Added multilabel reader in LibSVMFile #2073

Jiaolong · 2014-03-23T15:11:54Z

There are several issues need to be discussed:
(1) Use SGVector or SGSparseVector to store labels. Currently, it is SGVector but there should be no trouble to change it into SGVector.

(2) There is just one unified function for parsing single-label and multi-label files. However, I kept the olde API of reading single-label file. So the SGSparseVector labels are converted internally. To move this converter outside, I guess many files dependent on the old API need to be changed.

@tklein23 @vigsterkr
For (1), if you all agree, I can use the unified type SGVector, since it is more compatible with @tklein23 requirement.

@vigsterkr
For(2), I need your help since I don't know how to put the converter outside and how many files need to be changed correspondingly. To be honest, I don't fully understand your design. But I think all the necessary code are already in LibSVMFile right now.

Jiaolong · 2014-03-26T07:55:28Z

@tklein23 @vigsterkr
I have changed the multiple label type into SGVector<float64_t>*.
The Travis reports all is well now.

Jiaolong · 2014-03-26T08:03:14Z

@vigsterkr

(1) when user tries to read singlelabel file by calling
get_sparse_matrix(..., float_64* label) , it is fine.

(2) when user tries to read multilabel file by calling
get_sparse_matrix(..., float_64* label) , it will report an error to remind using get_sparse_matrix(..., SGVector<float_64>* label)

(3) when user uses get_sparse_matrix(..., SGVector<float_64>* label), reading single-label and multilabel are both fine.

tklein23 · 2014-03-28T23:00:50Z

src/shogun/io/LibSVMFile.cpp

-	get_sparse_matrix(matrix, num_feat, num_vec, labels, false); \
+        SGVector<float64_t>* mat_label; \
+        int32_t num_classes; \
+        get_sparse_matrix(mat_feat, num_feat, num_vec, mat_label, num_classes, false); \
 }


I suggest "mat_label" to "labels" to align naming in both functions. Even better would be "multilabel", so the name is telling exactly what it will contain.

Yes, I will change the naming.

tklein23 · 2014-03-28T23:17:37Z

All-in-all it looks really cool. It's almost ready to merge.

I'm "just" missing: a simply unit test, that reads an example file and compares the resulting labels in a few cases:

a line with "empty" multilabel, i.e. no label
a line with a single label
a line with more than one label (sorting shouldn't be changed, duplicates are allowed)

Please run your test(s) in valgrind and check if memory is clean.

Jiaolong · 2014-03-29T07:25:20Z

@tklein23 Thanks for your comments. Yes, the unit test is quite necessary. I will update the code soon.

Jiaolong · 2014-03-31T12:12:59Z

@tklein23 I have updated the LibSVMFile:
(1) Multilabel writer is added
(2) Unit test is updated to cover the suggested cases. The example file is like:

2:5 4:10 6:4 8:1 10:8 12:7 14:2 16:0 18:6
0,0.1,0.2 2:2 4:9 6:9 8:8
0,0.1,0 2:6 4:5 6:7 8:3 10:6 12:3 14:4 16:10 18:8
0 2:4 4:10 6:4 8:10 10:7 12:8 14:4 16:6
1 2:2 4:0 6:2 8:0 10:4
0 2:1
1 2:6 4:5 6:5 8:4 10:0 12:5
-1 2:5
-1 2:2 4:2 6:2 8:10 10:1 12:6 14:7 16:10
0 2:9 4:1 6:10 8:5 10:9 12:0 14:2 16:4 18:9 20:8 22:2

hushell · 2014-03-31T17:05:23Z

examples/undocumented/libshogun/io_libsvm_multilabel.cpp

+		SG_SPRINT("Unable to open file: %s\n", fname);
+		return;
+	}
+        fclose(pfile);


an additional space here.

hushell · 2014-03-31T17:30:40Z

Just go through the code, don't understand why you change float64_t* to SGVector<float64_t>* in some places.

