> L32: generalization to general

> L32: per-formance is just performance

> In general, do not use acronyms in your abstract if you never use them later (eg. CO2, TPS, GRU, LTSM)

> L37-38: This first sentence is just odd. Suggest rewording to something like, "In response to growing global demand for food (or do you mean specifically poultry?), the Chinese poultry industry has grown to be a leader in meat and egg production".

> L38-39: The first clause adds nothing to the sentence and so your sentence doesn't make sense. Why is there such a concern that poultry need to be grown in a controlled environment? You have not made that clear.

> L39-41: "In this sense" should be "because of this desire/need/concern" if you correct the sentence before. Then you have a sort of run-on here. I think what you are trying to say is that poultry farms need to be controlled environments that can maintain a healthy ecosystem and farm productivity? or something like that.

> L41-44: reword to "Thus the main goal of controlled environments for poultry production are to maintain optimal conditions for survival and growth by establishing a habitat similar to their typical natural environment." And with this sentence as such you may not need the sentence before as it would be redundant.

Reviewer #2: I have provided below some suggestions. But, the poor quality of the language did not help me to make a comprehensive review. I highly encourage the authors to reach out to some colleagues for help and get some editing done before re-submission. The topic is interesting, but, the manuscript contains mainly some generic information about the WT which are well known. Also, there should be more emphasis on the need for this study on global scale. please make some review work on this topic for other countries of the world.

Line 201: It is not clear, what is the projection time for these analyses! Authors mentioned “forecast the pollution index of waterfowl house”. Pleas provide an appropriate time scale.

On page 14, authors mentioned “Perform wavelet transform on the original signal s(k) to obtain wavelet coefficients of various scales.” These are very basic or generic statement about the WT. Please provide most useful information only related to this study. Authors are also encouraged to see other applications of WT in different fields and cite.

It will be useful if the authors could bring up a flow chart to guide the readers about step-by-step processes of making forecasts or projection which is the aim of this study.

It will be good if the authors take some serious time for a careful proofreading. There are some errors which automated word processor grammar and corrections can detect.

Fig. 10 outcome needs to be discussed well, being the key conclusion.

Once the pollutants are out in the atmosphere, there is also important consequences for the society. There are plenty of literature on this topic as well. But, I referred to one of them below.

A novel approach for the characterisation of transport and optical properties of aerosol particles near sources–Part I and Part II

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Reviewer #2: No

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PLoS One. 2021 Jul 23;16(7):e0254179. doi: 10.1371/journal.pone.0254179.r002

Author response to Decision Letter 0


31 Mar 2021

Response to Journal:

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Answer:Following your suggesstions we have updated ORCID.

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Answer: We have modified the changes following your suggesstion, which are:

Table.3 shown that TCN has the best performance in all simulation results compared with other

Reviewer #1: This manuscript develops a method to apply AI to predict a pollution index for a poultry farm in China. While I think the methods have promise, the authors need to address the following major issues before it is suitable for publication.

Major:

> The English and grammar are fair to poor throughout. I have included in the minor comments below some instances in just the abstract and first couple of paragraphs but I do not have time to edit the entire manuscript. This needs to be addressed as it made it difficult to follow along.

Answer: Thank you very much for you prestigious comments we have modified the manuscript and made changes following your suggestions which are given below.

Comment: The motivation for the paper is lacking. Why do we need such a robust prediction method? Can the facilities actually use it to make changes? If so, does the interval required to make adjustments align with the model's ability to predict (Figure 8). For example, L58-59 is the only place you mention that it would benefit farmers, but would it? In what way? How could it be used?

Answer: Provide a good growing environment for the goose to ensure the normal growth and development of the goose. For example, by predicting future changes in PI the farmer can make arrangements for the work time or power of environmental control equipment such as fans, exhaust fans, and/or nebulizers in advance.

Comment: At its most basic premise, this paper is quite simple. Calculate a very simple pollution index from a few variables and see if you can predict with ML methods. It would benefit by comparing these computationally intensive methods to simpler prediction methods...does it even warrant the use

of ML? What about other pollution indices? Or individual variables? Another example is you state that (L56-58) traditional methods have bad performance. So why not show that with your data to really make the case for your work?

