PhD thesis proposal defended

The 1st of December I defended the doctorate thesis proposal, which was approved with important remarks for take into account. The most important comment was to define a more close problem to explore the proposed research, for example in an interest problem in histopathology.The other important remark was how evaluate the 3th stage of the proposed methodology addressed to knowledge discovery? definitly we need the experts (pathologists) to determine if is interesting, relevant or not the visual patterns that we find. Then, interaction with phicisians is a key issue for my phd research.
Now, I have many thing to deep, read, explore and understand. The proposal is just the first step to achieve my PhD. Whereas, I share the slides used, if it is of your interest, comments, feedback, etc. is welcome.

Doctoral Thesis Proposal: An Automatic Knowledge Discovery Strategy In Biomedical Images

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ICVSS 2011: Selected Presentations

ICVSS 2011: Selected Presentations

Angel Cruz and Andrea Rueda

Bioingenium Seminar 2011-II, August 25, 2011

This is a presentation to share the experiences and selected presentation from International Computer Vision Summer School (ICVSS2011) attended by Angel Cruz and Andrea Rueda from Bioingenium Research Group of Universidad Nacional de Colombia.ICVSS2011 Selected Presentations

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Beyond of pixels - ICVSS 2011 Report (Part 2)

Finally I publish the second (and last) part of ICVSS 2011 Report... thanks for your patience ;)

The lectures were very interesting by high-experience speakers in the state-of-art of computer vision. The speakers and the lectures acording with the final program were:

Monday 11

• Steven Seitz - Landmarks in 3D Computer Vision
• Steven Seitz - A Trillion Photos
• Ramesh Raskar - Computational Light Transport and Computational Photography: Camera Culture Inverse problems (slides)

Tuesday 12

• Jiri Matas - Tracking, Learning, Detection, Modeling All Working Together
• Ivan Laptev - Human Action Recognition
• Shmuel Peleg - Image Rearrangement & Video Synopsis

Wednesday 13

• Martial Hebert - Scene Understanding
• Guillermo Sapiro - The Life of Structured Learned Dictionaries
• Kari Pulli - Mobile Computational Photography with FCam

Thursday 14

• Steve Zucker - Visual Cortex and Perceptual Organization: what neurobiology can teach us about visual information processing
• Josef Sivic - Large Scale Visual Search for Particular Objects and Places
• Lorenzo Torresani - Efficient Novel-Class Recognition and Search

Friday 15

• Vitorrio Murino - Socially Intelligent Survillance and Monitoring
• William T. Freeman - Photographing Events over Time (Slides) (Video)
• Andrew Fitzgibbon - Convex and Nonlinear Optimization for Computer Vision

Hot topics in Computer Vision

• Large scale image/video analysis
• Inverse problems
• Image and video understanding
• Photo tourism
• Pose recognition & Kinect (Shotton, Fitzgibbon, Cook, Blake CVPR2011 PDF, supplementary material, videos, project)
• Survilence

Impressive works

Among these lectures some of works are amazing and really look like 'magic' :D. For example:

(Building Rome in a day)

(Photo bios - Face Movies Picassa)

More details and videos:

• Photo tourism (e.g. Building Rome in a Day, Finding paths though World's photos, Photosynth, PhotoCity)
• Towards Internet-scale Multi-view Stereo (video)
• Photobios (Video)
• Being John Malkovich
• Reconstructing Building Interiors from Images
• 3D Stereo Panorama
• Video Synopsis and Indexing
• Dynamosaics: Video Mosaics with Non-Chronological Time
• Shift-Map Image Editing

Some ideas and papers to check

• Multiple kernel learning (Non-linear model + feature combination)
• Winning recipe: Many features +non -linear classifiers (e.g. [Gehler and Nowozin, CVPR’09])

• Represent each image x in terms of its “closeness” to a set of basis classes (“classemes”)
• Classemes: a compact descriptor for efficient recognition [Torresani et al., 2010]

Final remarks

• Most of poster of Ph.D students were about computer vision, few works were related with medical imaging. Just one poster had a part of work with histopathological images (75. MACHINE LEARNING FOR TARGET DETECTION Vink J.P.).
• Other poster shows an interesting relation between two kind of graphical models, LDA (latent dirichled allocation) and population structure ( 68. FROM LDA TO VISION VIA POPULATION STRUCTURE Sharmanska V., Lampert C.H.).
• To work in progress, compare against the state of the art methods that the source code publicly available.
• Do not forget next time to bring business cards. This lesson had already learned in the CIARP2009 and forgot :S.
• The awards were won by some end of doctoral work, completed and / or published. No need to bring something totally original or preliminary results, especially if you are interested in the prize, at least one of these was 700 euros (not bad).
• I need to improve English. I could defend, but I still lack a lot, sometimes one feels limited to express some ideas, especially outside the technical and academic environment, such as lunches.
• You must travel light. Better a bag that two (especially in the metro).
• My final comment about the course is that it is highly recommended. The winning combination of conferences in the state of the art, high-level speakers, experts from around the world in computer vision, excellent food and wine, in a quiet place next to a beach along the Mediterranean sea, what more you want? ICVSS2012 Coming soon...

