J. Biomedical Science and Engineering, 2010, 3, 785-790 JBiSE
doi:10.4236/jbise.2010.38104 Published Online August 2010 (http://www.SciRP.org/journal/jbise/).
Published Online August 2010 in SciRes. http:// www. scirp. org/journal/jbise
Categorizing HIV-1 subtypes using an ant-based clustering
David King*, Wei Hu
Department of Computer Science, Houghton College, Houghton, USA.
Email: David.King@Houghton.edu
Received 28 May 2010; revised 17 June 2010; accepted 22 June 2010.
Human Immunodeficiency Virus (HIV) is especially
difficult to treat due to its rapid mutation rate. There
are currently eleven different genomic subtypes of
HIV-1, as well as a number of recombinant subtypes.
An area of study in bioinformatics is the development
of algorithms to identify the subtypes of HIV-1 ge-
nomes. Ant-based algorithms have the ability to find
global solutions in optimizations problems, and are
also able to process complex data efficiently. We pro-
posed a new technique named Ant Colony Anchor Al-
gorithm (ACAA), using anchors of training data on a
topographic map to categorize HIV-1 sequences based
on ant-based clustering. We used three sets of se-
quences from the POL region of the HIV-1 genome.
We categorized these three dataset with the Subtype
Analyzer (STAR), a current HIV-1 categorization al-
gorithm, and the ACAA. We found that the ACAA
returned higher accuracy values of 83.2%, 67.1%, and
53.5% for our three datasets respectively, than the
STAR’s 47.3%, 49.4% and 18%. The results of the
ACAA are the average results of 20 runs of the algo-
rithm. We also observed the performance of the algo-
rithm on specific subtypes, and observed that while the
STAR and ACAA performed with similar accuracy on
several subtypes (A, B, and C in particular), the ACAA
had a significant advantage over the STAR in others,
especially in categorizing recombinant subtypes.
Keywords: Ants; Clustering; HIV; Classification;
Subtype; STAR; ATTA; Bioinformatics
1.1. HIV-1 Subtype Categorization
Human Immunodeficiency Virus (HIV), which causes
Acquired Immunodeficiency Syndrome (AIDS), falls
into two broad categories: HIV-1 and HIV-2. HIV-2 is
largely constrained to West Africa, and has a relatively
lower transmission rate. HIV-1, on the other hand, has a
very high transmission rate, and accounts for most HIV
infections on a global scale.
Treatment of HIV-1 is a difficult process because of
the virus’ exceptionally high mutation rate. When DNA
is replicated in the reproductive cycle of the virus, any-
where between 1 in 1000 and 1 in 10000 nucleotides will
be improperly transcribed. This has lead to an exception-
ally diverse pool of viruses, genetically speaking. HIV-1
has been classified into 11 subtypes based on genomic
patterns and variations (subtypes A-H, J, N, and O).
Additionally, there are recombinant types of these vi-
ruses, which contain combined DNA from two or more
viruses. These recombinant subtypes are caused by the
infection of a single cell by multiple viruses [1].
There is neither a cure for HIV-1 nor a preventative
vaccine. Antiretroviral drugs have been shown to be an
effective treatment. These drugs interfere with the DNA
of the virus. As such, the genetic makeup of the virus has
tremendous effect on its resistance to the treatments.
Because the subtype has such a significant impact on the
effectiveness of the drugs, categorization of different
subtypes of HIV-1 is critical to the treatment process.
The development of an algorithm to effectively cate-
gorize HIV-1 is of prime interest in this area of study.
One current categorization algorithm is the STAR (Sub-
type Analyzer), developed by University College Lon-
don Centre for Virology. The STAR functions by main-
taining profiles of these 11 categories. These profiles are
calculated based on aligned training sequence data. Each
profile is a two-dimensional frequency matrix, where the
number of rows in the matrix is the length of the train ing
sequences in amino acid positions, and the number of
columns is 20—one for each possible amino acid. These
profiles are calculated based on training sequence data,
where each position in a subtype profile is the frequency
of that particular amino acid at that position in all train-
ing sequences of that subtype. A global profile matrix is
786 D. King et al. / J. Biomedical Science and Engineering 3 (2010) 785-790
Copyright © 2010 SciRes. JBiSE
also calculated, using the amino acid frequency from
all training sequences rather than just a single subtype
Each test sequence to be categorized receives a
Z-score based on each subtype profile. The test se-
quence is categorized as the subtype which gives the
score closest to the mean. If the sequence is not within
1.5 standard deviations of the mean for any of the sub-
types, the virus is categorized into the lump category,
‘unassigned’ [1]. This is not an innately helpful cate-
gory; however neither is it innately harmful. It is pre-
ferred to leave a sequence unclassified rather than mis-
There are other algorithms, similar in nature to the
STAR, which have also been turned towards the purpose
of subtype categorization. The SUDI algorithm1, devel-
oped by Los Alamos National Laboratory, uses phylo-
genic analysis to determine subtype. The HIV Genotyp-
ing algorithm2, developed by NCBI uses both a similar-
ity search as well as a bootscanning similarity process to
categorize subtypes. Stanford’s HIVseq3 algorithm cate-
gorizes based only on a simple similarity search [2].