Answer: Following your suggestion we make comparison with tradition method and the results are given below:

Table.3 Comparison of model performance.

MAE RMSE R2

Hours 12 24 48 12 24 48 12 48 48

TCN 0.0842 0.0859 0.1115 0.0154 0.0167 0.0273 0.9789 0.9791 0.9635

GRU 0.1728 0.1810 0.1922 0.0759 0.0789 0.0789 0.8937 0.8903 0.8898

LSTM 0.1892 0.2523 0.4434 0.0824 0.1388 0.2953 0.8896 0.8082 0.6078

SVM 0.5919 0.7245 0.8991 0.3292 0.3537 0.8181 0.8512 0.7748 0.6617

RF 0.2744 0.5794 0.9571 0.3407 0.3555 0.7513 0.8809 0.8050 0.6799

Comm

Attachment

Submitted filename: Response to Reviewers.docx

Decision Letter 1

Chi-Hua Chen

26 Apr 2021

PONE-D-21-03161R1

Pollution index of waterfowl farm assessment and prediction based on temporal convoluted network

PLOS ONE

Dear Dr. Liu,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Jun 10 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

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If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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Academic Editor

PLOS ONE

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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: (No Response)

Reviewer #2: 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: Partly

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: 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: No

Reviewer #2: 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: No

Reviewer #2: 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: While I commend the authors for working diligently on the suggested comments by both reviewers, the manuscript is still not in a publishable state. I still maintain that the work is interesting and prudent, but the authors have not fully addressed some of the major comments brought up previously. First being the English is still not at a level of an academic paper and really needs major edits which I cannot put forth the time to do. Second, the paper is still very methods focus despite the fact that both reviewers pointed out that there needs to be more on the "why" do the study. What's the motivation? How can it help farmers. The authors added a few lines here and there but it is still not compelling. Other things that have come up with this new version include:

1. While the first table highlights the data chosen for the PI. The text does not go into much detail about why these were chosen, and what are the acceptable limits. I still do not see a mention of other similar studies on waterfowl or poultry in the introduction.

2. There is now way too much detail in the methods. I'm not sure you need every detail and plot for each AI technique in your paper unless this is the first time they are introduced. You should provide a brief summary of each and then if you want to include this detail move to SI.

3. Conclusions and future research again focus way too much on methods and not on the "why".

Reviewer #2: All comments were addresses and could be accepted as it is. I do not have additional comments at this stage.

**********

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.

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Reviewer #1: No

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.]

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PLoS One. 2021 Jul 23;16(7):e0254179. doi: 10.1371/journal.pone.0254179.r004

Author response to Decision Letter 1


6 May 2021

Response to Journal:

Reviewer #1: While I commend the authors for working diligently on the suggested comments by both reviewers, the manuscript is still not in a publishable state. I still maintain that the work is interesting and prudent, but the authors have not fully addressed some of the major comments brought up previously. First being the English is still not at a level of an academic paper and really needs major edits which I cannot put forth the time to do.

Answer: Thank you very much for your prestigious comments. This paper was edited for proper English language, grammar, punctuation, spelling, and overall style by one or more of the highly qualified native English speaking editors at AJE.

Second, the paper is still very methods focus despite the fact that both reviewers pointed out that there needs to be more on the "why" do the study. What's the motivation? How can it help farmers. The authors added a few lines here and there but it is still not compelling.

Answer: We have added more references to this study. It includes why we need to monitor and control the poultry house environment, what methods have been used to do that thing by others, how can they help the farmer and why we need the new method.

Labor shortages and increasing biosecurity practices will make it more difficult for producers to monitor and manage the production, health, and welfare status of all of their birds. Employing modern poultry management technology is necessary to increase production [6]. An example of how modern management technology can be used to monitor and control the poultry house environment is exemplified by humidity regulation via ventilation rate changes mediated by relative humidity sensors, as relative humidity is one of the more important environmental aspects of a poultry house [7]. In addition, more advanced systems are being researched. Bustamante et al. used a multisensor system to effectively assess barn ventilation system function by tracking temperature, air velocity and differential pressure in broiler houses [8]. Hanif et al. proposed an internet of things technology-based protection and monitoring of the environment of a poultry house to monitor the environment-related parameters such as air temperature, air humidity, CO2 level of concentration and ammonia concentration., which has been implemented successfully, leading to a safe environment and profit for the poultry industry [9]. The techniques mentioned above are both solutions for real-time environmental monitoring and control; however, relying on hardware monitoring in real time cannot capture the trend of environmental changes [10], and it is easy to miss the best time for adjustment, which leads to waterfowl health damage and property loss.

