---
title: "Non Metric Space ( Approximate ) Library in R"
author: "Lampros Mouselimis"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Non Metric Space ( Approximate ) Library in R}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---



The **nmslibR** package is a wrapper of [*NMSLIB*](https://github.com/nmslib/nmslib), which according to the authors "... is a similarity search library and a toolkit for evaluation of similarity search methods. The goal of the project is to create an effective and comprehensive toolkit for searching in generic non-metric spaces. Being comprehensive is important, because no single method is likely to be sufficient in all cases. Also note that exact solutions are hardly efficient in high dimensions and/or non-metric spaces. Hence, the main focus is on approximate methods".

I've searched for some time (before wrapping NMSLIB) for a nearest neighbor library which can work with high dimensional data and can scale with big datasets. I've already written a package for k-nearest-neighbor search ([KernelKnn](https://CRAN.R-project.org/package=KernelKnn)), however, it's based on brute force and unfortunately, it requires a certain computation time if the data consists of many rows. The *nmslibR* package, besides the main functionality of the NMSLIB python library, also includes an Approximate Kernel k-nearest function, which as I will show in the next lines is both fast and accurate. A comparison of NMSLIB with other popular approximate k-nearest-neighbor methods can be found [here](https://github.com/erikbern/ann-benchmarks).

<br>

The NMSLIB Library,

* is a collection of search methods for generic spaces
* has both metric and non-metric search algorithms
* has both exact and approximate search algorithms
* is an evaluation toolkit that simplifies experimentation and processing of results
* is extensible (new spaces and methods can be added)
* It was designed to be efficient

<br>

Details can be found in the [NMSLIB-manual](https://github.com/nmslib/nmslib/blob/master/manual/latex/manual.pdf).


<br>

#### The nmslibR package

<br> 

The *nmslibR* package includes the following R6-class / functions,

<br>

##### **class** 


<br>


|    NMSlib            | 
| :------------------: | 
|   Knn_Query()        | 
|   knn_Query_Batch()  | 
|   save_Index()       |



<br>
  
  
##### **functions**


**UPDATE 10-05-2018** : Beginning from version **1.0.2** the **dgCMatrix_2scipy_sparse** function was renamed to **TO_scipy_sparse** and now accepts either a *dgCMatrix* or a *dgRMatrix* as input. The appropriate format for the nmslibR package in case of sparse matrices is the **dgRMatrix** format (*scipy.sparse.csr_matrix*) 


<br>

| KernelKnn_nmslib() |
| :------------------------|

| KernelKnnCV_nmslib() |
| :------------------------|

| TO_scipy_sparse() |
| :-----------------|

| mat_2scipy_sparse() |
| :-------------------|

<br>


The package documentation includes details and examples for the R6-class and functions. I'll start explaining how a user can work with sparse matrices as the input can also be a **python sparse matrix**. 

<br>


#### Sparse matrices as input

<br>

The nmslibR package includes two functions (**mat_2scipy_sparse** and **TO_scipy_sparse**) which allow the user to convert from a *matrix* / *sparse matrix* (*dgCMatrix*, *dgRMatrix*) to a *scipy sparse matrix* (*scipy.sparse.csc_matrix*, *scipy.sparse.csr_matrix*),

<br>

```{r, eval = F, echo = T}

library(nmslibR)

# conversion from a matrix object to a scipy sparse matrix
#----------------------------------------------------------

set.seed(1)

x = matrix(runif(1000), nrow = 100, ncol = 10)

x_sparse = mat_2scipy_sparse(x, format = "sparse_row_matrix")

print(dim(x))

[1] 100  10

print(x_sparse$shape)

(100, 10)
  
```

<br>


```{r, eval = F, echo = T}

# conversion from a dgCMatrix object to a scipy sparse matrix
#-------------------------------------------------------------

data = c(1, 0, 2, 0, 0, 3, 4, 5, 6)


# 'dgCMatrix' sparse matrix
#--------------------------

dgcM = Matrix::Matrix(data = data, nrow = 3,

                      ncol = 3, byrow = TRUE,

                      sparse = TRUE)

print(dim(dgcM))

[1] 3 3

x_sparse = TO_scipy_sparse(dgcM)

print(x_sparse$shape)

(3, 3)


# 'dgRMatrix' sparse matrix
#--------------------------

dgrM = as(dgcM, "RsparseMatrix")

class(dgrM)

# [1] "dgRMatrix"
# attr(,"package")
# [1] "Matrix"

print(dim(dgrM))

[1] 3 3

res_dgr = TO_scipy_sparse(dgrM)

print(res_dgr$shape)

(3, 3)
  