1.2. Ant-Bas ed Clustering Algorithms
Ant-based algorithms fall under a category of algorithms
which model their behavior from ants in th e wild. These
algorithms have found effective applications in bioin-
formatics because of their ability to find global solutions
in optimization problems, as well as for their ability to
efficiently process complex data quickly [3].
Ant-based clustering algorithms refer specifically to
those algorithms which model the clustering behavior of
ants in the wild. The behavior of these social insects
displays a high level of swarm intelligence. In this in-
stance, the habits of many relatively simple individuals
form a pattern of behavior with distinct order and pur-
pose. In the same way that real ants will cluster objects
into like p iles within a space (e.g., within a colony, eggs
will be clustered into one chamber, while food will be
clustered into another), the algorithm will cluster like
pieces of data into the same area on a two-dimensional
topographic map, forming clusters. Clustering data on a
two dimensional map can greatly reduce the dimension-
ality which needs to be analyzed, allowing for much
more efficient analysis and evaluation than would be
possibl e w ith the raw data [4].
Ant-based clustering algorithms were originally pro-
posed in 1991 by Deneubourg et al. [5], and were de-
signed to emulate the sorting and clustering behaviors of
ants. Early algorithms of this variety were ineffective,
but showed enough potential for clustering data that new
improvements continued to occur [3].
One such improvement, called ATTA (Adaptive Time-
dependent Transporter Ants), was proposed by Julia
Handl [3], and is effective at clustering like data points
on a two dimensional map. A sample output of the ATTA
can be seen in Figure 1. The ATTA utilized formulae
which were altered from those used in previous algo-
rithms. Several other changes were made to the process
of the algorithm which increased the ability of the algo-
rithm to produce a distinct clustering [6].
The goal of this study is to develop a new algorithm
based on the ATTA to categorize HIV-1 subtypes, and to
compare the performance of our algorithm with that of
the STAR (http://www.vgb.ucl.ac.uk/starn.shtml).
2.1. HIV-1 Sequence Data
An analysis of the STAR algorithm used sequence data
which includes the entire protease region of the HIV-1
genome and 340 amino acids of the reverse transcriptase
(RT), making for a total sequence length of 439. The
protease and RT regions of HIV-1 play a role in the re-
productive cycle of the virus. Common antiretroviral
treatments interfere with the functions of these regions.
Because of their medical significance, sequence data of
Figure 1. ATTA. This is visual representation of the ATTA. To
generate this plot, 800 two-dimensional vectors were generated,
each containing values close (within a vector distance of 1) to
one of the points [2, 2], [2, 8], [8, 2] or [8, 8]. The points were
assigned colors based on which of the four points they were
associated with, then clustered using the ATTA.
D. King et al. / J. Biomedical Science and Engineering 3 (2010) 785-790 787
Copyright © 2010 SciRes. JBiSE
protease and RT has a high availability, making them
prime for use in categorization algorithms [1]. In this
study, we used three datasets, each covering different
subtypes and different portions of these genomic re-
Dataset 1 contained sequences of the same 439 amino
acid region as in Myers et al. [1]. We include data from
8 subtypes (Table 1). We obtained these sequences from
the Los Alamos National Laboratory HIV Sequence Da-
tabase. Each subtype contained no more than 50 se-
quences and no less than 35.
Dataset 2 contained sequences of a shorter length: 99
amino acids from the protease, and only 240 amino acids
from the RT (339 amino acids total, nucleotide positions
2253 to 3270). These were also downloaded from the
Los Alamos National Laboratory HIV Sequence Data-
base. 10 subtypes were covered, with sequence numbers
between 35 and 50 (Table 1).
