The New PhD

Les comparto una interesante nota sobre un tipo de doctorado en ingeniería que esta emergiendo y se esta haciendo necesario cada vez mas en la actualidad, en particular en paises como el nuestro (Colombia), para adquirir habilidades tanto de investigación como negocios con el fin de proprender por la generación de empresas, starp-ups y spin-offs, de base tecnológica e innovación.

The New PhD

Student entrepreneurship and a dearth of academic jobs prompt schools to re-engineer doctoral programs for the business world

http://www.prism-magazine.org/jan13/feature_02.cfm

"..., the majority of today’s new Ph.D. engineers face a tough choice: They can seek temporary and comparatively low-paid postdoctoral fellowships, or look to industry, which has tended to view research-trained doctoral graduates as destined for academe and therefore an unlikely fit. ..."

"But now, a number of institutions have begun to prepare Ph.D. engineers to grasp opportunities and thrive in the industrial, commercial, and business worlds, either as employees of large or small enterprises or as entrepreneurs seeking to turn their own research into marketable products."

2012 Year Balance / Balance del Año 2012

(English)

Finally the world does not end and many superstitious people ends disappointed, as we expected. Anyway, it not was the last date of end of world that the 'prophets' and multiple media exploit with questionable purposes. Meanwhile the world keeps turning, and as another year is over it's time to take a balance of the past year.

• A publication was achieved in conference MICCAI'2012, the most important conference on medical imaging. A paper in Digital Pathology that was achieved thanks to a collaboration between our research group Bioingenium and Laboratory for Computational Imaging & Bioinformatics - Rutgers University LCIB. In total there were four international and four national publications, this year we will hope and work for journal publications :)
• Thanks to a year's work of a team led by Professor Fabio González and Raúl Ramos postdoc, born BIGS, a framework for image processing and machine learning using large-scale parallel computing power to use power computing any environment, from a computer room, clusters or cloud. Available in www.3igs.org
• This was my first year as a beneficiary of the credit-grant from Colciencias and really was a very good decision. I can be 100% focused on my PhD with the reassurance of full funding (tuition and maintenance). It is one of the recommended options for doctoral study, since it is a credit (not forget) but can be 100% forgivable.
• Thanks to a conference where my wife presented a work about e-learning in education, we met Panama City, a great experience where we were The Panama Canal, ate good food, and saw old buildings and giant skyscrapers. A city of contrasts (mainly economic and social issues)
• Thanks to the article presented in MICCAI I was in Nice, conference venue, a very beautiful city of 'Côte d'Azur' in France, where I met incidentally Monaco (where one of my favorite GP of Formula One). Definitely another world where Ferraris, Maseratis, Jaguars, Porsches and Alpha Romeos roam the streets with impunity :D.
• Finally I could take my parents and my brother to San Andrés, a beautiful Caribbean paradise of our Colombia to visit and enjoy. This trip was an old purpose which I had and was finally done thanks of my wife's support, which I'm very grateful. :) Was great!
• Starting this 2013, my wife and me had the pleasure of visiting Leticia (Amazonas) and we were that other natural paradise, a wonderful experience in the majestic Colombian Amazon jungle, beautiful and varied wildlife, and delicious food. Excellent choice of ecotourism. Recommended!

It was a great year and certainly this new year will be no exception, I start very motivated and eager to move forward with my PhD and other personal purposes. One of them, I'm interested in sharing and call, it's to play a more active role in the socialization and dissemination of science and education, and to promote critical thinking and skepticism in our society. We all have something to give to improve our society, we contribute something. :)

Happy new year!


(Español)

Finalmente el mundo no se acabo y mucho supersticioso termino decepcionado, como era de esperarse. De todas formas no será la última fecha del fin del mundo que los 'profetas' y medios explotan con múltiples y cuestionables objetivos. Mientras tanto el mundo seguirá girando, y como otro año ha terminado es momento para hacer el balance del año pasado.