```


<br>


#### The NMSlib R6-class


<br>

The parameter settings for the *NMSlib* R6-class can be found in the [Non-Metric Space Library (NMSLIB) Manual](https://github.com/nmslib/nmslib/blob/master/manual/latex/manual.pdf), which explains the NMSLIB Library in detail. In the following code chunk, I'll show the functionality of the methods included using a [data set from my Github repository](https://github.com/mlampros/DataSets) (it appears as [.ipynb notebook in the nmslib Github repository](https://github.com/nmslib/nmslib/blob/master/python_bindings/notebooks/search_sift_uint8.ipynb))

<br>

```{r, eval = F, echo = T}


library(nmslibR)


# download the data from my Github repository (tested on a Linux OS)
#-------------------------------------------------------------------

system("wget https://raw.githubusercontent.com/mlampros/DataSets/master/sift_10k.txt")


# load the data in the R session
#-------------------------------

sift_10k = read.table("~/sift_10k.txt", quote="\"", comment.char="")


# index parameters
#-----------------

M = 15
efC = 100
num_threads = 5

index_params = list('M'= M, 'indexThreadQty' = num_threads, 'efConstruction' = efC, 
                    
                    'post' = 0, 'skip_optimized_index' = 1 )


# query-time parameters
#----------------------

efS = 100

query_time_params = list('efSearch' = efS)


# Number of neighbors 
#--------------------

K = 100


# space to use
#---------------

space_name = 'l2sqr_sift'     


# initialize NMSlib [ the data should be a matrix ]
#--------------------------------------------------

init_nms = NMSlib$new(input_data = as.matrix(sift_10k), Index_Params = index_params, 
                      
                      Time_Params = query_time_params, space = space_name, 
                      
                      space_params = NULL, method = 'hnsw', 
                      
                      data_type = 'DENSE_UINT8_VECTOR', dtype = 'INT',
                      
                      index_filepath = NULL, print_progress = FALSE)

```

<br>

```{r, eval = F, echo = T}

# returns a 1-dimensional vector
#-------------------------------

init_nms$Knn_Query(query_data_row = as.matrix(sift_10k[1, ]), k = 5)

```

<br>

```{r, eval = F, echo = T}

[[1]]
[1]    2    6 4585 9256  140                    # indices

[[2]]
[1] 18724 24320 68158 69067 70321               # distances
 
```

<br>

```{r, eval = F, echo = T}

# returns knn's for all data
#---------------------------

all_dat = init_nms$knn_Query_Batch(as.matrix(sift_10k), k = 5, num_threads = 1)

str(all_dat)

```

<br>

```{r, eval = F, echo = T}

# a list of indices and distances for all observations
#------------------------------------------------------

List of 2
 $ knn_idx : num [1:10000, 1:5] 3 4 1 2 13 14 1 2 30 31 ...
 $ knn_dist: num [1:10000, 1:5] 18724 14995 18724 14995 21038 ...

```

<br> 

Details on the various methods and parameter settings can be found in the [manual of the NMSLIB python Library](https://github.com/nmslib/nmslib/blob/master/manual/latex/manual.pdf). 


<br>

#### KernelKnn using the nmslibR package

<br>


In the [Vignette of the KernelKnn](https://CRAN.R-project.org/package=KernelKnn) (*Image classification of the MNIST and CIFAR-10 data using KernelKnn and HOG (histogram of oriented gradients)*) package I experimented with the **mnist dataset** and a cross-validated kernel k-nearest-neighbors model gave **98.4 % accuracy** based on **HOG** (histogram of oriented gradients) features. However, it took almost **30 minutes** (depending on the system configuration) to complete using **6 threads**. I've implemented a similar function using NMSLIB (**KernelKnnCV_nmslib**), so in the next code chunk I'll use the *same parameter setting* and I'll compare *computation time* and *accuracy*. 

<br>

First load the data,

<br>

```{r, eval = F, echo = T}

# using system('wget..') on a linux OS 

system("wget https://raw.githubusercontent.com/mlampros/DataSets/master/mnist.zip")             

mnist <- read.table(unz("mnist.zip", "mnist.csv"), nrows = 70000, header = T, 
                    
                    quote = "\"", sep = ",")

```

<br>


```{r, eval = F, echo = T}

X = mnist[, -ncol(mnist)]
dim(X)

## [1] 70000   784

# the 'KernelKnnCV_nmslib' function requires that the labels are numeric and start from 1 : Inf

y = mnist[, ncol(mnist)] + 1          
table(y)

## y
##    1    2    3    4    5    6    7    8    9   10 
## 6903 7877 6990 7141 6824 6313 6876 7293 6825 6958


# evaluation metric

acc = function (y_true, preds) {
  
  out = table(y_true, max.col(preds, ties.method = "random"))
  
  acc = sum(diag(out))/sum(out)
  
  acc
}