Dataset 3 contained sequences of the protease ge-
nomic region (99 amino acids, ranging from nucleotide
positions 2253 to 2550). These were downloaded from
the Stanford drug resistance database. This dataset con-
tained 10 subtypes (Table 1). Again, each data type had
no more than 50 and no less than 35 sequences.
Because misaligned sequences can significantly re-
duce the effectiveness of sequence analysis, we per-
formed a multiple alignment on all sequences in each
dataset using the ClustalW2 algorithm.
In each dataset, every subtype was separated into
training and test data. For the purposes of consistency,
we used 30 sequences as training data for every subtype.
All other sequences (between 5 and 20 in number) were
used as test data to be categorized.
All datasets are available on request from the author.
2.2. HIV-1 Sequence Encoding
Each dataset was a collection of sequenced HIV-1 ge-
nomes. Each sequence consisted of a list of amino acids.
In order to properly analyze these sequences, we con-
verted each into a binary vector. Because there are
twenty different possible amino acids, we mapped each
amino acid to a unique twenty-dimensional binary vector.
For example, we mapped the amino acid Alanine to the
point [1, 0, 0, 0, 0...], while we mapped Arginine to [0, 1,
0, 0, 0...]. After all the amino acids in a sequence were
converted, we concatenated these individual vectors into
an ordered, high-dimensional sequence vector, with di-
mensionality of 20N, where N is the number of amino
acids in the sequence. In this manner, each unique amino
acid was represented in the sequence vector.
3.1 The ATTA Algorithm
The ATTA takes as input a collection of vectors, called
documents—a term used by the ATTA. These documents
are distributed randomly across a two dimensional grid
called a topographic map. The vector data of the docu-
ments bears no relation to their initial coord inates on the
topographic map. The goal of the algorithm is to cluster
the documents on the topographic map such that the
documents which are similar to one another will be lo-
cated near one another on the map.
The ants are simple entities which have the ability to
wander freely across the map. They are able to pick up,
carry, and drop documents as the algorithm runs. The
probability that a document is picked up or dropped by
an ant is dependent on the nearby documents.
For each iteration of the algorithm, a random ant from
the colony is chosen. The ant moves to a different loca-
tion on the map within a user-defined distance (our
maximum movement distance was 50). At the beginning
of the algorithm, this movement is randomly generated,
but later is based partially on previous movements of
that ant. The ant attempts to drop the document it is car-
rying based on a probability calculated from the pdrop
formula. If the drop action is successful, the ant will
choose a new document at random, and attempt to pick
with a probability calculated from the ppick formula. If
this operation is unsuccessful, the ant will choose an-
other document at random, and try again. This continues
until the ant has successfully picked a new document [3].
The ppick and pdrop formulae are defined as:
pdrop 4*
Table 1. This table contains the subtypes used for each dataset, as well as the number of test data sequences for each subtype. Any
subtype with the heading N/A was not included in that dataset.
Subtype A B C D F F1 G J K O U AE AG
Dataset 1 20 20 20 20 N/A 7 19 N/A N/A N/A N/A 20 20
Dataset 2 20 20 20 20 N/A 20 20 N/A N/A 8 10 20 20
Dataset 3 20 20 20 20 20 N/A 20 20 20 N/A N/A 20 20
788 D. King et al. / J. Biomedical Science and Engineering 3 (2010) 785-790
Copyright © 2010 SciRes. JBiSE
)( *
if Jif
where i is the candidate document, σ is the neighborhoo d
size, J is the set of documents in the neighborhood, j is
the current document in J, δ(i, j) is the vector distance
between document i and document j, and α is a
user-defined constant. It is important to note that since
the vector information of all documents is constant,
δ(i, j) need only be calculated once for all possible
document pairs. Because the algorithm merely refer-
ences pre-calculated values, it is able to process even
high dimensional vectors very efficiently.
The value of f* becomes larger as i becomes more
similar with the other elements in J. As such, ppick¸
which has an inverse relation to f*, becomes smaller as
f* increases, leading to a dramatically decreased likeli-
hood that the element is picked up when it is nearby
similar elements. By contrast, pdrop skyrockets when f*
increases, leading to a very high likelihood that an ele-
ment will be dropped amongst like elements. These
formulae are specific to the ATTA, and are revised fro m
those used in previous ant-based clustering algorithms
In this manner, after a large number of successive it-
erations, the documents with similar vectors are likely to
have similar Euclidian positions, forming clusters of like
documents on the map.
