1 Introduction

Infectious disease imposes a significant threat to human health and pose substantial healthcare costs. Infectious diseases result from the cross-talks between hosts and pathogens, which are mainly mediated by protein-protein interactions between hosts and pathogen proteins (HP-PPIs). The potential (HP-PPIs) represents the crucial elements of the infection mechanism as they decide the outcome, leading to either pathogen clearance or spread of the pathogen in the host due to evading the host immune response (Rahmatbakhsh et al., 2021). Therefore, the study of the host-pathogen interactome is increasingly vital to uncover the molecular attributes of infectious diseases and potentially discover novel pharmacological targets or laying a strong foundation for repurposing of existing drugs.

In the past decades, several high throughput experimental approaches have been developed to chart HP-PPIs on a large scale (e.g., yeast two-hybrid (Y2H) system (Ito et al., 2001) or affinity purification (AP) coupled to mass spectrometry (MS) (Puig et al., 2001)). However, such high-throughput experimental screens are typically laborious, time-consuming, and challenging to capture the complete interactome, resulting in limited number of experimentally validated interactome in a database of HP-PPIs (Hart et al., 2006). In-silico prediction of HP-PPIs can complement wet-lab experiments by suggesting candidate interaction partners for all the host proteins and excluding partners with low interacting probability scores to reduce the range of possible PPI candidates that need to be validated via wet-lab experiments. Specialized computational approaches to predict HP-PPIs are therefore of significant importance. While many computational tools have been developed to predict intra-species PPIs (i.e., PPIs within the same species) (Wu et al., 2006; Shen et al., 2007; Nourani et al., 2015), the availability of computational tools to predict inter-species PPIs such as HP-PPIs are rare.

For this purpose, we describe HPiP (host-pathogen interaction prediction), an R package for automated prediction of HP-PPIs using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins. Briefly, HPiP extracts gold-standard of experimentally verified HP-PPIs (i.e., positive interactions) from public repository, construct negative interactions via negative sampling, retrieve and convert protein sequences to numerical representation via various descriptors, applies multivariate feature selection based on correlation and recursive feature elimination (RFE)-embedded, and finally applies ensemble averaging to predict interactions. Taken together, we hope that the HPiP package not only contributes a useful predictor to accelerate the exploration of host-pathogen PPIs, but also provides some meaningful insights into host-pathogen relationships.

2 Overview of HPiP

Briefly, HPiP downloads the gold-standard data sets of experimentally verified host-pathogen PPIs from the BioGRID database (Stark et al., 2006). Such interactions serve as a positive set. In the absence of ground truth negative examples, HPiP uses negative sampling to construct a negative set. Following the construction of gold-standard data, HPiP retrieves the FASTA sequences of associated proteins. HPiP then represents protein sequences into a fixed-length feature vector using a series of structural and physicochemical descriptors. Host-pathogen feature vectors and the accompanying gold standard reference set also called the training set, are fed into the hybrid filter-wrapper feature selection method to select the most relevant features in inferring the target variable. In the following step, HPiP uses a training set to train a series of individual machine learning models (base learners) provided in the caret package (Kuhn et al., 2020). For each applied model, hyperparameters are tweaked throughout training via resampling techniques (e.g., k-fold cross-validation), and the best set of hyperparameters are selected based on the accuracy performance measure. The optimized models will then be applied to host-pathogen feature vectors with an unknown class label to return a classification result for each pair. The HPiP then uses ensemble averaging to average classification results over an ensemble of classifiers for each possible interaction. Finally, HPiP compares the algorithmic performance of the ensemble model with individual base learners through resampling technique (e.g., k-fold cross-validation) and various performance metrics (e.g., accuracy).

3 An Example of Predicting HP-PPIs

In the following sections, we explain the main components of the HPiP package, including dataset preparation (i.e., construction of the gold-standard set, FASTA sequence retrieval), feature extraction, data processing steps (i.e., imputation of missing values, feature selection), ensemble model generation and evaluation, prediction of HP-PPIs, network visualization and external validation of the predicted network using functional enrichment analysis. Furthermore, we guide users through each step by applying the HPiP to sample data derived from public databases.

3.1 Data Set Preparation

3.1.1 Gold Standard Reference Dataset of Host-Pathogen PPIs

In this tutorial, we use the data provided by Samavarchi-Tehrani et al. (2020) as our benchmark dataset. In this study, the authors mapped interaction between 27 SARS-CoV-2 and host proteins via the proximity-dependent biotinylation (BioID) approach. We then randomly selected 500 SARS-CoV-2-host interaction pairs from all pairs as the positive samples. Since ground truth negatives are not available, here negative examples are generated from the positive set using negative sampling (Eid et al., 2016). In this approach, negative instances are sampled from all the possible pairwise combinations of host and viral proteins, as long as the possible pairs do not occur in the positive reference set. To prevent statistical differences, the same scale is assumed for the negative and positive instances (i.e., the ratio of positive to negative 1:1) (Zhou et al., 2018). The gold-reference data set can be loaded with the following command:

# Loading packages required for data handling & data manipulation
library(dplyr)
library(tibble)
library(stringr)
# Loading HPiP package
library(HPiP)
# Loading data 
data(Gold_ReferenceSet)
dim(Gold_ReferenceSet)

## [1] 1000    6

As stated by dim() the gold reference set includes 1000 HP-PPIs interaction between 27 SARS-CoV-2 and 784 host proteins.

In addition, users can use get_positivePPI in the HPiP package to construct positive set from the BioGRID database (Stark et al., 2006).

This function takes the following parameters:

organism.taxID Taxonomy identifier for the pathogen.
access.key Access key for using BioGRID webpage. To retrieve interactions from the BioGRID database, the users are first required to register for access key.
filename A character string, indicating the output filename as an RData object to store the retrieved interactions.
path A character string indicating the path to the project directory that contains the interaction data. If the directory is missing, it will be stored in the current directory.

local = tempdir()
#Get positive interactions from BioGrid 
TP <- get_positivePPI(organism.taxID = 2697049,
                      access.key = 'XXXX',
                            filename = "PositiveInt.RData",
                            path = local)

Subsequently, we can construct negative set via negative sampling using the following command:

#pathogen proteins
prot1 <- unique(TP$`Official Symbol Interactor A`)
#host proteins
prot2 <- unique(TP$`Official Symbol Interactor B`)
#true positive PPIs 
TPset <- TP$PPI
TN <- get_negativePPI(prot1 , prot2, TPset)
dim(TN)

## [1] 2600    1

3.1.2 FASTA Sequence extraction

To compute different features from protein sequences, we must first extract their sequences (in FASTA format). The getFASTA function in the HPiP package can retrieve the sequences for any organism from the UniProt database.

local = tempdir()
#retrieve FASTA sequences of SARS-CoV-2 virus 
id = unique(Gold_ReferenceSet$Pathogen_Protein)
fasta_list <- getFASTA(id, filename = 'FASTA.RData', path = local)

3.2 Sequence-based Features Extraction

To apply a learning algorithm on a host or pathogen protein sequence, it is needed to encode sequence information as numerical features. However, one of the critical challenges in inferring protein-protein interactions from the protein sequences is finding an appropriate way to encode protein sequences’ important information fully. Also, the amino-acid sequences of different lengths should be converted to fixed-length feature vectors, which is crucial in classifying training data using machine-learning techniques as such techniques require fixed-length patterns. The HPiP offers multiple functions for generating various numerical features from protein sequences.

These feature coding schemes listed in HPiP include amino acid composition (AAC) , dipeptide composition (DC), tripeptide composition (TC), tripeptide composition (TC) from biochemical similarity classes, quadruplets composition (QC), F1, F2, CTD (composition/transition/distribution), conjoint triad, autocorrelation, k-spaced amino acid pairs, and binary encoding.

