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Multiple Minor Enhancements #42

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645cf8e
prettify README
hadisfr Feb 19, 2021
0902ff1
add makefile
hadisfr Feb 19, 2021
6e2ed7b
refactor python files
hadisfr Feb 19, 2021
d0af2c0
make some args required in python files
hadisfr Feb 19, 2021
8f19629
handle new style label file
hadisfr Feb 19, 2021
af8d103
change args to use double dash
hadisfr Feb 19, 2021
1ebb98f
add no-axis and legend options to plot script
hadisfr Feb 19, 2021
130c4af
change colormap
hadisfr Feb 19, 2021
b1d6b8e
check required args
hadisfr Feb 19, 2021
cf63bc9
unify indentations
hadisfr Feb 19, 2021
4483228
handle inputs without weight
hadisfr Feb 19, 2021
012dcf4
fix warnings
hadisfr Feb 19, 2021
b1d45ac
Make module Python3 compatible.
lmcinnes Apr 4, 2017
dfa2a4b
As per requested changes.
lmcinnes Oct 19, 2017
174f3d8
Support py3 and loading numpy arrays
lmcinnes Sep 2, 2018
a62e8e0
use empty string as default cluster name
hadisfr Feb 21, 2021
e08d50e
make plot square
hadisfr Feb 21, 2021
925852b
add annotation
hadisfr Feb 24, 2021
62a277d
handle overcomplete lable list
hadisfr Feb 24, 2021
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58 changes: 30 additions & 28 deletions LargeVis_run.py
100644 → 100755
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Original file line number Diff line number Diff line change
@@ -1,28 +1,30 @@
import LargeVis
import argparse

parser = argparse.ArgumentParser()
parser.add_argument('-fea', default = 1, type = int, help = 'whether to visualize high-dimensional feature vectors or networks')
parser.add_argument('-input', default = '', help = 'input file')
parser.add_argument('-output', default = '', help = 'output file')
parser.add_argument('-outdim', default = -1, type = int, help = 'output dimensionality')
parser.add_argument('-threads', default = -1, type = int, help = 'number of training threads')
parser.add_argument('-samples', default = -1, type = int, help = 'number of training mini-batches')
parser.add_argument('-prop', default = -1, type = int, help = 'number of propagations')
parser.add_argument('-alpha', default = -1, type = float, help = 'learning rate')
parser.add_argument('-trees', default = -1, type = int, help = 'number of rp-trees')
parser.add_argument('-neg', default = -1, type = int, help = 'number of negative samples')
parser.add_argument('-neigh', default = -1, type = int, help = 'number of neighbors in the NN-graph')
parser.add_argument('-gamma', default = -1, type = float, help = 'weight assigned to negative edges')
parser.add_argument('-perp', default = -1, type = float, help = 'perplexity for the NN-grapn')

args = parser.parse_args()

if args.fea == 1:
LargeVis.loadfile(args.input)
else:
LargeVis.loadgraph(args.input)

Y = LargeVis.run(args.outdim, args.threads, args.samples, args.prop, args.alpha, args.trees, args.neg, args.neigh, args.gamma, args.perp)

LargeVis.save(args.output)
#!/usr/bin/env python

import LargeVis
import argparse

parser = argparse.ArgumentParser()
parser.add_argument('--fea', default=1, type=int, help='whether to visualize high-dimensional feature vectors or networks')
parser.add_argument('--input', default='', help='input file', required=True)
parser.add_argument('--output', default='', help='output file', required=True)
parser.add_argument('--outdim', default=-1, type=int, help='output dimensionality')
parser.add_argument('--threads', default=-1, type=int, help='number of training threads')
parser.add_argument('--samples', default=-1, type=int, help='number of training mini-batches')
parser.add_argument('--prop', default=-1, type=int, help='number of propagations')
parser.add_argument('--alpha', default=-1, type=float, help='learning rate')
parser.add_argument('--trees', default=-1, type=int, help='number of rp-trees')
parser.add_argument('--neg', default=-1, type=int, help='number of negative samples')
parser.add_argument('--neigh', default=-1, type=int, help='number of neighbors in the NN-graph')
parser.add_argument('--gamma', default=-1, type=float, help='weight assigned to negative edges')
parser.add_argument('--perp', default=-1, type=float, help='perplexity for the NN-grapn')

args = parser.parse_args()

if args.fea == 1:
LargeVis.loadfile(args.input)
else:
LargeVis.loadgraph(args.input)

