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Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison.
Results
We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach.
Conclusion
In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.
Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.
This paper outlines the design and testing of a z-scan spectrometer capable of measuring the third order refraction index of liquids. The spectrometer underwent multiple redesigns, with each explored in this paper with their benefits and drawbacks discussed. The first design was capable of measuring the third order refraction index for glass, and found a value of 8.43 +- 0.392 x 10^(-16) cm^2/W for the glass sample, with the literature stating glass has a refraction index between 1-100 x 10^(-16) cm^2/W. The second design was capable of measuring the third order refraction index of liquids, and found values of 1.23 $\pm$ 0.121 $\e{-16}$ and 9.43 +- 1.00 x 10^(-17) cm^2/W for water and ethanol respectively, with literature values of 2.7 x 10^(-16) and 5.0 x 10^(-17) cm^2/W respectively. The third design gave inconclusive results due to extreme variability in testing, and and the fourth design outlined has not been tested yet due to time constraints.
Affective computing allows computers to monitor and influence people’s affects, in other words emotions. Currently, there is a lot of research exploring what can be done with this technology. There are many fields, such as education, healthcare, and marketing, that this technology can transform. However, it is important to question what should be done. There are unique ethical considerations in regards to affective computing that haven't been explored. The purpose of this study is to understand the user’s perspective of affective computing in regards to the Association of Computing Machinery (ACM) Code of Ethics, to ultimately start developing a better understanding of these ethical concerns. For this study, participants were required to watch three different videos and answer a questionnaire, all while wearing an Emotiv EPOC+ EEG headset that measures their emotions. Using the information gathered, the study explores the ethics of affective computing through the user’s perspective.
Cryptojacking is a process in which a program utilizes a user’s CPU to mine cryptocurrencies unknown to the user. Since cryptojacking is a relatively new problem and its impact is still limited, very little has been done to combat it. Multiple studies have been conducted where a cryptojacking detection system is implemented, but none of these systems have truly solved the problem. This thesis surveys existing studies and provides a classification and evaluation of each detection system with the aim of determining their pros and cons. The result of the evaluation indicates that it might be possible to bypass detection of existing systems by modifying the cryptojacking code. In addition to this classification, I developed an automatic code instrumentation program that replaces specific instructions with functionally similar sequences as a way to show how easy it is to implement simple obfuscation to bypass detection by existing systems.
This research endeavor explores the 1964 reasoning of Irish physicist John Bell and how it pertains to the provoking Einstein-Podolsky-Rosen Paradox. It is necessary to establish the machinations of formalisms ranging from conservation laws to quantum mechanical principles. The notion that locality is unable to be reconciled with the quantum paradigm is upheld through analysis and the subsequent Aspect experiments in the years 1980-1982. No matter the complexity, any local hidden variable theory is incompatible with the formulation of standard quantum mechanics. A number of strikingly ambiguous and abstract concepts are addressed in this pursuit to deduce quantum's validity, including separability and reality. `Elements of reality' characteristic of unique spaces are defined using basis terminology and logic from EPR. The discussion draws directly from Bell's succinct 1964 Physics 1 paper as well as numerous other useful sources. The fundamental principle and insight gleaned is that quantum physics is indeed nonlocal; the door into its metaphysical and philosophical implications has long since been opened. Yet the nexus of information pertaining to Bell's inequality and EPR logic does nothing but assert the impeccable success of quantum physics' ability to describe nature.