Jiaolong · 2014-03-31T17:42:06Z

@hushell Thanks for your comments. There are a lot of details I didn't check carefully. Regarding to your main concern float64_t and SGVector<float64_t>*, I have replied in the above section. I will update the code soon.

tklein23 · 2014-03-31T20:55:47Z

On Monday 31 March 2014 05:13:02 Jiaolong wrote:

@tklein23 I have updated the LibSVMFile:
(1) Multilabel writer is added
(2) Unit test is updated to cover the suggested cases. The example file is
like: ```
2:5 4:10 6:4 8:1 10:8 12:7 14:2 16:0 18:6
0,0.1,0.2 2:2 4:9 6:9 8:8
0,0.1,0 2:6 4:5 6:7 8:3 10:6 12:3 14:4 16:10 18:8
0 2:4 4:10 6:4 8:10 10:7 12:8 14:4 16:6
1 2:2 4:0 6:2 8:0 10:4
0 2:1
1 2:6 4:5 6:5 8:4 10:0 12:5
-1 2:5
-1 2:2 4:2 6:2 8:10 10:1 12:6 14:7 16:10
0 2:9 4:1 6:10 8:5 10:9 12:0 14:2 16:4 18:9 20:8 22:2

"empty" multilabels are valid es well; just a line that starts with a
space and then the features. Can you do that?

Jiaolong · 2014-03-31T21:04:43Z

@tklein23 Note that in the above example 2:5 4:10 6:4 8:1 10:8 12:7 14:2 16:0 18:6 is a sample with "empty" multilabels, but without a space at the head. Is it OK?

tklein23 · 2014-03-31T21:08:53Z

On Monday 31 March 2014 14:04:47 Jiaolong wrote:

@tklein23 Note that in the above example 2:5 4:10 6:4 8:1 10:8 12:7 14:2 16:0 18:6 is a sample with "empty" multilabels, but without a space at
the head. Is it OK?

I missed that. That's okay. (I guess the space is important to let
the parser distinguish between labels and features.)

Jiaolong · 2014-03-31T21:12:30Z

@tklein23 Given a space at the head, I think it can be parsed by the current code as well. Anyway, I will add this in the unit test.

tklein23 · 2014-03-31T21:13:59Z

If you ran some tests, let me know if it worked!

Jiaolong · 2014-03-31T21:20:55Z

@tklein23 There is an example in libshogun: io_libsvm_multilabel, which reads and displays multilabels from yeast dataset. I pasted the output as follows:

......
vector=[0,1,11,12]
vector=[1,2,6,7,11,12]
vector=[0,1,5,6,10,11]
Number of the samples: 917
Dimention of the feature: 103
Number of classes: 14

Jiaolong · 2014-04-01T22:39:23Z

@tklein23 I got a Travis error:
The command "git fetch origin +refs/pull/2073/merge:" failed
https://travis-ci.org/shogun-toolbox/shogun/jobs/22037649

Could you help me to check it? I only changed the format issue and the previous versions have all passed the Travis test.

Jiaolong · 2014-04-01T23:47:21Z

@tklein23 For the memory leak issue, I pasted the the valgrind output in gist
https://gist.github.com/Jiaolong/9925271
Thank you very much!

tklein23 · 2014-04-01T23:51:39Z

examples/undocumented/libshogun/io_libsvm_multilabel.cpp

+ */
+#include <shogun/io/LibSVMFile.h>
+#include <shogun/lib/SGVector.h>
+#include <shogun/lib/SGVector.h>


Including SGVector.h more than once? ;)

Jiaolong · 2014-04-02T11:07:51Z

@tklein23 I have updated the code with minor changes. Now the tests are passed.

Added multilabel reader in LibSVMFile - thanks to Jiaolong

tklein23 reviewed Mar 28, 2014
View reviewed changes

hushell reviewed Mar 31, 2014
View reviewed changes

Jiaolong added 2 commits April 1, 2014 16:17

Added multilabel reader in LibSVMFile.

7903a39

Added multilabel writer in LibSVMFile. Updated LibSVMFile unit test.

80d2bb1

tklein23 reviewed Apr 1, 2014
View reviewed changes

Jiaolong closed this Apr 2, 2014

Jiaolong deleted the io_multilabel branch April 2, 2014 09:02

Jiaolong reopened this Apr 2, 2014

Corrected indent issues and memory leak.

309fc08

tklein23 added a commit that referenced this pull request Apr 3, 2014

Merge pull request #2073 from Jiaolong/io_multilabel

a9c4864

Added multilabel reader in LibSVMFile - thanks to Jiaolong

tklein23 merged commit a9c4864 into shogun-toolbox:develop Apr 3, 2014

tklein23 mentioned this pull request Apr 3, 2014

Add reader/writer for MultilabelLabels #1987

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Added multilabel reader in LibSVMFile #2073

Added multilabel reader in LibSVMFile #2073

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Added multilabel reader in LibSVMFile #2073

Added multilabel reader in LibSVMFile #2073

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