Y = LargeVis.run(args.outdim, args.threads, args.samples, args.prop, args.alpha, args.trees, args.neg, args.neigh, args.gamma, args.perp)

LargeVis.save(args.output)
63 changes: 41 additions & 22 deletions Linux/LargeVis.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ LargeVis::LargeVis()
knn_vec = old_knn_vec = NULL;
annoy_index = NULL;
head = alias = NULL;
neg_table = NULL;
neg_table = NULL;
}

const gsl_rng_type *LargeVis::gsl_T = NULL;
Expand All @@ -26,8 +26,8 @@ void LargeVis::clean_model()
vis = prob = NULL;
knn_vec = old_knn_vec = NULL;
annoy_index = NULL;
neg_table = NULL;
alias = NULL;
neg_table = NULL;
alias = NULL;

edge_count_actual = 0;
neg_size = 1e8;
Expand Down Expand Up @@ -56,14 +56,23 @@ void LargeVis::load_from_file(char *infile)
printf("\nFile not found!\n");
return;
}
printf("Reading input file %s ......", infile); fflush(stdout);
fscanf(fin, "%lld%lld", &n_vertices, &n_dim);
printf("Reading input file %s ......", infile); fflush(stdout);
if (fscanf(fin, "%lld%lld", &n_vertices, &n_dim) != 2) {
printf("Could not read dimensions\n");
fclose(fin);
exit(1);
}
vec = new real[n_vertices * n_dim];
for (long long i = 0; i < n_vertices; ++i)
{
for (long long j = 0; j < n_dim; ++j)
{
fscanf(fin, "%f", &vec[i * n_dim + j]);
if (fscanf(fin, "%f", &vec[i * n_dim + j]) != 1)
{
fclose(fin);
printf("Could not read line %lld\n", i + 1);
exit(1);
}
}
}
fclose(fin);
Expand All @@ -80,7 +89,17 @@ void LargeVis::load_from_data(real *data, long long n_vert, long long n_di)
printf("Total vertices : %lld\tDimension : %lld\n", n_vertices, n_dim);
}

void LargeVis::load_from_graph(char *infile)
bool load_edge_from_graph(FILE *fin, char *w1, char *w2, real *weight, bool use_default_weight) {
if (use_default_weight)
{
(*weight) = 1;
return fscanf(fin, "%s%s", w1, w2) == 2;
}
else
return fscanf(fin, "%s%s%f", w1, w2, weight) == 3;
}

void LargeVis::load_from_graph(char *infile, bool use_default_weight)
{
clean_data();
char *w1 = new char[1000];
Expand All @@ -96,7 +115,7 @@ void LargeVis::load_from_graph(char *infile)
return;
}
printf("Reading input file %s ......%c", infile, 13);
while (fscanf(fin, "%s%s%f", w1, w2, &weight) == 3)
while (load_edge_from_graph(fin, w1, w2, &weight, use_default_weight))
{
if (!dict.count(w1)) { dict[w1] = n_vertices++; names.push_back(w1); }
if (!dict.count(w2)) { dict[w2] = n_vertices++; names.push_back(w2); }
Expand Down Expand Up @@ -162,7 +181,7 @@ long long LargeVis::get_out_dim()

void LargeVis::normalize()
{
printf("Normalizing ......"); fflush(stdout);
printf("Normalizing ......"); fflush(stdout);
real *mean = new real[n_dim];
for (long long i = 0; i < n_dim; ++i) mean[i] = 0;
for (long long i = 0, ll = 0; i < n_vertices; ++i, ll += n_dim)
Expand Down Expand Up @@ -281,7 +300,7 @@ void *LargeVis::annoy_thread_caller(void *arg)

void LargeVis::run_annoy()
{
printf("Running ANNOY ......"); fflush(stdout);
printf("Running ANNOY ......"); fflush(stdout);
annoy_index = new AnnoyIndex<int, real, Euclidean, Kiss64Random>(n_dim);
for (long long i = 0; i < n_vertices; ++i)
annoy_index->add_item(i, &vec[i * n_dim]);
Expand All @@ -293,7 +312,7 @@ void LargeVis::run_annoy()
for (int j = 0; j < n_threads; ++j) pthread_create(&pt[j], NULL, LargeVis::annoy_thread_caller, new arg_struct(this, j));
for (int j = 0; j < n_threads; ++j) pthread_join(pt[j], NULL);
delete[] pt;
delete annoy_index; annoy_index = NULL;
delete annoy_index; annoy_index = NULL;
printf(" Done.\n");
}