• Se logró una publicación en la conferencia principal de MICCAI'2012, la más importante conferencia en imagen médica. Un trabajo en Digital Pathology que se logró gracias a una colaboración entre nuestro grupo de investigación Bioingenium y 'Laboratory for Computational Imaging & Bioinformatics - LCIB Rutgers University'. En total fueron 4 publicaciones internacionales y 4 nacionales, este año aspiramos y trabajaremos por las publicaciones de journal :)
• Gracias a un año de trabajo de todo un equipo, liderado por el profesor Fabio González y el posdoc Raúl Ramos, nació BIGS, un framework para el procesamiento de imágenes y aprendizaje de máquina a gran escala usando el poder computacional en paralelo para usar el poder de cómputo de cualquier entorno, desde una sala de informática, clusters o computación en la nube. Disponible en www.3igs.org
• Este fue mi primer año como beneficiario del crédito-beca de Colciencias y realmente fue una muy buena decisión. Puedo estar concentrado 100% en mi doctorado con la tranquilidad de la financiación completa (matrícula y sostenimiento). Es una de las opciones recomendadas para estudiar doctorado, puesto que es un crédito (no olvidarlo) pero que puede ser 100% condonable.
• Gracias a una conferencia donde presentó mi esposa un trabajo en e-learning, conocimos Ciudad de Panamá, una gran experiencia donde conocimos el canal, probamos buena comida, y vimos antiguas construcciones y gigantescos rascacielos. Una ciudad de contrastes (principalmente económicos y sociales)
• Gracias al artículo de MICCAI estuve en Niza, lugar de la conferencia, muy bonita ciudad de Côte d'Azur de Francia, donde de paso conocí Mónaco (donde esta una de mis pistas favoritas de F1). Definitivamente otro mundo en donde los Ferraris, Maseratis, Jaguars, Porsches y Alpha Romeos se pasean impunemente en las calles :D.
• Finalmente pude llevar a mis padres y mi hermano a San Andrés, un hermoso paraíso caribeño de nuestra Colombia para visitar y disfrutar. Este viaje era ya un viejo propósito que tenía y que finalmente se pudo dar gracias al apoyo conjunto de mi esposa, de lo cual estoy muy agradecido. :) la pasamos genial!
• Empezando este 2013, tuvimos el gusto de visitar Leticia (Amazonas) y conocer este otro paraíso natural, una maravillosa experiencia en la majestuosa selva amazónica colombiana, hermosa y variada fauna, así como deliciosa comida. Excelente opción de ecoturismo. Recomendado!

Fue un gran año y de seguro este nuevo año no será la excepción, empiezo muy motivado y con muchas ganas de sacar adelante mi doctorado y demás propósitos personales. Uno de ellos, que me interesa compartir y convocar, es jugar un rol más activo en la socialización y divulgación de la ciencia y la educación, así en promover el pensamiento crítico y escéptico en nuestra sociedad. Todos tenemos algo que dar para mejorar nuestra sociedad, aportemos algo. :)

Feliz año!

2011 Year Balance

One month after started a new year I look back motivated by a previous blog in order to analyse if was an appropriate approach a balance between reason and instinct to achieve the goals (professional and personal) with personal satisfaction.  The main goals were:

• I defended my M.Sc. thesis successfully with meritorious mention. One of the academic challenges achieved.
• I traveled for first time to Europe (I knew Spain, Italy and Portugal). This was an amazing experience.
• I did my first internship outside in other lab in CETA-Ciemat (Trujillo, Spain) working in Grid Computing. Other people and other kind of challenges, a complete and enrich experience.
• I attended to my first summer school in ICVSS2011 (Sicily, Italy). This great moment was detailed in [Part 1, Part 2]
• I defended my PhD thesis proposal successfully.
• I get married with Diana Marcela Cardona (the most excited moment of year for me :D), in fact she also defended her M.Sc. thesis in last days and I am very proud of her :)
• I was selected by Colciencias for a National PhD grant (508/2011).

So I am pleased and happy by the last year :), this was an amazing year for me, and I have learned a lot and I have expanded my vision. 

I just hope this new year is not the end of the world as many people naively think, but rather be a year of many successes, growth and progress with new goals and challenges living fully and with passion balancing between reason and instinct.

That all may have a great 2012 (if not the world ends ¬¬ ')

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...