Towards Image-based Cancer Cell Lines Authentication Using Deep Neural Networks

Although short tandem repeat (STR) analysis is available as a reliable method for the determination of the genetic origin of cell lines, the occurrence of misauthenticated cell lines remains an important issue. Reasons include the cost, effort and time associated with STR analysis. Moreover, there are currently no methods for the discrimination between isogenic cell lines (cell lines of the same genetic origin, e.g. different cell lines derived from the same organism, clonal sublines, sublines adapted to grow under certain conditions). Hence, additional complementary, ideally low-cost and low-effort methods are required that enable 1) the monitoring of cell line identity as part of the daily laboratory routine and 2) the authentication of isogenic cell lines. In this research, we automate the process of cell line identification by image-based analysis using deep convolutional neural networks. Two different convolutional neural networks models (MobileNet and InceptionResNet V2) were trained to automatically identify four parental cancer cell line (COLO 704, EFO-21, EFO-27 and UKF-NB-3) and their sublines adapted to the anti-cancer drugs cisplatin (COLO-704rCDDP1000, EFO-21rCDDP2000, EFO-27rCDDP2000) or oxaliplatin (UKF-NB-3rOXALI2000), hence resulting in an eight-class problem. Our best performing model, InceptionResNet V2, achieved an average of 0.91 F1-score on 10-fold cross validation with an average area under the curve (AUC) of 0.95, for the 8-class problem. Our best model also achieved an average F1-score of 0.94 and 0.96 on the authentication through a classification process of the four parental cell lines and the respective drug-adapted cells, respectively, on a four-class problem separately. These findings provide the basis for further development of the application of deep learning for the automation of cell line authentication into a readily available easy-to-use methodology that enables routine monitoring of the identity of cell lines including isogenic cell lines. It should be noted that, this is just a proof of principal that, images can also be used as a method for authentication of cancer cell lines and not a replacement for the STR method

PROFILING - CONCEPTS AND APPLICATIONS

Profiling is an approach to put a label or a set of labels on a subject, considering the characteristics of this subject. The New Oxford American Dictionary defines profiling as: “recording and analysis of a person’s psychological and behavioral characteristics, so as to assess or predict his/her capabilities in a certain sphere or to assist in identifying a particular subgroup of people”. This research extends this definition towards things demonstrating that many methods used for profiling of people may be applied for a different type of subjects, namely things. The goal of this research concerns proposing methods for discovery of profiles of users and things with application of Data Science methods. The profiles are utilized in vertical and 2 horizontal scenarios and concern such domains as smart grid and telecommunication (vertical scenarios), and support provided both for the needs of authorization and personalization (horizontal usage).:The thesis consists of eight chapters including an introduction and a summary. First chapter describes motivation for work that was carried out for the last 8 years together with discussion on its importance both for research and business practice. The motivation for this work is much broader and emerges also from business importance of profiling and personalization. The introduction summarizes major research directions, provides research questions, goals and supplementary objectives addressed in the thesis. Research methodology is also described, showing impact of methodological aspects on the work undertaken. Chapter 2 provides introduction to the notion of profiling. The definition of profiling is introduced. Here, also a relation of a user profile to an identity is discussed. The papers included in this chapter show not only how broadly a profile may be understood, but also how a profile may be constructed considering different data sources. Profiling methods are introduced in Chapter 3. This chapter refers to the notion of a profile developed using the BFI-44 personality test and outcomes of a survey related to color preferences of people with a specific personality. Moreover, insights into profiling of relations between people are provided, with a focus on quality of a relation emerging from contacts between two entities. Chapters from 4 to 7 present different scenarios that benefit from application of profiling methods. Chapter 4 starts with introducing the notion of a public utility company that in the thesis is discussed using examples from smart grid and telecommunication. Then, in chapter 4 follows a description of research results regarding profiling for the smart grid, focusing on a profile of a prosumer and forecasting demand and production of the electric energy in the smart grid what can be influenced e.g. by weather or profiles of appliances. Chapter 5 presents application of profiling techniques in the field of telecommunication. Besides presenting profiling methods based on telecommunication data, in particular on Call Detail Records, also scenarios and issues related to privacy and trust are addressed. Chapter 6 and Chapter 7 target at horizontal applications of profiling that may be of benefit for multiple domains. Chapter 6 concerns profiling for authentication using un-typical data sources such as Call Detail Records or data from a mobile phone describing the user behavior. Besides proposing methods, also limitations are discussed. In addition, as a side research effect a methodology for evaluation of authentication methods is proposed. Chapter 7 concerns personalization and consists of two diverse parts. Firstly, behavioral profiles to change interface and behavior of the system are proposed and applied. The performance of solutions personalizing content either locally or on the server is studied. Then, profiles of customers of shopping centers are created based on paths identified using Call Detail Records. The analysis demonstrates that the data that is collected for one purpose, may significantly influence other business scenarios. Chapter 8 summarizes the research results achieved by the author of this document. It presents contribution over state of the art as well as some insights into the future work planned