3.2.1 Amino acid Composition (AAC) Descriptor

The amino acid composition (AAC) has low complexity and has been widely used to predict protein-protein interactions (PPIs) (Beltran et al., 2019; Dey et al., 2020).The AAC explains the fraction of a type of amino acid found within a protein sequence (Dey et al., 2020). This gives 20-dimensional feature vectors. For example, the fraction of all 20 natural amino acids is computed as follow:

\[ f_{(i)}=\frac{n_i}{L} \text{ }\ (i = 1,2,3,....,20) \]

where n_i is the number of amino acid type and L is the sequence length. The ACC descriptor from the protein sequences can be loaded with the following command:

# Convert the list of sequences obtained in the previous section to data.frame 
fasta_df <- do.call(rbind, fasta_list) 
fasta_df <- data.frame(UniprotID = row.names(fasta_df), 
                       sequence = as.character(fasta_df))

#calculate AAC
acc_df <- calculateAAC(fasta_df)
#only print out the result for the first row 
acc_df[1,-1]

##           A           C           D           E           F           G 
## 0.062058130 0.031421838 0.048703849 0.037706206 0.060487038 0.064414768 
##           H           I           K           L           M           N 
## 0.013354281 0.059701493 0.047918303 0.084838963 0.010997643 0.069128044 
##           P           Q           R           S           T           V 
## 0.045561665 0.048703849 0.032992930 0.077769049 0.076197958 0.076197958 
##           W           Y 
## 0.009426551 0.042419482

3.2.2 Dipeptide Composition (DC) Descriptor

The dipeptide composition (DC) is simply the fraction of the different adjacent pairs of amino acids within a protein sequence (Bhasin and Raghava, 2004). Also, this descriptor encapsulates the properties of neighboring amino acids. Dipeptide composition converts a protein sequence to a vector of 400 dimensions. The composition of all 400 natural amino acids can be calculated using the following equation:

\[ f_{(m,k)}=\frac{n_{m,k}}{L-1} \text{ }\ (m,k = 1,2,3,....,20) \]

where n_m,k corresponds to the number of dipeptide compositions characterized by amino acid type m and type k, while L is the sequence length.The DC descriptor from the protein sequences can be loaded with the following command:

# using data.frame provided by getFASTA function as data input
dc_df <- calculateDC(fasta_df)
#only print out the first 30 elements for the first row 
dc_df[1, c(2:31)]

##           AA           AC           AD           AE           AF           AG 
## 0.0047169811 0.0000000000 0.0047169811 0.0031446541 0.0000000000 0.0062893082 
##           AH           AI           AK           AL           AM           AN 
## 0.0007861635 0.0055031447 0.0007861635 0.0062893082 0.0007861635 0.0023584906 
##           AP           AQ           AR           AS           AT           AV 
## 0.0031446541 0.0039308176 0.0015723270 0.0062893082 0.0031446541 0.0031446541 
##           AW           AY           CA           CC           CD           CE 
## 0.0015723270 0.0039308176 0.0023584906 0.0031446541 0.0015723270 0.0007861635 
##           CF           CG           CH           CI           CK           CL 
## 0.0007861635 0.0031446541 0.0007861635 0.0000000000 0.0007861635 0.0023584906

3.2.3 Tripeptide Composition (TC) Descriptor

The tripeptide composition explains the occurrence of adjacent triune residues in a protein sequence (Liao et al., 2011). Tripeptide composition converts a protein sequence to a vector of 8,000 dimensions. The composition of all 8,000-dimensional descriptor can be calculated using the following equation: \[ f_{(m,k,j)}=\frac{n_{m,k,j}}{L-2} \text{ }\ (m,k,j = 1,2,3,....,20) \] where n_m,k,j corresponds to the number of tripeptide compositions characterized by amino acid type m, k and j, while L is the sequence length.The TC descriptor from the protein sequences can be loaded with the following command:

# using data.frame provided by getFASTA function as data input
tc_df <- calculateTC(fasta_df)
#only print out the first 30 elements for the first row 
tc_df[1, c(2:31)]

##          AAA          AAC          AAD          AAE          AAF          AAG 
## 0.0007867821 0.0000000000 0.0000000000 0.0007867821 0.0000000000 0.0000000000 
##          AAH          AAI          AAK          AAL          AAM          AAN 
## 0.0000000000 0.0000000000 0.0000000000 0.0007867821 0.0000000000 0.0000000000 
##          AAP          AAQ          AAR          AAS          AAT          AAV 
## 0.0000000000 0.0000000000 0.0007867821 0.0000000000 0.0007867821 0.0000000000 
##          AAW          AAY          ACA          ACC          ACD          ACE 
## 0.0000000000 0.0007867821 0.0000000000 0.0000000000 0.0000000000 0.0000000000 
##          ACF          ACG          ACH          ACI          ACK          ACL 
## 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000

3.2.4 Tripeptide Composition (TC) from Biochemical Similarity Classes Descriptor

In order to reduce the dimension of length-8,000 TC descriptor, the sequence alphabet is reduced from 20 amino acids to six classes based on biochemical similarity. The classes are [{IVLM}, {FYW}, {HKR}, {DE}, {QNTP}, and {ACGS} (Ahmed et al., 2018)]. This classification of amino acids converts a protein sequence to a vector of 216 (i.e., 6 * 6 * 6) different combinations of possible substrings of length 3. The frequency of triplet for each encoded class in the protein sequence can be calculated as follows:

\[ q_{(i)}=\frac{f_i - M_0}{M_1-M_0} \] \[ M_0 = min(f_1,f_2,...,f_{216})\text { and}\ M_1 = max(f_1,f_2,...,f_{216}) \]

Here f_i is the frequency of i^th triplet in the sequence i=1,2,…,216. To get 216-dimensional descriptor from the protein sequences, the following command can be used:

# using data.frame provided by getFASTA function as data input
TC_Sm_df <- calculateTC_Sm(fasta_df)
#only print out the first 30 elements for the first row 
TC_Sm_df[1, c(2:31)]

##         1         2         3         4         5         6         7         8 
## 0.7053571 0.2946429 0.4732143 0.4910714 0.8392857 0.8660714 0.2857143 0.1517857 
##         9        10        11        12        13        14        15        16 
## 0.2142857 0.1875000 0.2946429 0.3482143 0.4107143 0.1964286 0.2053571 0.1160714 
##        17        18        19        20        21        22        23        24 
## 0.2589286 0.3571429 0.3035714 0.1428571 0.2321429 0.1517857 0.2410714 0.3928571 
##        25        26        27        28        29        30 
## 0.7321429 0.3035714 0.4285714 0.3303571 0.7500000 0.6250000

3.2.5 Quadruplets Composition from Biochemical Similarity Classes Descriptor

To compute these features, the sequence alphabet is first reduced to six classes reported above (section 3.3.2.4). This reduction converts a protein sequence to a vector of 1296 (i.e., 6 * 6 * 6 * 6) different combinations of possible substrings of length 4 (Ahmed et al., 2018). The frequency of quadruplets for each encoded class in the protein sequence can be calculated similarly to the equation mentioned above:

\[ q_{(i)}=\frac{f_i - M_0}{M_1-M_0} \] \[ M_0 = min(f_1,f_2,...,f_{1296})\text { and}\ M_1 = max(f_1,f_2,...,f_{1296}) \] To get 1296-dimensional descriptor from the protein sequences, the following command can be used:

# using data.frame provided by getFASTA function as data input
QD_df <- calculateQD_Sm(fasta_df)
#only print out the first 30 elements for the first row 
QD_df[1, c(2:31)]

##          1          2          3          4          5          6          7 
## 0.42424242 0.18181818 0.27272727 0.48484848 0.48484848 0.66666667 0.15151515 
##          8          9         10         11         12         13         14 
## 0.21212121 0.15151515 0.09090909 0.24242424 0.27272727 0.45454545 0.06060606 
##         15         16         17         18         19         20         21 
## 0.24242424 0.18181818 0.21212121 0.57575758 0.24242424 0.15151515 0.36363636 
##         22         23         24         25         26         27         28 
## 0.24242424 0.27272727 0.51515152 0.66666667 0.42424242 0.54545455 0.21212121 
##         29         30 
## 0.63636364 0.48484848

3.2.6 F1/F2 Composition Descriptor

F1 composition gives 20-dimensional description, defined as:

\[ F1(SAR)=\sum_{SAR\text{ }\epsilon\text{ } sequence}length(SAR)^2 \]

Where SAR is the sum of squared length of single amino acid repeats (SARs) in the entire protein sequence. Since F1 includes SAR of length 1, the F1 descriptor reveals global composition of amino acids and amino acid repeats (Alguwaizani et al., 2018).