Curiosities

• Other two Colombian guys were in the school!!. They are doing their Ph.D in France and Belgium. Santiago Velasco and Jorge Niño.
• The Italians are superstitious, Alitalia's planes jumped from positions 12 to Post 14.
• Many participants wore shirts geeks, many of the participants passed it connected to the laptop and smart-phone with the pool and the beach nearby, there are more nerds than us :D jeje.
• The hotel had a bad internet connection was slow or had no connection, especially when they had the breaks between talks.
• There was plenty of delicious food and not go hungry:) Quite the contrary (it was buffet). In fact we ate particular things as horse meat and octopus in Catania and Ragusa respectively.

References

Torresani, L., Szummer, M., & Fitzgibbon, A. (2010). Efficient object category recognition using classemes. Computer Vision–ECCV 2010, 776–789. Springer. Retrieved from http://www.springerlink.com/index/800852076P3467J2.pdf

Griffin, G., & Perona, P. (2008). Learning and using taxonomies for fast visual categorization. Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on (pp. 1–8). IEEE. Retrieved from http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4587410

Bart, E., Porteous, I., Perona, P., & Welling, M. (2008). Unsupervised learning of visual taxonomies. Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on (pp. 1–8). IEEE. Retrieved from http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4587620

Sivic, J., Russell, B. C., Zisserman, A., Freeman, W. T., & Efros, A. A. (2008). Unsupervised discovery of visual object class hierarchies. Computer Vision and Pattern Recognition, 2008. CVPR 2008. IEEE Conference on (pp. 1–8). IEEE. Retrieved from http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4587622

Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945. Genetics Soc America. Retrieved from http://www.genetics.org/content/155/2/945.short

Beyond of pixels - ICVSS 2011 Report (Part 1)

I am back from de ICVSS2011 in Sicily (Italy), which was an amazing experience in several aspects attended by around of 160 Ph.D students and 15 speakers that work in the state-of-art in computer vision. Then, I want to share this experience in this post.

Before of ICVSS

The friday 8 of July Andrea Rueda and me traveled (in different flights) to Catania from Madrid. I arrived after of Andrea without know any of Italian but thanks of Google Maps and ask for the address showing a paper I finally find the accomodation place :)

The next day we went to Mount Etna which is imposing and impressive. At the end of this tour we can listen eruptions in the distance, the curious thing was that in the afternoon whereas waking in the center of Catania there was a volcanic ash rain clossing the airport all night. This was interesting but it was not a pleasant experience to feel the ash all over the body, because is like a very small and solid stone. Some of the students of ICVSS had to wait for the flight by the airport closed.

(volcanic ash cloud is comming)

(After of volcanic ash rain)

ICVSS starts

The sunday the bus was waitting for first group of ICVSS students that took us to the place of event. After of two hours of travel finally we are in Hotel Villagio Baia Samuele.

Poster sessions

The Summer School starts the monday with the lectures all day with poster session of two hours at the final. The difficult degree was thanks of the hot inside of both floors where the poster session was performed. It was exhausting, I don't stop to talk in the all session without any drop of water :(

But were more the good things :D, many people like our proposed approach, in fact one of the things that the people likes was the way which we adapt Bag of Features approach (originally of Computer Vision area) in our context to represent Histopathological images.

One first conclusion is that I must improve the overall method diagram, still it is not clear enought. The description of Nonnegative Matrix Factorization problem must be included in the poster and the automatic annotation method also, step-by-step. Some persons also like the combination of BOF with NMF and the analysis that allows NMF for latent factors as a part-based representation, however few people didn´t know NMF and the people that know it said that is interesting because NMF has been applied in other areas for text and object recognition but is not common in biomedical images.

(The poster and me)

The common remarks about this work were:

It is a little weirdo the performance results obtained by SVM in accuracy and precision, in contrast with recall measure

• Maybe clarify that the classifiers are binaries and put how the performance measures were calculated over the average by image. Maybe use another measures like area under ROC curve, because the SVM model performance could be change according to threshold defined in the predicted labels.

NMF doesn't provide an unique solution, then how it must be take into account with results in order to reproduce this results?. How it affects the results of each latent factor?. How we can obtain an unique solution with a global minima?

• That is true, NMF doesn´t provide an unique solution. However the different solution are very closed. Maybe we must check this aspect, but in average NMF have similar results. This could be included in the way to present the results in future experiments. Nonnegative Tensor Factorization is a generalization of NMF that guarantees an unique solution, we must review and test this method.

Is it database available publicly?

• A: This database is not publicly yet, we are working in release but this take some time. We have another database that is publicly available of histology with images of tissues annotated by four concepts (http://www.informed.unal.edu.co/histologyDS/).