Advanced Biometrics with Deep Learning

Biometrics, such as fingerprint, iris, face, hand print, hand vein, speech and gait recognition, etc., as a means of identity management have become commonplace nowadays for various applications. Biometric systems follow a typical pipeline, that is composed of separate preprocessing, feature extraction and classification. Deep learning as a data-driven representation learning approach has been shown to be a promising alternative to conventional data-agnostic and handcrafted pre-processing and feature extraction for biometric systems. Furthermore, deep learning offers an end-to-end learning paradigm to unify preprocessing, feature extraction, and recognition, based solely on biometric data. This Special Issue has collected 12 high-quality, state-of-the-art research papers that deal with challenging issues in advanced biometric systems based on deep learning. The 12 papers can be divided into 4 categories according to biometric modality; namely, face biometrics, medical electronic signals (EEG and ECG), voice print, and others

CHEATING DETECTION IN ONLINE EXAMS BASED ON CAPTURED VIDEO USING DEEP LEARNING

Today, e-learning has become a reality and a global trend imposed and accelerated by the COVID-19 pandemic. However, there are many risks and challenges related to the credibility of online exams which are of widespread concern to educational institutions around the world. Online exam system continues to gain popularity, particularly during the pandemic, due to the rapid expansion of digitalization and globalization. To protect the integrity of the examination and provide objective and fair results, cheating detection and prevention in examination systems is a must. Therefore, the main objective of this thesis is to develop an effective way of detection of cheating in online exams. In this work, a system to track and prevent attempts to cheat on online exams is developed using artificial intelligence techniques. The suggested solution uses the webcam that is already connected to the computer to record videos of the examinee in real time and afterwards analyze them using different deep learning methods to find best combinations of models for face detection and classification if cheating/not cheating occurred. To evaluate the system, we use a benchmark dataset of exam videos from 24 participants who represented examinees in online exam. An object detection technique is used to detect face appeared in the image and crop the face portion, and then a deep learning based classification model is trained from the images to classify a face as cheating or not cheating. We have proposed an effective combination of data preprocessing, object detection, and classification models to obtain high detection accuracy. We believe that the suggested invigilation methodology can be used in colleges, institutions, and schools to look for and keep an eye on suspicious student behavior. Hopefully, by putting the proposed invigilation method into place, we can aid in eliminating and reducing cheating incidences as it undermines the integrity and fairness of the educational system