Figure 1: Example of calculating F1 (repeats of S) in the protein sequence.

While, to calculate feature F2, the sequence alphabet is first split into substrings of length 6 residues (Alguwaizani et al., 2018). There are two main differences between feature F2 and F1:

For F2, sum of square length of single amino acid repeats (SARS) is computed for every window of 6 residues.
The maximum of the sum of squared length of SARs is selected for F2.

F2 composition gives 20-dimensional description, defined as:

\[ F1(SAR)=max_{windows\text{ }\epsilon\text{ }sequence} \ sum_{SAR\text{ }\epsilon\text{ } sequence}length(SAR)^2 \]

Where SAR is the sum of squared length of single amino acid repeats (SARs) in the entire protein sequence.

Get feature F1 from the protein sequences:

# using data.frame provided by getFASTA function as data input
F1_df <- calculateF(fasta_df, type = "F1")
#only print out the result the first row 
F1_df[1,-1]

##   A   C   D   E   F   G   H   I   K   L   M   N   P   Q   R   S   T   V   W   Y 
##  93  48  66  50  79  88  17  82  65 130  14 102  64  66  44 117 109 113  12  60

Get feature F2 from the protein sequences:

# using data.frame provided by getFASTA function as data input
F2_df <- calculateF(fasta_df, type = "F2")
#only print out the result the first row 
F2_df[1,-1]

## A C D E F G H I K L M N P Q R S T V W Y 
## 9 4 4 4 4 4 1 4 4 9 1 4 4 4 4 9 4 9 1 4

3.2.7 Composition/Transition/Distribution (CTD) Descriptors

To calculate CTD descriptors developed by (Dubchak et al., 1995, 1999), the 20 standard amino acids is first clustered into three classes according to its attribute. Then, each amino acid in the protein sequence is encoded by one of the indices 1,2,3 depending on its grouping. The corresponding divisions for each group are shown in Table 1. According to Hydrophobicity grouping mentioned in Table 1, the protein sequence CLVIMFWGASTPHYRKEDQN is replaced by 11111112222222333333. Next, for a given attribute, three types of descriptors, composition (C), transition (T), and distribution (D) can be calculated, which will be explained in the following sections.

Table 1: Amino acid attributes and the division of amino acid into three-group.
Sl	Property	Group 1	Group 2	Group 3
1	Charge	Neutral	Negatively charged	Positively charged
	Amino acids	A,C,F,G,H,I,L,M,N,P,Q,S,
T,V,W,Y	D,E	K,R
2	Hydrophobicity	Hydrophobicity	Neutral	Polar
	Amino acids	C,F,I,L,M,V,W	A,G,H,P,S,T,Y	D,E,K,N,Q,R
3	Normalized vander Waals	0-2.78	2.95-4.0	4.03-8.08
	Amino acids	A,C,D,G,P,S,T	E,I,L,N,Q,V	F,H,K,M,R,W,Y
4	Polarity	4.9-6.2	8.0-9.2	10.4-13.0
	Amino acids	C,F,I,L,M,V,W,Y	A,G,P,S,T	D,E,H,K,N,Q,R
5	Polariizability	0 - .108	0.128-0.186	0.219-0.409
	Amino acids	A,D,G,S,T	C,E,I,L,N,P,Q,V	F,H,K,M,R,W,Y
6	Secondary Structure	Coil	Helix	Strand
	Amino acids	D,G,N,P,S	A,E,H,K,L,M,Q,R	C,F,I,T,V,W,Y
7	Solvent Accessibility	Buried	Intermediate	Exposed
	Amino acids	A,C,F,G,I,L,V,W	H,M,P,S,T,Y	D,E,K,N,R,Q

3.2.7.1 Composition (C) Descriptor

The composition represents the number of amino acids of a particular property (e.g., hydrophobicity) for each encoded class divided by the protein sequence length (You et al., 2014). In the above example using the hydrophobicity attribute, the number for encoded classes 1, 2, 3 are 7,7,6 respectively. Therefore, the compositions for each class are 7/20 =35%, 7/20 =35%, and 6/20 =30%, respectively. Composition descriptor can be defined as:

\[ C_{(i)}=\frac{n_i}{L} \text{ }\ (i = 1,2,3) \]

where n_i is the number of amino acid type i and L is the sequence length. The C descriptor from the protein sequences can be loaded with the following command:

# using data.frame provided by getFASTA function as data input
CTDC_df <- calculateCTDC(fasta_df)
CTDC_df[1, c(-1)]

##          G1.charge  G1.hydrophobicity G1.normwaalsvolume        G1.polarity 
##         0.08091123         0.28515318         0.40612726         0.37549097 
##  G1.polarizability G1.secondarystruct   G1.solventaccess          G2.charge 
##         0.32914375         0.33857031         0.44854674         0.83267871 
##  G2.hydrophobicity G2.normwaalsvolume        G2.polarity  G2.polarizability 
##         0.38177533         0.37627651         0.32600157         0.45326002 
## G2.secondarystruct   G2.solventaccess          G3.charge  G3.hydrophobicity 
##         0.35585232         0.28515318         0.08641005         0.33307148 
## G3.normwaalsvolume        G3.polarity  G3.polarizability G3.secondarystruct 
##         0.21759623         0.29850746         0.21759623         0.30557738 
##   G3.solventaccess 
##         0.26630008

3.2.7.2 Transition (T) Descriptor

Transition (T) characterizes the percent frequency from a type of amino acids to another type (Wang et al., 2017). For instance, a transition from class 1 to 2 or 2 to 1 is the percent frequency with which class 1 is followed by class 2 or vice versa (Xiao et al., 2015). The frequency of these transitions can be computed as follow:

\[ T_{(rs)}=\frac{n_{rs} + n_{sr}}{L-1} \text{ }\ (rs = 12,13,23) \]

where n_rs,n_sr are the number of dipeptide encoded as rs and sr in the sequence and and L is the sequence length.The T descriptor from the
protein sequences can be calculated with the following command:

# using data.frame provided by getFASTA function as data input
CTDT_df <- calculateCTDT(fasta_df)
#only print out the result for the first row 
CTDT_df[1, -1]

##          charge.Tr1221.prob          charge.Tr1331.prop 
##                  0.13207547                  0.01572327 
##          charge.Tr2332.prob  hydrophobicity.Tr1221.prob 
##                  0.14465409                  0.21462264 
##  hydrophobicity.Tr1331.prop  hydrophobicity.Tr2332.prob 
##                  0.20047170                  0.26415094 
## normwaalsvolume.Tr1221.prob normwaalsvolume.Tr1331.prop 
##                  0.31367925                  0.16823899 
## normwaalsvolume.Tr2332.prob        polarity.Tr1221.prob 
##                  0.16902516                  0.25000000 
##        polarity.Tr1331.prop        polarity.Tr2332.prob 
##                  0.23977987                  0.19261006 
##  polarizability.Tr1221.prob  polarizability.Tr1331.prop 
##                  0.30660377                  0.14072327 
##  polarizability.Tr2332.prob secondarystruct.Tr1221.prob 
##                  0.19654088                  0.24371069 
## secondarystruct.Tr1331.prop secondarystruct.Tr2332.prob 
##                  0.20676101                  0.23663522 
##   solventaccess.Tr1221.prob   solventaccess.Tr1331.prop 
##                  0.25943396                  0.23899371 
##   solventaccess.Tr2332.prob 
##                  0.15566038

3.2.7.3 Distribution (D) Descriptor

The distribution measures the chain length within which the first, 25%, 50%, 75%, and 100% of the amino acids of a particular property (e.g., hydrophobicity) for a certain encoded class are located, respectively (Dubchak et al., 1995). For example, as shown in Figure 3, there are 8 residues as 1, the position for the first residue 1 , the 2nd residue 1 (25% * 8 = 2), the 5th 1 residue (50% * 8 = 4), the 7th 1 (75% * 8= 6) and the 10th residue 2 (100% * 8 =8) in the encoded sequence are 1, 2, 13, 17, 22 respectively, so that the distribution descriptors for residue 1 are : (1/22) ×100% = 4.55%, (2/22)×100% = 9.09%, (13/22) ×100% = 59.09%, (17/22)×100% = 77.27%, (22/22)×100% = 100%, respectively. Likewise, the distribution descriptor for 2 and 3 is (18.18%, 18.18%, 27.27%, 63.64%, 95.45%) and (13.64%, 31.82%, 45.45%, 54.55%, 86.36%), respectively.