Are you going to test their method with other (similar and publicly) datasets?

• Yes, we must test with another datasets in histopathology images with several annotation by image. In fact also we can try with other kind of biomedical images, e.g. radiological images like ImageClef Medical database.

How the dataset was built? Who performs the annotations?

• A set of samples of basal cell carcinoma stained with Hematoxylin-eosin were digitalized from microscopy at the same magnification, which were globally annotated by an expert physician in pathology.

Why you used NMF and SVD not? Why is important the nonnegative constraint over the matrix factors?

• Because NMF allows provide an interpretability layer of intermediate representation of images in latent space as a part-based representation in additive terms and not in terms of sums and substractions. The image, the concept or the latent factor is represented with mixtures in additive way of parts.

End of this part...

Designing poster for ICVSS 2011

Coming soon the ICVSS2011 will start and a poster about our preliminar results was accepted for its presentation.

A preliminar version was sent (see here in pdf) with the constraint that must be designed in LaTeX :S.

The second version (the last) is available here in pdf format or the image is depicted above (using the same template in latex):

(click in the image)

I just have two days for print the poster :O, so thanks in advance for your valuable and quickly feedback :$ . Apologies for that special request :)

Otro día del fin del mundo que se acaba...

Hoy 21 de Mayo de 2011, al igual que en 1994, otro fin del mundo había sido pronosticado por Harold Camping, cristiano y presidente de la emisora Family Radio (http://nymag.com/daily/intel/2011/05/a_conversation_with_harold_cam.html).

Es curioso como ha pesar de las innumerables veces que este día ha sido pronosticado erróneamente, la mayoría por líderes o fanáticos religiosos, aun existen personas que siguen creyendo en ellos, aun cuando se equivocan ellos mismos mas de una vez como Harol Camping. En medio de su locura, la gente fanática y creyentes de este tipo de profecías llegan a realizar cualquier cantidad de estupideces para purgar sus pecados por temor del final de los tiempos, incluso atentar contra su propia vida.

Para no gastarle tanta tinta simplemente termino este Blog compartiendo la respuesta de la pregunta obvia que uno se debe hacer siempre en estos caso, ¿Cuantos días de fin del mundo han sido pronosticados (erróneamente por supuesto) en la historia de la humanidad?, buscando en Google encontré este enlace en donde se resumen distintas fechas del fin del mundo: http://www.taringa.net/posts/noticias/1409367/Profecias-incumplidas-del-Fin-del-Mundo.html

Los dejo con algunas noticias un día después del fin del mundo. Feliz fin del mundo No. 382!!, espero que hayan aprovechado el día porque seguro vendrán mas profecías para celebrar otro día como hoy. Nos vemos en el día del juicio final... Bazinga! :D

http://www.voanews.com/english/news/Biblical-Soothsayer-Predicting-Worlds-Demise-but-Americans-Scoffing-122387634.html

http://www.cbsnews.com/stories/2011/05/21/eveningnews/main20065059.shtml

http://www.guardian.co.uk/world/2011/may/22/rapture-harold-camping-end-world

http://edition.cnn.com/2011/US/05/21/doomsday/?hpt=C2

Starting a new year: Between reasons and instincts

After of something more than a year without write in my blog, I think that a good way to start this year is follow my instinct. This instinct said me that I must share the introspection which I have in these last days of 2010 and two days starting this 2011.

I know that the most people did the same things in this season, review the goals reached, the failures, and planning the "new" list of objectives (normally are similar for all ¬¬). However one important conclusion that I have is that this list of goals are good, but is not enough. I mean, set goals is good for our lives in short and long time, but this question brings two problems that we don't take into account. The first is that we don't planning how to reach these goals (in general), and the end, when you evaluate them the number of goals are near the number of deceptions, which can be an unpleasant question. The second conclusion is we must not forget our instinct. Many times due to the routine, responsibilities, or other things, we repress some things that we want to do but finally we did not.

The two conclusions are related, because both can provide a disappointment or satisfaction. When we list the goals of year also we must planning how we reach them (step by step) in order to ensuring the goal. The time needed to reach each goal is different and we must take into account too. On the other hand, follow the instinct mean that, if we are doing the routine things and the tasks necessary to reach the planning goals and we have a feeling that we want to do something and we believe that we must do, just do it!. Try do it, is better than regretting not doing so.

Finally I just want that you keep in your mind these reflexions. Maybe you think that these are obvious but the point is put into practice. As far as I'm concerned, for years I've forgotten these thoughts and I just hope this year 2011 to start putting into practice the result of my introspection. To do this I hope to have a proper balance between my reason and instinct. Surely this will achieve different goals (both personal and professional) with the personal satisfaction of accomplishment.

Happy New Year!!! let omens aside, schedule and fight your goals, and don't forget to follow your instincts.