Expand Down Expand Up @@ -348,7 +367,7 @@ void LargeVis::run_propagation()
{
for (int i = 0; i < n_propagations; ++i)
{
printf("Running propagation %d/%d%c", i + 1, n_propagations, 13);
printf("Running propagation %d/%lld%c", i + 1, n_propagations, 13);
fflush(stdout);
old_knn_vec = knn_vec;
knn_vec = new std::vector<int>[n_vertices];
Expand All @@ -375,7 +394,7 @@ void LargeVis::compute_similarity_thread(int id)
for (iter = 0; iter < 200; ++iter)
{
H = 0;
sum_weight = FLT_MIN;
sum_weight = FLT_MIN;
for (p = head[x]; p >= 0; p = next[p])
{
sum_weight += tmp = exp(-beta * edge_weight[p]);
Expand All @@ -392,8 +411,8 @@ void LargeVis::compute_similarity_thread(int id)
hi_beta = beta;
if (lo_beta < 0) beta /= 2; else beta = (lo_beta + beta) / 2;
}
if(beta > FLT_MAX) beta = FLT_MAX;
}
if(beta > FLT_MAX) beta = FLT_MAX;
}
for (p = head[x], sum_weight = FLT_MIN; p >= 0; p = next[p])
{
sum_weight += edge_weight[p] = exp(-beta * edge_weight[p]);
Expand Down Expand Up @@ -440,7 +459,7 @@ void *LargeVis::search_reverse_thread_caller(void *arg)

void LargeVis::compute_similarity()
{
printf("Computing similarities ......"); fflush(stdout);
printf("Computing similarities ......"); fflush(stdout);
n_edge = 0;
head = new long long[n_vertices];
long long i, x, y, p, q;
Expand All @@ -458,8 +477,8 @@ void LargeVis::compute_similarity()
head[x] = n_edge++;
}
}
delete[] vec; vec = NULL;
delete[] knn_vec; knn_vec = NULL;
delete[] vec; vec = NULL;
delete[] knn_vec; knn_vec = NULL;
pthread_t *pt = new pthread_t[n_threads];
for (int j = 0; j < n_threads; ++j) pthread_create(&pt[j], NULL, LargeVis::compute_similarity_thread_caller, new arg_struct(this, j));
for (int j = 0; j < n_threads; ++j) pthread_join(pt[j], NULL);
Expand Down Expand Up @@ -515,7 +534,7 @@ void LargeVis::test_accuracy()
++hit_case;
}
}
delete heap;
delete heap;
printf("Test knn accuracy : %.2f%%\n", hit_case * 100.0 / (test_case * n_neighbors));
}

Expand All @@ -542,7 +561,7 @@ void LargeVis::init_neg_table()
{
long long x, p, i;
neg_size = 1e8;
reverse.clear(); vector<long long> (reverse).swap(reverse);
reverse.clear(); vector<long long> (reverse).swap(reverse);
real sum_weights = 0, dd, *weights = new real[n_vertices];
for (i = 0; i < n_vertices; ++i) weights[i] = 0;
for (x = 0; x < n_vertices; ++x)
Expand All @@ -553,8 +572,8 @@ void LargeVis::init_neg_table()
}
sum_weights += weights[x] = pow(weights[x], 0.75);
}
next.clear(); vector<long long> (next).swap(next);
delete[] head; head = NULL;
next.clear(); vector<long long> (next).swap(next);
delete[] head; head = NULL;
neg_table = new int[neg_size];
dd = weights[0];
for (i = x = 0; i < neg_size; ++i)
Expand Down
2 changes: 1 addition & 1 deletion Linux/LargeVis.h
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ class LargeVis{
public:
LargeVis();
void load_from_file(char *infile);
void load_from_graph(char *infile);
void load_from_graph(char *infile, bool use_default_weight = false);
void load_from_data(real *data, long long n_vert, long long n_di);
void save(char *outfile);
void run(long long out_d = -1, long long n_thre = -1, long long n_samp = -1, long long n_prop = -1, real alph = -1, long long n_tree = -1, long long n_nega = -1, long long n_neig = -1, real gamm = -1, real perp = -1);
Expand Down
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