Figure 2:The sequence of hypothetical protein showing the construction of CTD descriptors of a protein. The index 1, 2 and 3 indicates the position of amino acid for each encoded class. 1-2 transitions indicated the position of 12 or 21 pairs in the sequence. Similarly, 1-3 and 2-3 transitions are defined in the same way.

The D descriptor from the protein sequences can be calculated with the following command:

# using data.frame provided by getFASTA function as data input
CTDD_df <- calculateCTDD(fasta_df)
#only print out the first 30 elements for the first row 
CTDD_df[1, c(2:31)]

##           charge.g1.residue0         charge.g1.residue100 
##                    1.6496465                   99.6857816 
##          charge.g1.residue25          charge.g1.residue50 
##                   23.5663786                   43.7549097 
##          charge.g1.residue75           charge.g2.residue0 
##                   75.7266300                    0.0785546 
##         charge.g2.residue100          charge.g2.residue25 
##                  100.0000000                   24.9018068 
##          charge.g2.residue50          charge.g2.residue75 
##                   49.9607227                   74.1555381 
##           charge.g3.residue0         charge.g3.residue100 
##                    3.1421838                   99.1358995 
##          charge.g3.residue25          charge.g3.residue50 
##                   26.7085625                   55.1453260 
##          charge.g3.residue75   hydrophobicity.g1.residue0 
##                   80.9897879                    1.0997643 
## hydrophobicity.g1.residue100  hydrophobicity.g1.residue25 
##                   99.6857816                   25.7659073 
##  hydrophobicity.g1.residue50  hydrophobicity.g1.residue75 
##                   50.3534957                   75.8051846 
##   hydrophobicity.g2.residue0 hydrophobicity.g2.residue100 
##                    0.7069914                  100.0000000 
##  hydrophobicity.g2.residue25  hydrophobicity.g2.residue50 
##                   24.7446976                   49.4893951 
##  hydrophobicity.g2.residue75   hydrophobicity.g3.residue0 
##                   71.4846819                    0.0785546 
## hydrophobicity.g3.residue100  hydrophobicity.g3.residue25 
##                   99.7643362                   23.8020424 
##  hydrophobicity.g3.residue50  hydrophobicity.g3.residue75 
##                   50.5106049                   76.9835035

3.2.8 Conjoint Triad Descriptor

The conjoint triad is one of the popular sequence-based approaches for protein-protein interactions prediction (Shen et al., 2007). This method encodes a protein sequence as a feature vector by calculating the frequency of amino acid triplets as follows (Figure 2) :

Similar to section 3.3.2.4, it encodes 20 amino acids to seven classes based on their dipoles and volumes of the side chains. These seven classes are [{AGV}, {DE}, {FILP}, {KR}, {MSTY}, and {C} (Shen et al., 2007)]
A given protein sequence is then represented using three consecutive amino acids (i.e., amino acid triple).
It uses 343-dimensional feature vectors to represent a given protein sequence, where then each feature vector v is then mapped to frequency vector d_i (i= 1,2,…343), which is defined as follow:

\[ d_i = \frac{f_i - \min\{\,f_1, f_2 , \ldots, f_{343}\,\}}{\max\{\,f_1, f_2, \ ldots, f_{343}\,\}} \]

Where f_i is the frequency of i-th triplet type in the protein sequence. The numerical value of d_i of each protein ranges between 0 to 1, which therefore allows the comparison between proteins.

Figure 3: Schematic diagram for constructing conjoint triad method. V is the vector space of feature vectors that includes a fixed number of features; each feature (v_i) includes amino acid triplet; F represents the frequency vector corresponding to V, and the value of i-th dimension of F(f_i) corresponds to the frequency of that v_i-triad observed in the sequence.

The conjoint triad Descriptor descriptor from the protein sequences can be calculated with the following command:

# using data.frame provided by getFASTA function as data input
CTriad_df <- calculateCTriad(fasta_df)
#only print out the first 30 elements for the first row 
CTriad_df[1, c(2:31)]

##          1          2          3          4          5          6          7 
## 0.78409091 0.78409091 0.61363636 0.53409091 0.38636364 0.56818182 0.09090909 
##          8          9         10         11         12         13         14 
## 0.72727273 0.79545455 0.77272727 0.42045455 0.35227273 0.42045455 0.10227273 
##         15         16         17         18         19         20         21 
## 0.68181818 0.76136364 0.63636364 0.43181818 0.34090909 0.30681818 0.11363636 
##         22         23         24         25         26         27         28 
## 0.46590909 0.46590909 0.39772727 0.20454545 0.35227273 0.14772727 0.07954545 
##         29         30 
## 0.29545455 0.44318182

3.2.9 Autocorrelation (Auto) Descriptors

Autocorrelation descriptors, also known as molecular connectivity indices, explain the magnitude of the correlation between protein or peptide sequences based on their particular structural or physiochemical information, which are defined according to the distribution of amino acid properties along the protein sequence (Ong et al., 2007). Eight default properties (Xiao et al., 2015) are used here for deriving the autocorrelation descriptors: normalized average hydrophobicity scales (AccNo. CIDH920105), average flexibility indices (AccNo. BHAR88010), polarizability parameter (AccNo. CHAM820101), free energy of solution in water(AccNo. CHAM820102), residue accessible surface area in tripeptide (AccNo. CHOC760101), residue volume (AccNo. BIGC670101), steric parameter (AccNo. CHAM810101), and relative mutability (AccNo. DAYM780201). Autocorrelation descriptors includes three types of descriptors (Morean-Broto, Moran, and Geary) which are described below. Prior to integrating any of the physiochemical attributes into the autocorrelation formula, these attributes need to be normalized by the following equation:

\[ P_r = \frac{P_r - \bar{P}}{\sigma} \] where $\bar{P}$ is the mean value of the eight physiochemical attributes, and sigma represents the standard deviation, in which both can be defined as:

\[ \bar{P} = \frac{\sum_{r=1}^{20} P_r}{20} \quad \textrm{and} \quad \sigma = \sqrt{\frac{1}{2} \sum_{r=1}^{20} (P_r - \bar{P})^2} \]

The first type of autocorrelation is known as Moreau-Broto autocorrelation (Broto et al., 1984). Application of Moreau-Broto autocorrelation to protein sequence is calculated by the following equation:

\[ AC(d) = \sum_{i=1}^{L-d} P_i P_{i + d} \quad d = 1, 2, \ldots, \textrm{nlag} \]

where $P_i$ and $P_{i+d}$ represent the amino acid property at position $i$ and $i+d$ and $d$ is termed the lag of the autocorrelation along the protein sequence; $P_i$ and $P_{i+d}$. While, $\textrm{nlag}$ is the maximum value of the lag. This equation can be normalized based on peptide length to get normalized Moreau-Broto autocorrelation:

\[ ATS(d) = \frac{AC(d)}{L-d} \quad d = 1, 2, \ldots, \textrm{nlag} \]

The second type of autocorrelation, named the Moran autocorrelation (Moran, 1950), can be defined as:

\[ I(d) = \frac{\frac{1}{L-d} \sum_{i=1}^{L-d} (P_i - \bar{P}') (P_{i+d} - \bar{P}')}{\frac{1}{L} \sum_{i=1}^{L} (P_i - \bar{P}')^2} \quad d = 1, 2, \ldots, 30 \]

where $d$, $P_i$, and $P_{i+d}$ are described in the same fashion as that for Moreau-Broto autocorrelation; $\bar{P}'$ is the mean of the given amino acid property $P$ across the protein sequence, i.e.,

\[ \bar{P}' = \frac{\sum_{i=1}^L P_i}{L} \]

$d$, $P$, $P_i$ and $P_{i+d}$, $\textrm{nlag}$ are defined as above. The main difference between Moran and Moreau-Broto autocorrelation is that, unlike Moreau-Broto, the Moran autocorrelation utilizes the mean value of the given amino acid property instead of the actual value of the property (Al-Barakati et al., 2019).