The output of the ATTA is a clustering of the input
vectors. The quality of these clusters is measured by a
Pearson Correlation, which evaluates the correlation
between the distances of two documents on the topog-
raphic map and the distances between the vectors of the
two document s [7] .
3.2 Modifications to the ATTA
The ATTA is a clustering algorithm, not originally in-
tended for categorization purposes. Where the ATTA
takes in all documents at once, and clusters them all in
the same manner, categorization algorithms build a clas-
sifier based on training data, and then apply the classifier
to the test data to categorize. Using the ATTA as a base,
we built a categorization algorithm to categorize input
test sequences using a classifier build from training se-
Our classifier takes the form of anchors of training
data in fixed positions on the topographic map. We as-
sign each subtype of training data a unique square region
on the topographic map, called the anchor area. The
Euclidian positions of the training documents are fixed.
This anchoring technique ensures that the training
documents of each subtype are well separated, and will
not move through the clustering phase of the algorithm.
As a result, the ants will tend to drop test documents of a
given subtype near the pre-defined anchor of the same
subtype. We call this the Ant Colony Anchor Algorithm
(ACAA). A sample output of the ACAA is visible in
Figure 2. The pseudo- code for the AC AA is available in
Section 1 of the supplementary file.
3.3 Subtype Categorization Based on Clustering
When running the ACAA on HIV-1 sequences, we con-
verted each sequence to a binary vector as in Subsection
2.2. Each document in the ACAA represents one HIV-1
After the clustering process of the ACAA is finished,
we defined a local area for each test document. The ra-
dius of this local area was one half the width of the an-
chor areas. Each test document was classified as the
subtype which has the highest representation of training
documents within the test document’s local area. This is
a modified version of the classification strategy used in
the study by Lee et al. [8].
Because the ACAA is non-deterministic, we utilized
repetition to stabilize the results of the categorization.
We recorded each test sequence’s predicted subtype in
each repetition of the ACAA. There are a total of 20
repetitions in our experiment—further repetitions did not
Figure 2. ACAA. This figure clearly shows the anchors of
training data on the topographic map, with test data clustering
around the training anchors of appropriate type.
D. King et al. / J. Biomedical Science and Engineering 3 (2010) 785-790 789
Copyright © 2010 SciRes. JBiSE
improve performan ce significantly. The final categoriza-
tion is based on majority votes.
We categorized our test data using the ACAA and the
STAR’s online interface. For each dataset, we main-
tained a record of the number of sequences correctly
classified, the number incorrectly classified, and the
number left unclassified.
The STAR is deterministic in nature, and so the cate-
gorization was only run a single time. Because the
ACAA is non-deterministic in nature, we ran the algo-
rithm on each dataset twenty times, taking the average
values of the twenty runs. We also recorded the individ-
ual run which produced the highest rate of correct cate-
gorization (Table 2).
The ACAA yields a more accurate classification than
the STAR for all datasets. For the ACAA, the lengthier
Dataset 1 yields the best results, while Dataset 2 still
gives reasonable accuracy. The STAR was able to cate-
gorize both Datasets 1 and 2 with approximately the
same level of accuracy. In both the STAR and the ACAA,
the categorization of Dataset 3 was not very successful,
although the ACAA did categorize with a much higher
accuracy than the STAR.
In all datasets, we observe that the ratio of inaccuracy
to unclassified sequences is higher in our algorithm than
in the STAR. In addition, in Datasets 2 and 3, we ob-
serve a higher number of misclassified sequences in the
ACAA than in the STAR.
The statistical significance of these results is undeni-
able—every accuracy rating of the ACAA had a P-v alue
of 0.0. The accuracies generated by the STAR had
P-values of 0.0 for Datasets 1 and 2, and 0.004 for
Dataset 3.
The statistical significance was determined by gener-
ating 10,000 randomized classification predictions for
each dataset, and comparing the accuracy of each against
the accuracy of the prediction generated by the ACAA.
The statistical significance was the percentage of ran-
domly generated predictions with accuracies greater than
those produced by the ACAA.
In addition to analysis on each specific dataset, we
also observed distinct differences in the ability of both
algorithms to categorize specific subtypes. To measure
this, we maintained records of the accuracy for each
specific subtype in each dataset (Table 3).