Cultivation environment forecasting has been studied for many years and has made some achievements in aquaculture and livestock breeding [11–14]. The technique estimates or predicts the future changes in target variables that cannot be obtained directly. For example, Jackman et al. generated a prediction model by using sensor inputs of relative humidity, carbon dioxide, temperature, and ammonia for environmental parameter and crop yield prediction [15]. In waterfowl production, a system such as this would allow for actions to be taken sooner by farmers if the environment is projected to be bad. However, few studies have applied prediction in waterfowl breeding. Therefore, it is necessary to apply environmental prediction technology to waterfowl production to fill this gap.

1. While the first table highlights the data chosen for the PI. The text does not go into much detail about why these were chosen, and what are the acceptable limits. I still do not see a mention of other similar studies on waterfowl or poultry in the introduction.

Answer: We have added more references to detail describe why data were chosen, and what are the acceptable limits.

Labor shortages and increasing biosecurity practices will make it more difficult for producers to monitor and manage the production, health, and welfare status of all of their birds. Employing modern poultry management technology is necessary to increase production [6]. An example of how modern management technology can be used to monitor and control the poultry house environment is exemplified by humidity regulation via ventilation rate changes mediated by relative humidity sensors, as relative humidity is one of the more important environmental aspects of a poultry house [7]. In addition, more advanced systems are being researched. Bustamante et al. used a multisensor system to effectively assess barn ventilation system function by tracking temperature, air velocity and differential pressure in broiler houses [8]. Hanif et al. proposed an internet of things technology-based protection and monitoring of the environment of a poultry house to monitor the environment-related parameters such as air temperature, air humidity, CO2 level of concentration and ammonia concentration., which has been implemented successfully, leading to a safe environment and profit for the poultry industry [9]. The techniques mentioned above are both solutions for real-time environmental monitoring and control; however, relying on hardware monitoring in real time cannot capture the trend of environmental changes [10], and it is easy to miss the best time for adjustment, which leads to waterfowl health damage and property loss.

Cultivation environment forecasting has been studied for many years and has made some achievements in aquaculture and livestock breeding [11–14]. The technique estimates or predicts the future changes in target variables that cannot be obtained directly. For example, Jackman et al. generated a prediction model by using sensor inputs of relative humidity, carbon dioxide, temperature, and ammonia for environmental parameter and crop yield prediction [15]. In waterfowl production, a system such as this would allow for actions to be taken sooner by farmers if the environment is projected to be bad. However, few studies have applied prediction in waterfowl breeding. Therefore, it is necessary to apply environmental prediction technology to waterfowl production to fill this gap.

According to the importance of the environment and expert research, we selected 5 environmental factors, as shown in Table 1. Among them, ammonia is a toxic gas and the greatest concern of environmental pollution in waterfowl production, adversely affecting the ecosystem, environment, and health of birds and people. Less than 10 ppm is the ideal limit [42]. Relative humidity can impact bird health, and high relative humidity may worsen broiler geese performance; the ideal value is 70% [43]. Heat stress is a major concern in waterfowl production; high and low temperatures will reduce the growth performance and survivability of waterfowl, and temperatures less than 27°C and more than 10°C are ideal [44]. TSP is from the birds themselves as well as from the feed, litter, and building materials and may serve as a pathogen disseminator and bring about lung damage; less than 10 mg/m3 is the ideal limit [42]. Additionally, the levels of relative humidity, ammonia, carbon dioxide, temperature and TSP are known to be correlated with each other [6]. These factors are important for waterfowl production and can be monitored and optimized.