The last type of autocorrelation , known as the Geary autocorrelation, can be calculated as: \[ C(d) = \frac{\frac{1}{2(L-d)} \sum_{i=1}^{L-d} (P_i - P_{i+d})^2}{\frac{1}{L-1} \sum_{i=1}^{L} (P_i - \bar{P}')^2} \quad d = 1, 2, \ldots, 30 \]

where $d$, $P$, $P_i$, $P_{i+d}$, and $\textrm{nlag}$ are defined above. The key difference between Geary and the other two autocorrelations is that the Geary autocorrelation utilizes the square difference of the property values (Al-Barakati et al., 2019).

Computing autocorrelation with HPiP is simple as the following commands:

Get Moran autocorrelation:

# using data.frame provided by getFASTA function as data input
moran_df <- calculateAutocor(fasta_df,type = "moran", nlag = 10)
#only print out the first 30 elements for the first row 
moran_df[1, c(2:31)]

##  CIDH920105.lag1  CIDH920105.lag2  CIDH920105.lag3  CIDH920105.lag4 
##    -2.277533e-02    -6.586333e-02    -6.065475e-03     7.793094e-03 
##  CIDH920105.lag5  CIDH920105.lag6  CIDH920105.lag7  CIDH920105.lag8 
##    -1.965556e-02    -2.291896e-02     3.609957e-02     2.404702e-02 
##  CIDH920105.lag9 CIDH920105.lag10  BHAR880101.lag1  BHAR880101.lag2 
##    -7.224129e-03    -1.962279e-02     5.838844e-04    -3.936188e-02 
##  BHAR880101.lag3  BHAR880101.lag4  BHAR880101.lag5  BHAR880101.lag6 
##    -4.993847e-04     1.610445e-02     7.256299e-03     2.432986e-03 
##  BHAR880101.lag7  BHAR880101.lag8  BHAR880101.lag9 BHAR880101.lag10 
##     2.951910e-02     1.431268e-02    -9.954176e-03    -6.734817e-03 
##  CHAM820101.lag1  CHAM820101.lag2  CHAM820101.lag3  CHAM820101.lag4 
##     2.246027e-02     1.045731e-04     1.598308e-02    -2.012865e-02 
##  CHAM820101.lag5  CHAM820101.lag6  CHAM820101.lag7  CHAM820101.lag8 
##    -3.081543e-05    -2.027915e-02     2.091813e-02     1.198716e-02 
##  CHAM820101.lag9 CHAM820101.lag10 
##    -3.860567e-03    -2.132450e-02

Get Normalized Moreau-Broto autocorrelation:

# using data.frame provided by getFASTA function as data input
mb_df <- calculateAutocor(fasta_df,type = "moreaubroto", nlag = 10)
#only print out the first 30 elements for the first row 
mb_df[1, c(2:31)]

##  CIDH920105.lag1  CIDH920105.lag2  CIDH920105.lag3  CIDH920105.lag4 
##    -0.0188245843    -0.0605085976    -0.0026823499     0.0107362310 
##  CIDH920105.lag5  CIDH920105.lag6  CIDH920105.lag7  CIDH920105.lag8 
##    -0.0157906557    -0.0189568440     0.0381003015     0.0264468353 
##  CIDH920105.lag9 CIDH920105.lag10  BHAR880101.lag1  BHAR880101.lag2 
##    -0.0037862857    -0.0157775749     0.0082438732    -0.0239249619 
##  BHAR880101.lag3  BHAR880101.lag4  BHAR880101.lag5  BHAR880101.lag6 
##     0.0073538778     0.0207404479     0.0136327763     0.0097268396 
##  BHAR880101.lag7  BHAR880101.lag8  BHAR880101.lag9 BHAR880101.lag10 
##     0.0315019066     0.0192685645    -0.0002740419     0.0023150775 
##  CHAM820101.lag1  CHAM820101.lag2  CHAM820101.lag3  CHAM820101.lag4 
##     0.0646786378     0.0473994319     0.0596316658     0.0317531550 
##  CHAM820101.lag5  CHAM820101.lag6  CHAM820101.lag7  CHAM820101.lag8 
##     0.0472702127     0.0316032556     0.0633505635     0.0564643542 
##  CHAM820101.lag9 CHAM820101.lag10 
##     0.0442242141     0.0307261016

Get Geary autocorrelation:

# using data.frame provided by getFASTA function as data input
geary_df <- calculateAutocor(fasta_df,type = "geary", nlag = 10)
#only print out the first 30 elements for the first row 
geary_df[1, c(2:31)]

##  CIDH920105.lag1  CIDH920105.lag2  CIDH920105.lag3  CIDH920105.lag4 
##        1.0226568        1.0657160        1.0059053        0.9920253 
##  CIDH920105.lag5  CIDH920105.lag6  CIDH920105.lag7  CIDH920105.lag8 
##        1.0194498        1.0227587        0.9637505        0.9757426 
##  CIDH920105.lag9 CIDH920105.lag10  BHAR880101.lag1  BHAR880101.lag2 
##        1.0068772        1.0192243        0.9991465        1.0391630 
##  BHAR880101.lag3  BHAR880101.lag4  BHAR880101.lag5  BHAR880101.lag6 
##        1.0003447        0.9837570        0.9926833        0.9974919 
##  BHAR880101.lag7  BHAR880101.lag8  BHAR880101.lag9 BHAR880101.lag10 
##        0.9703168        0.9853979        1.0097805        1.0066186 
##  CHAM820101.lag1  CHAM820101.lag2  CHAM820101.lag3  CHAM820101.lag4 
##        0.9774946        0.9999835        0.9841586        1.0203869 
##  CHAM820101.lag5  CHAM820101.lag6  CHAM820101.lag7  CHAM820101.lag8 
##        1.0004284        1.0207839        0.9794036        0.9882033 
##  CHAM820101.lag9 CHAM820101.lag10 
##        1.0041758        1.0217759

3.2.10 k-Spaced Amino Acid Pairs

The k-spaced amino acid pairs (KSAAP) feature describes the number of occurrences of all possible amino acid pairs by a distance of k, which can be any number of residues up to two less than the protein length (Al-Barakati et al., 2019). For instance, given 400 (20 x 20) amino acid pairs and four values for k (k = 1-4), there would be 1600 attributes resulted from the KSAAP feature, and the frequency of each amino acid pair with k spaces is calculated by sliding through protein sequence one by once. Table 2 illustrates the outputs of using KSAAP features with various values of k for protein sequence ARAQRTAAADARAKAAKAGCAARRAAATANYN.

Table 2: Composition of k-spaced amino acid pairs
Given 400 (20 × 20) amino acid pairs and four values for k (k=1–4), there are 1600 attributes generated for the KSAAP feature.