In so doing, we observed that there are clear differ-
ences in how certain subtypes categorize. Typically the
subtypes A-D are easier to categorize than others. The
ACAA gives a more accurate classification on recombi-
nant subtypes, especially AE. Other subtypes, particu-
larly J, K, and U were problematic to classify in both
We observed in both algorithms that, while the accu-
racy for some subtypes increased as sequence length
increased, there were some subtypes which were more
accurately categorized when the sequence length was
shorter—the G subtype, for instance.
Overall, however, we find that the ACAA gives a more
consistently accurate categorization for the subtypes used
in this study than the STAR gives for all sequence lengths.
Table 2. Results of Analysis. This table shows a synopsis of the performance of the ACAA and STAR. Accuracy is the percentage of
sequences correctly classified, inaccuracy is the percentage incorrectly classified, and unclassified is the number of sequences which
were not assigned a category. The ACAA results are the average values from 20 runs of the algorithm, with the values in parentheses
being the results of the run which.
STAR accuracy STAR inaccuracy STAR unclassifiedACAA accuracyACAA inaccuracy ACAA unclassified
Dataset 1 47.3% 16.4% 36.3% 83.2% (85.6%) 6.9% (6.1%) 10.1% (8.2%)
Dataset 2 49.4% 16.9% 33.7% 67.1% (70.2%) 19.9% (16.9%) 13.0% (12.9%)
Dataset 3 18% 17% 65% 53.5% (57%) 27.3% (30.5%) 19.2% (19.5%)
Table 3. Subtype specific Results. This table shows the accuracy for each subtype for both the ACAA and the STAR. Results of the
ACAA are the average of the same twenty runs as used in Table 2.
Subtype A B C D F F1 G J K O U AE AG
Dataset 1
Dataset 2
Dataset 3
790 D. King et al. / J. Biomedical Science and Engineering 3 (2010) 785-790
Copyright © 2010 SciRes. JBiSE
We proposed to use ant-based clustering as a method to
categorize HIV-1 sequences according to subtype. We
developed the ACAA algorithm to utilize the approach
of anchoring test data on a topographic map in order to
categorize test data.
We ran our algorithm on three distinct datasets, con-
taining varied HIV-1 subtypes and sequence lengths. For
comparison, we also ran the STAR algorithm, a previ-
ously developed algorithm for HIV-1 subtype classifica-
tion, on each dataset.
We have demonstrated increased accuracy of the
ACAA algorithm over the STAR algorithm based on
HIV-1 subtype classification. Our results imply that the
ACAA is a viable alternative for the algorithmic classi-
fication of binary vector-based data.
We would like to thank Julia Handl for providing the original java code
of the ATTA, and also for her quick and helpful responses to our en-
quiries about the code.
We would also like to thank Thomas Leitner of the Los Alamos Na-
tional Laboratories HIV Database, who also responded to queries in an
expedient and helpful manner.
[1] Myers, E.R., et al. (2005) A stati stical model for HIV- 1
sequence classification using the subtype analyzer (STAR).
Bioinformatics, 21(17), 3535-3540.
[2] Oliveira, T., et al. (2005) An automated genotyping
system for analysis of HIV-1 and other microbial se-
quences. Bioinformatics, 21(19), 3797-380 0.
[3] Handl, J. (2003) Ant-based methods for tasks of cluster-
ing and topographic mapping: Improvements, evaluation
and comparison with alternative methods. Ph.D. Thesis,
Friedrich-Alexander University, Erlangen-Nürnberg.
[4] Chen, L., et al. (2004) An adaptive ant colony clustering
algorithm. Proceedings of the 3rd International Confer-
ence on Machine Learning and Cybernetics, Shanghai,
26-29 August 2004, 1387-1392.
[5] Deneubourg, J.L., et al. (1991) The dynamics of collec-
tive sorting: Robot-like ants and ant-like robots. Pro-
ceedings of the 1st International Conference on Simula-
tion of Adaptive Behavior: From Animals to Animats,
MIT Press, Cambridge, 1, 356-365.
[6] Handl, J., et al. (2004) Strategies for increased robustness
of ant-based clustering. Engineering Self-Organising Sys-
tems (Lecture Notes in Computer Science), 2977, 90-
[7] Handl, J., et al. (2004) Ant-based clustering and topog-
raphic mapping. Artificial Life, 12(1), 35-61.
[8] Lee, M., et al. (2007) An ant-based clustering system for
knowledge discovery in DNA chip analysis data. Pro-
ceedings of World Academy of Science, Engineering and
Technology, 32, 261-266.