2. There is now way too much detail in the methods. I'm not sure you need every detail and plot for each AI technique in your paper unless this is the first time they are introduced. You should provide a brief summary of each and then if you want to include this detail move to SI.

Answer: We have simplify introduction of some methods.

Wavelet transform

Continuous wavelet transforms for a given waterfowl environment signal s(k) can be described as follows:

(3)

where denotes the complex conjugate, is the wavelet function, a is the time scale dilation and b is the time translation. By controlling the values of parameters a and b, signal time-frequency positioning can be achieved. The wavelet transform can decompose signals into multiple resolutions. However, the symbols in realization communication are discrete data, so the continuous wavelet transform needs to be discretized. Suppose , when :

(4)

The discrete waterfowl environment signal s(n) can be transformed as:

(5)

The Mallat algorithm can quickly calculate the orthogonal wavelet transform coefficients and realize signal decomposition and reconstruction [47]. The approximation coefficients and detail coefficients can be recurrently related by the Mallat algorithm as follows:

(6)

(7)

where h0 and h1 are the high-pass filter and low-pass filter, respectively. The reconstruction is the inverse process of decomposition:

(8)

The wavelet transform can decompose noise signals into different signal channels at various levels of resolution. In general, the useful signals are distributed in the high-level resolution channel, and the noise signal is likely to be distributed in the lower-level channel. Therefore, the noise of the original data can be reduced as much as possible based on a reasonable threshold. Therefore, the wavelet denoised algorithm can be described as follows:

(1) Perform wavelet transform on the original signal s(k) to obtain wavelet coefficients of various scales.

(2) Determine the threshold and perform threshold denoising on different wavelet coefficients to obtain estimated wavelet coefficients.

(3) Conduct wavelet reconstruction by equation 11 to obtain the denoise signal .

Support vector machine

SVM has good generalization ability in solving nonlinear, small sample, and high-dimensional pattern recognition, and the optimal solution obtained is global, which solves the local optimal problem that cannot be avoided in other algorithms. The prediction process of the SVM includes support vector determination, kernel function selection, kernel parameter determination, and solution. The mathematical expression as follow:

(9)

Where SVS is the number of support vectors, αi is the Lagrangian coefficient of each training sample, yi (-1 or 1) is the vector label, K (xi, x) is the selected kernel function, and b0 is the bias. The kernel function replaces the linear quantity in the traditional linear equation and maps the data to high-dimensional space processing. After selected the kernel function, the samples are trained to establish the SVM model and the prediction result Nt is finally obtained.

Long short-term memory neural network

The LSTM neural network is a special kind of recurrent neural network. It was first proposed by Ho-chreiter and Schmidhuber [49]. Its appearance effectively solved the gradient explosion problem of traditional recurrent neural networks. At the same time, the LSTM neural network has long-term memory to handle long-term sequence data. The LSTM cell structure consists of forget gate, input gate, output gate and cell state. LSTM structure is shown in Fig 2 At the time t, there are three input parameters of the LSTM network: input value xt, at time t, output value ht-1 and cell state Ct-1 at t-1. There are two output parameters of the LSTM network: output value ht and cell state Ct at time t. Through the activation function σ LSTM realizes the control of the three gates so as to realize the retention and forgetting of historical information.

Fig.2. The structure of LSTM

Gated recurrent unit

A gated recurrent unit (GRU) is a type of recurrent neural network (RNN). Similar to a long short-term memory neural network (LSTM), it is also proposed to solve long-term and gradient backpropagation problems. LSTM and GRU have similar performances, but compared with LSTM, GRU is computationally cheaper. The structure of GRU is shown in Fig 3 GRU can be descried as follows:

Firstly, two output gateds, r (reset gated) and z (update gated), were obtained by the input X(t) at t time and the output h(t − 1) at t − 1 time.

(10)

(11)

Where CJ is a sigmoid function. Parameter h' selective re- members X(t). Trough the reset gated r we can obtain h’ as follows:

(12)

Finally, the output y(t) and hidden state h(t) at t time can be calculated as follows:

(13)

(14)

Where [ ] denoted the connection of two vectors and * denoted the product of matrices.