K = 1	Amino Acid pairs	AXA	AXC	AXD	AXE	—-	YXY
	Numbe of occurances	8	1	1	0	—-	1
K =2	Amino Acid pairs	AXXA	AXXC	AXXD	AXXE	—-	YXXY
	Numbe of occurances	7	0	1	0	—-	0
K = 3	Amino Acid pairs	AXXXA	AXXXC	AXXXD	AXXXE	—-	YXXXY
	Numbe of occurances	8	1	1	0	—-	0
K = 4	Amino Acid pairs	AXXXXA	AXXXXC	AXXXXD	AXXXXE	—-	YXXXXY
	Numbe of occurances	7	1	0	0	—-	0

The KSAAP descriptor from the protein sequences can be calculated with the following command:

# using data.frame provided by getFASTA function as data input
KSAAP_df <- calculateKSAAP(fasta_df)
#only print out the first 30 elements for the first row 
KSAAP_df[1, c(2:31)]

##        AsssA        RsssA        NsssA        DsssA        CsssA        EsssA 
## 0.0067643743 0.0018320180 0.0026775648 0.0028184893 0.0028184893 0.0031003382 
##        QsssA        GsssA        HsssA        IsssA        LsssA        KsssA 
## 0.0011273957 0.0036640361 0.0047914318 0.0066234498 0.0025366404 0.0040868095 
##        MsssA        FsssA        PsssA        SsssA        TsssA        WsssA 
## 0.0022547914 0.0016910936 0.0016910936 0.0039458850 0.0059188275 0.0056369786 
##        YsssA        VsssA        AsssR        RsssR        NsssR        DsssR 
## 0.0009864713 0.0036640361 0.0025366404 0.0012683202 0.0016910936 0.0009864713 
##        CsssR        EsssR        QsssR        GsssR        HsssR        IsssR 
## 0.0007046223 0.0023957159 0.0015501691 0.0012683202 0.0021138670 0.0029594138

3.2.11 Binary encoding

Binary encoding (BE) can be used to transform each residue in a protein sequence into 20 coding values (Al-Barakati et al., 2019). For example, ALa is described as (10000000000000000000) while Cys is defined as (01000000000000000000), etc. Thus, the total length of this feature is 400(20 * 20) vectors.

# using data.frame provided by getFASTA function as data input
BE_df <- calculateBE(fasta_df)
#only print out the first 30 elements for the first row 
BE_df[1, c(2:31)]

3.2.12 BString Object as Data Input

Alternatively, we can directly read the FASTA sequences into R using Biostrings
package (Pagès et al., 2019), followed by converting the protein sequences into numerical features.

#loading the package 
library(Biostrings)

#Read fasta sequences provided by HPiP package using Biostrings
fasta <- 
  readAAStringSet(system.file("extdata/UP000464024.fasta", package="HPiP"),
                  use.names=TRUE)
#Convert to df
fasta_bios = data.frame(ID=names(fasta),sequences=as.character(fasta))
#Extract the UniProt identifier
fasta_bios$ID <- sub(".*[|]([^.]+)[|].*", "\\1", fasta_bios$ID)
# for example, run ACC
acc_bios <- calculateAAC(fasta_bios)

Note that fasta_bios can be used as data input for all the descriptors listed in section 3.3.2.

3.2.13 Generate a SummarizedExperiment Objects

SummerizedExperiment objects can be used to store and merge rectangular matrices of different outputs, as long as they have similar rownames or colnames. As illustrated in section 3.3.2, all the computed data.frames have the same rownames but different features; therefore, we can easily use the cbind functions to merge multiple SummerizedExperiment objects to one object. The HPiP package provides two example SummarizedExperiment objects: viral_se and host_se. viral_se includes pre-computed (CTD) numerical features per viral proteins present in the Gold_ReferenceSet. Similarly,host_se includes (CTD) pre-computed numerical features per host proteins in the Gold_ReferenceSet.

#loading viral_se object
data(viral_se)
viral_se

## class: SummarizedExperiment 
## dim: 13 147 
## metadata(0):
## assays(1): counts
## rownames(13): P0DTD1 P0DTC7 ... P0DTC9 P0DTC2
## rowData names(0):
## colnames(147): G1.charge G1.hydrophobicity ...
##   solventaccess.Tr1331.prop solventaccess.Tr2332.prob
## colData names(1): X

#loading host_se object
data(host_se)
host_se

## class: SummarizedExperiment 
## dim: 785 147 
## metadata(0):
## assays(1): counts
## rownames(785): Q9Y2Z0 Q6NUM9 ... Q02880 Q7KZF4
## rowData names(0):
## colnames(147): G1.charge G1.hydrophobicity ...
##   solventaccess.Tr1331.prop solventaccess.Tr2332.prob
## colData names(1): X

The numerical features from each SummarizedExperiment object can be easily retrieved using the assays()$counts, where each row represent the viral or host proteins and each column represents one of the numerical features.

As an example, construction of SummarizedExperiment for viral proteins using CTD descriptors is as follows:

#generate descriptors
CTDC_df <- calculateCTDC(fasta_df)
CTDC_m <- as.matrix(CTDC_df[, -1])
row.names(CTDC_m) <- CTDC_df$identifier

CTDT_df <- calculateCTDT(fasta_df)
CTDT_m <- as.matrix(CTDT_df[, -1])
row.names(CTDT_m) <- CTDT_df$identifier

CTDD_df <- calculateCTDD(fasta_df)
CTDD_m <- as.matrix(CTDD_df[, -1])
row.names(CTDD_m) <- CTDD_df$identifier

#convert matrix to se object
ctdc_se <- SummarizedExperiment(assays = list(counts = CTDC_m),
                                colData = paste0(colnames(CTDC_df[,-1]),
                                                 "CTDC"))
ctdt_se <- SummarizedExperiment(assays = list(counts = CTDT_m),
                                colData = paste0(colnames(CTDT_df[,-1]),
                                                 "CTDT"))
ctdd_se <- SummarizedExperiment(assays = list(counts = CTDD_m),
                                colData = paste0(colnames(CTDD_df[,-1]),
                                                 "CTDD"))
#combine all se objects to one 
viral_se <- cbind(ctdc_se,ctdd_se,ctdt_se)

3.2.14 Table of Summary Descriptors

Table 3: List of commonly used descriptors in HPiP.
Descriptor name	Length vectors	Function
Amino Acid Composition	20	calculateAAC()
Dipeptide Composition	400	calculateDC()
Tripeptide Composition	8000	calculateTC()
Tripeptide Composition (TC) from BS Classes	216	calculateTC_Sm()
Quadruples Composition (QC)	1296	calculateQD_Sm()
F1	20	calculateF1()
F2	20	calculateF2()
Composition	21	calculateCTDC()
Transition	21	calculateCTDT()
Distribution	105	calculateCTDD()
Conjoint Triad	343	calculateCTriad()
Geary (Default nlag = 30)	240	calculateGeary()
Moran (Default nlag = 30)	240	calculateMoran()
Normalized (Default nlag = 30)	240	calculateMoreauBroto()
k-Spaced Amino Acid Pairs	400	calculateKSAAP()
Binary encoding	400	calculateBE()

Note that we can calculate protein sequence descriptors for the host proteins using the functions described above (i.e., section 3.2.1-3.2.14).