```
<br>

then compute the HOG features,

<br>

```{r, eval = F, echo = T}

library(OpenImageR)

hog = HOG_apply(X, cells = 6, orientations = 9, rows = 28, columns = 28, threads = 6)

## 
## time to complete : 2.101281 secs  

dim(hog)

## [1] 70000   324

```
<br>

then compute the **approximate** kernel k-nearest-neighbors using the **cosine** distance,

<br>


```{r, eval = F, echo = T}

# parameters for 'KernelKnnCV_nmslib'
#------------------------------------

M = 30
efC = 100
num_threads = 6

index_params = list('M'= M, 'indexThreadQty' = num_threads, 'efConstruction' = efC,
                    
                    'post' = 0, 'skip_optimized_index' = 1 )


efS = 100

query_time_params = list('efSearch' = efS)


# approximate kernel knn
#-----------------------

fit_hog = KernelKnnCV_nmslib(hog, y, k = 20, folds = 4, h = 1, 
                             weights_function = 'biweight_tricube_MULT', 
                             Levels = sort(unique(y)), Index_Params = index_params,
                             Time_Params = query_time_params, space = "cosinesimil", 
                             space_params = NULL, method = "hnsw", data_type = "DENSE_VECTOR", 
                             dtype = "FLOAT", index_filepath = NULL, print_progress = FALSE, 
                             num_threads = 6, seed_num = 1)


# cross-validation starts .. 

# |=================================================================================| 100%

# time to complete : 32.88805 secs 


str(fit_hog)


```

<br>

```{r, eval = F, echo = T}

List of 2
 $ preds:List of 4
  ..$ : num [1:17500, 1:10] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ : num [1:17500, 1:10] 0 0 0 0 1 ...
  ..$ : num [1:17500, 1:10] 0 0 0 0 0 ...
  ..$ : num [1:17500, 1:10] 0 0 0 0 0 0 0 0 0 0 ...
 $ folds:List of 4
  ..$ fold_1: int [1:17500] 49808 21991 42918 7967 49782 28979 64440 49809 30522 36673 ...
  ..$ fold_2: int [1:17500] 51122 9469 58021 45228 2944 58052 65074 17709 2532 31262 ...
  ..$ fold_3: int [1:17500] 33205 40078 68177 32620 52721 18981 19417 53922 19102 67206 ...
  ..$ fold_4: int [1:17500] 28267 41652 28514 34525 68534 13294 48759 47521 69395 41408 ...

```

<br>

```{r, eval = F, echo = T}

acc_fit_hog = unlist(lapply(1:length(fit_hog$preds), 
                            
                            function(x) acc(y[fit_hog$folds[[x]]], 
                                            
                                            fit_hog$preds[[x]])))
acc_fit_hog

## [1] 0.9768000 0.9786857 0.9763429 0.9760000

cat('mean accuracy for hog-features using cross-validation :', mean(acc_fit_hog), '\n')

## mean accuracy for hog-features using cross-validation : 0.9769571

```
<br>

It took approx. **33 seconds** to return with an accuracy of **97.7 %** . Almost **47 times faster** than KernelKnn's corresponding function (brute force) with a **slight lower accuracy** rate (the *braycurtis* distance metric might be better suited for this dataset).

I also run the corresponding brute-force algorithm of the NMSLIB Library by setting the *method* parameter to **seq_search**,

<br>

```{r, eval = F, echo = T}


# brute force of NMSLIB   [ here we set 'Index_Params' and 'Time_Params' to NULL ]
#----------------------

fit_hog_seq = KernelKnnCV_nmslib(hog, y, k = 20, folds = 4, h = 1, 
                                weights_function = 'biweight_tricube_MULT', 
                                Levels = sort(unique(y)), Index_Params = NULL,
                                Time_Params = NULL, space = "cosinesimil", 
                                space_params = NULL, method = "seq_search", 
                                data_type = "DENSE_VECTOR", dtype = "FLOAT", 
                                index_filepath = NULL, print_progress = FALSE, 
                                num_threads = 6, seed_num = 1)


# cross-validation starts .. 

# |=================================================================================| 100%

# time to complete : 4.506177 mins  


acc_fit_hog_seq = unlist(lapply(1:length(fit_hog_seq$preds), 
                                
                                function(x) acc(y[fit_hog_seq$folds[[x]]], 
                                                
                                                fit_hog_seq$preds[[x]])))
acc_fit_hog_seq

## [1] 0.9785143 0.9802286 0.9783429 0.9784571

cat('mean accuracy for hog-features using cross-validation :', mean(acc_fit_hog_seq), '\n')

## mean accuracy for hog-features using cross-validation : 0.9788857


```

<br>

The brute-force algorithm of the NMSLIB Library is almost **6 times faster** than KernelKnn giving an accuracy of approx. **97.9 %**.