Information embedding and retrieval in 3D printed objects

Deep learning and convolutional neural networks have become the main tools of computer vision. These techniques are good at using supervised learning to learn complex representations from data. In particular, under limited settings, the image recognition model now performs better than the human baseline. However, computer vision science aims to build machines that can see. It requires the model to be able to extract more valuable information from images and videos than recognition. Generally, it is much more challenging to apply these deep learning models from recognition to other problems in computer vision. This thesis presents end-to-end deep learning architectures for a new computer vision field: watermark retrieval from 3D printed objects. As it is a new area, there is no state-of-the-art on many challenging benchmarks. Hence, we first define the problems and introduce the traditional approach, Local Binary Pattern method, to set our baseline for further study. Our neural networks seem useful but straightfor- ward, which outperform traditional approaches. What is more, these networks have good generalization. However, because our research field is new, the problems we face are not only various unpredictable parameters but also limited and low-quality training data. To address this, we make two observations: (i) we do not need to learn everything from scratch, we know a lot about the image segmentation area, and (ii) we cannot know everything from data, our models should be aware what key features they should learn. This thesis explores these ideas and even explore more. We show how to use end-to-end deep learning models to learn to retrieve watermark bumps and tackle covariates from a few training images data. Secondly, we introduce ideas from synthetic image data and domain randomization to augment training data and understand various covariates that may affect retrieve real-world 3D watermark bumps. We also show how the illumination in synthetic images data to effect and even improve retrieval accuracy for real-world recognization applications

Insights into the role of gender in aesthetic design: a participatory study on the design of digital health wearables

The role of artificial intelligence (AI) in facilitating the real-time processing of data is revolutionising the future of healthcare through mobile diagnostics, remote monitoring devices, and wearable technology products. The rise in digital wearables for remote healthcare is evolving at an increasing pace towards patient-centred and personalised care with connected patients. This transformation is creating new opportunities for designers to increase patients' participation and sustain their engagement in remote healthcare. In this paper, the authors have investigated the role of gender in aesthetic design in the context of digital health wearables to enhance user engagement and interaction. The investigations were conducted through participatory design sessions and showed a constructive relationship between aesthetic preferences and understanding the influence of gender as a means of facilitating user engagement with digital health wearables. This paper presents a novel user response model that leads to suggestions for future work, including research in the areas of gender awareness in aesthetics to move beyond traditional, stereotypical, and pre-identified gendered characteristics related to femininity and masculinity. The findings conclude with a path forwards for design research to promote gender awareness in aesthetic design for the realisation of healthcare wearables of the future

Change blindness: eradication of gestalt strategies

Arrays of eight, texture-defined rectangles were used as stimuli in a one-shot change blindness (CB) task where there was a 50% chance that one rectangle would change orientation between two successive presentations separated by an interval. CB was eliminated by cueing the target rectangle in the first stimulus, reduced by cueing in the interval and unaffected by cueing in the second presentation. This supports the idea that a representation was formed that persisted through the interval before being 'overwritten' by the second presentation (Landman et al, 2003 Vision Research 43149–164]. Another possibility is that participants used some kind of grouping or Gestalt strategy. To test this we changed the spatial position of the rectangles in the second presentation by shifting them along imaginary spokes (by ±1 degree) emanating from the central fixation point. There was no significant difference seen in performance between this and the standard task [F(1,4)=2.565, p=0.185]. This may suggest two things: (i) Gestalt grouping is not used as a strategy in these tasks, and (ii) it gives further weight to the argument that objects may be stored and retrieved from a pre-attentional store during this task

A locally activatable sensor for robust quantification of organellar glutathione

Glutathione (GSH) is the main determinant of intracellular redox potential and participates in multiple cellular signalling pathways. Achieving a detailed understanding of intracellular GSH homeostasis depends on the development of tools to map GSH compartmentalization and intra-organelle fluctuations. Here we present a GSH-sensing platform for live-cell imaging, termed targetable ratiometric quantitative GSH (TRaQ-G). This chemogenetic sensor possesses a unique reactivity turn-on mechanism, ensuring that the small molecule is only sensitive to GSH in a desired location. Furthermore, TRaQ-G can be fused to a fluorescent protein to give a ratiometric response. Using TRaQ-G fused to a redox-insensitive fluorescent protein, we demonstrate that the nuclear and cytosolic GSH pools are independently regulated during cell proliferation. This sensor was used in combination with a redox-sensitive fluorescent protein to quantify redox potential and GSH concentration simultaneously in the endoplasmic reticulum. Finally, by exchanging the fluorescent protein, we created a near-infrared, targetable and quantitative GSH sensor