3.3 Combine Host-Pathogen Interaction Descriptors

To generate host-pathogen protein-protein interaction descriptors, sequence-based descriptors can be combined into one vector space using getHPI(), which provides two types of interactions, controlled by argument type. To illustrate the usage of getHPI, we will continue our example from section 3.2.16

1.Extraction of numerical features from viral_se and host_se objects

#extract features from viral_se
counts_v <- assays(viral_se)$counts
#extract row.names from viral_Se
rnames_v <- row.names(counts_v)

#extract features from host_se
counts_h <- assays(host_se)$counts
#extract row.names from viral_Se
rnames_h <- row.names(counts_h)

2.Map the features to the gold-standard data:

#Loading gold-standard data
gd <- Gold_ReferenceSet

x1_viral <- matrix(NA, nrow = nrow(gd), ncol = ncol(counts_v))
for (i in 1:nrow(gd)) 
  x1_viral[i, ] <- counts_v[which(gd$Pathogen_Protein[i] == rnames_v), ]

x1_host <- matrix(NA, nrow = nrow(gd), ncol = ncol(counts_h))
for (i in 1:nrow(gd)) 
  x1_host[i, ] <- counts_h[which(gd$Host_Protein[i] == rnames_h), ]

3.Generate host-pathogen interaction descriptors using getHPI:

x <- getHPI(x1_viral,x1_host, type = "combine")
x <- as.data.frame(x)
x <- cbind(gd$PPI, gd$class, x)
colnames(x)[1:2] <- c("PPI", "class")

3.4 Data Processing

It is crucial to pre-process the data (i.e., remove the noise) before feeding it into the machine learning model as the quality of data and valuable information that can be extracted from it directly affect the model’s performance. The pre-processing steps are as follow:

Handling missing values: in any real-world data set, there are always missing values. The easiest option is to remove rows or columns including missing values; however, such an approach results in losing valuable information. The alternative method is to impute missing values using neighboring information (e.g., average or median) or replace the missing values with zeros. HPiP package provides two functions to deal with the missing values. The filter_missing_values allows the user to drop the missing values above a certain threshold, controlled by argument max_miss_rate, while the impute_missing_data function replaces the null values with mean/median or zero, controlled by argument method.
Feature selection: some of the sequence-based features are high dimensional, including hundreds to thousands of features. Unfortunately, such high-dimensional data includes many redundant features that reduce the predictive model’s accuracy and increase the training time. The FSmethodfunction in the HPiP package combines two feature selection (FS) methods, controlled by type() argument, to eliminate redundant features. The first FS method is based on correlation analysis that computes the correlation between features using Pearson correlation measure and removes highly correlated features above the user-defined threshold. The second FS method uses the Recursive Feature Elimination (RFE) algorithm (wrapped up with a random forest (rf) machine learning algorithm) to perform feature selection. RFE works by fitting the rf algorithm with all features in the training data set, ranking features by importance, removing the least important features, and re-fitting the model until the desired number of features remains. The feature importance can be computed using rf model-independent metric (e.g., ROC curve analysis or accuracy), which is controlled by argument metric().

The complete set of arguments for FSmethod function are:

x A data.frame containing protein-protein interactions, class labels and features.
type The feature selection type
cor.cutoff Correlation coefficient cutoff used for filtering.
resampling.method The re-sampling method (e.g., k-fold cross-validation) for RFE.
iter Number of partitions for cross-validation.
repeats For repeated k-fold cross validation only.
metric A string that specifies what summary metric will be used to select the optimal feature.
verbose Make the output verbose.

Continuing our example from section 3.3, feature selection using both correlation analysis and RFE approach can be performed using the following command:

#to use correlation analysis, make sure to drop the columns with sd zero
xx <- Filter(function(x) sd(x) != 0, x[,-c(1,2)])
xx <- cbind(x$PPI, x$class, xx)
colnames(xx)[1:2] <- c("PPI", "class")

#perform feature selection using both correlation analysis and RFE approach
set.seed(101)
x_FS <- FSmethod(xx, type = c("both"),
                 cor.cutoff = 0.8,resampling.method = "cv",
                 iter = 2,repeats =NULL, metric = "Accuracy", 
                 verbose = FALSE)

We can also visualize the results from the FSmethod analysis. For instance, the correlation matrix of unfiltered data can be visualized using the corr_plot. This will present us with a heatmap showing the correlation between all the features prior to filtration.

#cor plot
corr_plot(x_FS$cor.result$corProfile, method = 'square' , cex = 0.1)

In addition, the variable importance of retained features after the RFE feature selection approach can also be plotted using the var_imp function.

#var importance
var_imp(x_FS$rf.result$rfProfile, cex.x = 8, cex.y = 8)

3.5 Prediction Algorithm

Sequence features and a list of gold-standard HP-PPIs can be fed into an ensemble classifier to rank the potential HP-PPIs interaction. This is accomplished via the pred_ensmebel function. This function uses the ensemble averaging approach, to combine any base classifiers provided in the caret package to predict HP-PPIs. To score interactions, the pred_ensmebel function uses the the training data (i.e., labelled HP-PPIs with sequence features) as well as unlabeled HP-PPIs data set to learn features that allow reliable prediction of HP-PPIs, utilizing multiple ML algorithms. Following training, the trained models will be used to make predictions on unlabeled data. Then,ensemble averaging will be applied to average predictions over an ensemble of classifiers, each with different cross-validation splits. Finally, through resamplign techniques (e.g., k-fold cross-validation), this function also compares and evaluates the performance of ensemble model with individual machine learning models via commonly used measurements such as Recall (Sensitivity), Specificity, Accuracy , Precision, F1-score, and Matthews correlation coefficient (MCC). The corresponding formulae are as follows:

\[ Recall=Sensitivity=TPR=\frac{TP}{TP+FN} \]

\[ Specificity=1-FPR=\frac{TN}{TN+FP} \]

\[ Accuracy=\frac{TP+TN}{TP+TN+FP+FN} \]

\[ Precision=\frac{TP}{TP+FP} \]

\[ F1=2 \text{ × } \frac{Precision \text{ × } Recall}{Precision + Recall} \]

\[ MCC=\frac{TP \text{ × } TN - FP \text{ × } FN}{\sqrt{(TP+FP)\text{ × } (TP+FN)\text{ × } (TN+FP)\text{ × } (TN+FN)}} \]

The pred_ensemble takes the following parameters:

features A data frame with host-pathogen protein-protein interactions (HP-PPIs) in the first column, and features to be passed to the classifier in the remaining columns.
gold_standard A data frame with gold_standard HP-PPIs and class label indicating if such PPIs are positive or negative.
classifier The type of classifier to use. See caret package for all the available classifiers.
resampling.method The re-sampling technique (i.e., k-fold cross-validation).
ncross Number of partitions for cross-validation.
plots Logical value, indicating whether to plot the performance of ensemble learning algorithm as compared to individual classifiers.If the argument set to TRUE, plots will be saved in current working directory.
verboseIter Make the output verbose.
filename A character string, indicating the output filename as an pdf object.

As an example, we will use three base learners , support vector machine (svmRadial), Fitting Generalized Linear Models (glm), and random forest (ranger), controlled by argument classifier, to rank potential interaction. For the sake of time, we use only five-fold cross-validation (ncross = 5). In order to perform prediction, we will use unlabel_data, retrieved from Supplementary Table 1 presented in (Gordon et al., 2020) , which includes unlabeled HP-PPIs along with pre-computed CTD features, as well as constructed data containing labeled HP-PPIs from section 3.4.

#load the unlabeled HP-PPIs
data('unlabel_data')
#Constructed labeled HP-PPIs
labeled_dat <- x_FS$rf.result$rfdf
labeled_dat <- labeled_dat[,-1] 
#select important features
unlabel_data <- 
  unlabel_data[names(unlabel_data) %in% names(x_FS$rf.result$rfdf)]

#merge them 
ind_data <- rbind(unlabel_data,labeled_dat)

# Get class labels
gd <-  x_FS$rf.result$rfdf
gd <-  gd[, c(2,1)]

Now we can predict interactions using pred_ensembel:

set.seed(102)
ppi <- pred_ensembel(ind_data,
                     gd,
                     classifier = c("svmRadial", "glm", "ranger"),
                     resampling.method = "cv",
                     ncross = 5,
                     verboseIter = TRUE,
                     plots = TRUE,
                     filename=file.path(tempdir(), "plots.pdf"))

To retrieve predicted interactions from the result generated by pred_ensembel function, we can just type:

pred_interactions <- ppi[["predicted_interactions"]]
head(pred_interactions)

##                  PPI Pathogen_protein Host_protein  ensemble
## 1    M:P0DTC5~Q9UBM1         M:P0DTC5       Q9UBM1 0.7008682
## 2 nsp6:P0DTD1~Q8WVX9      nsp6:P0DTD1       Q8WVX9 0.6857571
## 3 ORF6:P0DTC6~P62861      ORF6:P0DTC6       P62861 0.6921793
## 4 nsp4:P0DTD1~Q6P2Q9      nsp4:P0DTD1       Q6P2Q9 0.6889793
## 5    M:P0DTC5~O75489         M:P0DTC5       O75489 0.6986460
## 6 nsp6:P0DTD1~Q8TEM1      nsp6:P0DTD1       Q8TEM1 0.6923126

Finally, users can subset their list of high-confidence interactions for further analysis, using a stringent classifier confidence ensemble score cutoff of 0.7:

pred_interactions <- filter(pred_interactions, ensemble >= 0.7)
dim(pred_interactions)

## [1] 100   4

When the plots argument set to TRUE, the pred_ensembel function generates one pdf file indicating the performance of the ensemble classier as compared to individual base learners

The first plot shows the Receiver Operating Characteristic (ROC) curve.