Fig.3. The structure of GRU

3. Conclusions and future research again focus way too much on methods and not on the "why".

Answer: We have modified the conclusions.

To further promote waterfowl house environment monitoring and controlling technology, reduce labor and increase the production effect, this study analyses the shortcomings of existing methods and introduces a new way to guide waterfowl house environment management by learning from other fields.

The new method investigates the application of denoised WT and the performance of three neural network models and two mechanical learning models in predicting the pollution index of the waterfowl house environment using environmental quality parameters at different intervals. The results indicate that the TCN model has the best performance in predicting PI. The GRU model has similar performance but lower performance when the prediction time interval changed, and the LSTM model performed the worst among the three models, although it still provided fairly accurate PI predictions.

The models presented in this paper, in particular the TCN model, could provide accurate and long-interval PI predictions of waterfowl house environments and monitor them in real time. The simulation results show that this method can be applied in waterfowl house environment prediction. The future trend of the environment can be estimated and predicted compared with traditional real-time monitoring technology, which can allow better waterfowl house environment management practices, better culture plan design, and, in general, contribute to a more sustainable waterfowl house management approach.

The environmental parameters selected in the present study may also pose a limitation because of the lack of equipment. Future work may include the use of more environmental parameters to evaluate PI and apply the model in more waterfowl breeding sites to improve the production effect and further verify the model.

Attachment

Submitted filename: Response to Reviewers.docx

Decision Letter 2

Chi-Hua Chen

25 May 2021

PONE-D-21-03161R2

Pollution index of waterfowl farm assessment and prediction based on temporal convoluted network

PLOS ONE

Dear Dr. Liu,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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We look forward to receiving your revised manuscript.

Kind regards,

Chi-Hua Chen, Ph.D.

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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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

Reviewer #2: 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

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: 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

Reviewer #2: 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: The authors have done a much better job addressing remaining concerns, especially with language. I made suggested grammatical changes in the attached document. I have some other minor things to address below, but then should be suitable for publication.

1. The order of the methods and results seems off. For example there is a wavelet transform section and then further section on wavelet transform starting on 270. Then you also have results of denoising in methods not results. I think rearranging for a better flow is needed.

2. Acronyms need to be fixed. You should define acronyms the first time only and then use the acronym after. You have many in the manuscript so this needs to be addressed.

3. Figures 6a-e are still hard to read. Maybe try removing the line on the original data so that the observed points can be seen overlain on denoised data?

Reviewer #2: Can be accepted as it is now. I do not have further comments at this stage. Authors have addressed all the comments.

**********

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Reviewer #1: No

Reviewer #2: No

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Attachment

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PLoS One. 2021 Jul 23;16(7):e0254179. doi: 10.1371/journal.pone.0254179.r006

Author response to Decision Letter 2


29 May 2021

Dear editor,

Thank you very much for your letter and advice. We have revised the paper, and would like to re-submit it for your consideration. We have addressed the comments raised by the reviewers, and the amendments are highlighted in the revised manuscript. We hope that the revision is acceptable, and I look forward to hearing from you soon.

Yours sincerely,

Shuangyin Liu

Dean and Professor

School of Information science and Technology

Zhongkai University of Agriculture and Engineering

Guangzhou, 510225, P.R. China;

E-mail: shuangyinliu@zhku.edu.cn

Fax: +86-020-8900-3114;

Tel: +86-13822211958;

Attachment

Submitted filename: Response to Reviewers.docx

Decision Letter 3

Chi-Hua Chen

22 Jun 2021

Pollution index of waterfowl farm assessment and prediction based on temporal convoluted network

PONE-D-21-03161R3

Dear Dr. Liu,

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,

Chi-Hua Chen, Ph.D.

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: (No Response)

**********

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Reviewer #1: No

Acceptance letter

Chi-Hua Chen

16 Jul 2021

PONE-D-21-03161R3

Pollution index of waterfowl farm assessment and prediction based on temporal convoluted network

Dear Dr. Liu:

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.

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PLOS ONE Editorial Office Staff

on behalf of

Professor Chi-Hua Chen

Academic Editor

PLOS ONE

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    Data Availability Statement

    All relevant data are within the paper and its Supporting Information files.


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