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.

CIARP 2009 - Report

After having returned from CIARP2009 in Guadalajara, MX in which I present in poster modality the paper Visual Pattern Analysis in Histopathology Images Using Bag of Features and then to return to work and academic activities (including assisting the SIB-SIPAIM 2009) I describe what I'm experience both academically and personally in my first trip abroad.

Feedback

I must thank in first place to Francisco Gomez for preparation before of poster presentation in 30 seconds, it was really useful to present the idea in such a short time. Moreover, in the poster session I present on several occasions this work (I was lucky that everyone were from hispanoamerica, so it was in Spanish jeje: P). The main remarks were about the possibility of building the visual vocabulary automatically by a method of unsupervised clustering, as control or linking semantic information and the magnification of the images, and finally on the methodology designed for automatic annotation tasks.

Works of interes

• Texture analysis methods and applications. Prof. Maria Petrou University of Cambridge, UK. This was an interesting tutorial about texture analysis and description methods, also she shows your book about this. This is very important for the relationship with histology images for tissue description.
• We are Building a Topological Pyramid. Prof. Walter G. Kropatsch. Vienna University of Technology, Viena. This was other interesting tutorial about graph representation of objects in image processing for segmentation and others using topological and connectivity information in order to reduce this representation.
• Randomized Probabilistic Latent Semantic Analysis for Scene Recognition. Erik Rodner and Joachim Denzler. This was an interesting work that use bag of feature and pLSA for image categorization in natural scene images.
• Classifier Selection in a Family of Polyhedron Classifiers. Tetsuji Takahashi, Mineichi Kudo and Atsuyoshi Nakamura. An interesting paper where the authors proposed a classifiers for SVM where choose the decision space with polyhedrons that reduce the convex hull with relative better results.
• Clustering Ensemble Method for Heterogeneous Partitions. Sandro Vega-Pons and José Ruiz-Shulcloper. This work is about clustering method addressed to ensemble for heterogeneous partitions. The application in hierarchical clustering can be explored.
• Improved Online Support Vector Machines Spam Filtering Using String Kernels. Ola Amayri and Nizar Bouguila. Good paper about machine learning using string kernels and Transductive Support Vector Machines. The more interesting of this work is the exhaustive experimentation and configuration setup.
• A New Incremental Algorithm for Overlapped Clustering. Airel Pérez Suárez, José Fco. Martínez Trinidad, Jesús A. Carrasco Ochoa, and José E. Medina Pagola. This is a good work about incremental clustering, very useful when we have large datasets and when a new data arrive, we don't want the clustering again. Closely related with our work and maybe a collaborative work is possible.

The procedings of CIARP2009 are available here.

Contacts

Ioannis A. Kakadiaris, Ph.D. He is Director of Computational Biomedicine Laboratory and Division of Bioimaging and Biocomputation Institute for Digital Informatics and Analysis at University of Houston, Houston, Texas, USA. He was the only keynote speaker who works in biomedical imaging. We spoke about cardiac image problems in 4D (spatial and time resolution trade-off) and the possibility of collaborative work and an invitation to Bioingenium Reseach Group for similiar research topics, to which he showed interest and possibilities under its schedule.

Lic. Airel Perez Suarez. He is a reseacher in computer science of Centro de Aplicaciones de Tecnologías Avanzadas (CENATAV). He works in data minning and information retrieval. He shows a paper about incremental algorithm for overlapped clustering and he is interested in test your algorithm with our histology images dataset and visual words for collaborative works.

Dr. José Ruiz Shulcloper. He is Director of Centro de Aplicaciones de Tecnologías Avanzadas (CENATAV) and president of the Cuban Association for Pattern Recognition. He invite us to start the fundation of Colombian Association for Pattern Recognition in order to enter at International Association of Pattern Recognition (IAPR). For this, he said that we can to start from an actual association related with pattern recognition (for example, Sociedad Colombiana de Computación), only we must send the information request for this purpose to your mail.

Erik Rodner. He is rearcher in chair of computer vision from Institute of Computer Science at University of Jena. He shows two works, one about image categorization using Bag of Features in natural scene images and object recognition using a visual feature combination with bag of features from 2D and 3D images.

Note: For future conferences is very important to carry presentation cards.

Photos

The Poster and me (academic evidence)

Pyramid of the sun, Teotihuacan. (evidence tourist)

El Lago, Chapultepec Forest. (like a picture-postcard)

Final version of CIARP poster

Hi, finally I publish the final version of CIARP Poster. Excuse me the delay. I appreciate the comment, because tomorrow I going to print. The saturday is the travel!! :P. The flickr link to more specific annotation is here.

Designing the poster for CIARP

Hi buddies, in a few days I hope to be in Guadalajara presenting a poster about the work that was accepted at 14th Iberoamerican Congress of Pattern Recognition. For this reason I must do it and I started to design it. So, I show the preliminar design to give me your opinion to improve it. Thank you very much.

The image is avaliable also in Flickr here.