Figure 4: ROC_Curve curve.
The second plot shows the Precision-Recall (PR) curve

Figure 5: Precision-Recall (PR) curve.
The third plot shows the accuracy (ACC), F1-score ,positive predictive value (PPV),sensitivity (SE),and Matthews correlation coefficient (MCC) of ensemble classifier vs selected individual classifiers.

Figure 6: Point plot.

3.6 Nework Visualization

Following PPI prediction, users can visualize the predicted PPI network using plotPPI and FreqInteractors functions.

The plotPPI function, which is based on the igraph plotting function (Csardi, 2013), provide visualization on interacting host protein partners of pathogen proteins. For instance, to get the PPI network of SARS-CoV2-ORF8-human, we can run the following command:

S_interc <- filter(pred_interactions, 
                           str_detect(Pathogen_protein, "^ORF8:"))
#drop the first column
ppi <- S_interc[,-1]

plotPPI(ppi, edge.name = "ensemble",
            node.color ="red",
            edge.color = "grey",
            cex.node = 10,
            node.label.dist= 2)

The FreqInteractors function, shows the degree distribution of pathogen proteins in the HP-PPI network:

ppi <- pred_interactions[,-1]
FreqInteractors(ppi,cex.size = 12)

3.7 GO Enrichment Analysis

To identify significantly enriched annotation terms in predicted interacting host protein partners of each pathogen protein, we can use the enrichfindP function based on the g:Profiler tool (Kolberg et al., 2020). Additionally, we can use the erichfind_hp function to analyze functional characteristics of all predicted human proteins in the predicted network.

For instance, the following command can be used to performs functional enrichment analysis of host protein partners of each pathogen protein:

enrich_result <- 
  enrichfindP(ppi,threshold = 0.05,
            sources = "GO",
            p.corrction.method = "bonferroni",
            org = "hsapiens")

3.8 Complex Prediction

for this analysis, we utilizes the predicted HP-PPIS network generated in section 3.5 as input data for complex prediction. For the community detection analysis, run_clustering function provided in the HPiP package includes the five most popular complex detection algorithms in including fast-greedy, walktrap, label propagation, multi-level community, and markov clustering. For example, to detect complexes using fast-greedy algorithm, we can run the following command:

ppi <- pred_interactions[,-1]
set.seed(103)
predcpx <- run_clustering(ppi, method = "FC")

Additionally, we can analyze the functional characteristics of these predicted modules via enrichfind_cpx function.

enrichcpx <- enrichfind_cpx(predcpx,
             threshold = 0.05,
             sources = "GO",
             p.corrction.method = "bonferroni",
             org = "hsapiens")

4 Session info

sessionInfo()

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] caret_6.0-94                lattice_0.22-6             
##  [3] ggplot2_3.5.1               HPiP_1.12.0                
##  [5] tibble_3.2.1                stringr_1.5.1              
##  [7] SummarizedExperiment_1.36.0 Biobase_2.66.0             
##  [9] GenomicRanges_1.58.0        MatrixGenerics_1.18.0      
## [11] matrixStats_1.4.1           Biostrings_2.74.0          
## [13] GenomeInfoDb_1.42.0         XVector_0.46.0             
## [15] IRanges_2.40.0              S4Vectors_0.44.0           
## [17] BiocGenerics_0.52.0         dplyr_1.1.4                
## [19] readr_2.1.5                 knitr_1.48                 
## [21] BiocStyle_2.34.0           
## 
## loaded via a namespace (and not attached):
##   [1] jsonlite_1.8.9          magrittr_2.0.3          magick_2.8.5           
##   [4] farver_2.1.2            corrplot_0.95           rmarkdown_2.28         
##   [7] zlibbioc_1.52.0         vctrs_0.6.5             RCurl_1.98-1.16        
##  [10] PRROC_1.3.1             tinytex_0.53            htmltools_0.5.8.1      
##  [13] S4Arrays_1.6.0          SparseArray_1.6.0       pROC_1.18.5            
##  [16] sass_0.4.9              parallelly_1.38.0       bslib_0.8.0            
##  [19] htmlwidgets_1.6.4       plyr_1.8.9              plotly_4.10.4          
##  [22] lubridate_1.9.3         cachem_1.1.0            igraph_2.1.1           
##  [25] lifecycle_1.0.4         iterators_1.0.14        pkgconfig_2.0.3        
##  [28] Matrix_1.7-1            R6_2.5.1                fastmap_1.2.0          
##  [31] GenomeInfoDbData_1.2.13 future_1.34.0           digest_0.6.37          
##  [34] colorspace_2.1-1        labeling_0.4.3          randomForest_4.7-1.2   
##  [37] fansi_1.0.6             timechange_0.3.0        httr_1.4.7             
##  [40] abind_1.4-8             compiler_4.4.1          proxy_0.4-27           
##  [43] bit64_4.5.2             withr_3.0.2             highr_0.11             
##  [46] MASS_7.3-61             lava_1.8.0              DelayedArray_0.32.0    
##  [49] ModelMetrics_1.2.2.2    tools_4.4.1             ranger_0.16.0          
##  [52] future.apply_1.11.3     nnet_7.3-19             glue_1.8.0             
##  [55] nlme_3.1-166            grid_4.4.1              reshape2_1.4.4         
##  [58] generics_0.1.3          recipes_1.1.0           gtable_0.3.6           
##  [61] tzdb_0.4.0              class_7.3-22            tidyr_1.3.1            
##  [64] data.table_1.16.2       hms_1.1.3               utf8_1.2.4             
##  [67] foreach_1.5.2           pillar_1.9.0            vroom_1.6.5            
##  [70] splines_4.4.1           survival_3.7-0          bit_4.5.0              
##  [73] tidyselect_1.2.1        MCL_1.0                 gridExtra_2.3          
##  [76] bookdown_0.41           xfun_0.48               expm_1.0-0             
##  [79] hardhat_1.4.0           timeDate_4041.110       stringi_1.8.4          
##  [82] UCSC.utils_1.2.0        lazyeval_0.2.2          yaml_2.3.10            
##  [85] evaluate_1.0.1          codetools_0.2-20        protr_1.7-4            
##  [88] kernlab_0.9-33          archive_1.1.9           BiocManager_1.30.25    
##  [91] cli_3.6.3               rpart_4.1.23            munsell_0.5.1          
##  [94] jquerylib_0.1.4         Rcpp_1.0.13             globals_0.16.3         
##  [97] gprofiler2_0.2.3        parallel_4.4.1          gower_1.0.1            
## [100] bitops_1.0-9            listenv_0.9.1           ggthemes_5.1.0         
## [103] viridisLite_0.4.2       ipred_0.9-15            scales_1.3.0           
## [106] prodlim_2024.06.25      e1071_1.7-16            purrr_1.0.2            
## [109] crayon_1.5.3            rlang_1.1.4

5 References

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Introduction to HPiP

29 October 2024

Package

Contents