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2.
  • Abbasi, Ahtisham Fazeel, et al. (creator_code:aut_t)
  • Deep learning architectures for the prediction of YY1-mediated chromatin loops
  • 2023
  • record:In_t: Bioinformatics research and applications. - : Springer. - 9789819970735 - 9789819970742 ; , s. 72-84
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • YY1-mediated chromatin loops play substantial roles in basic biological processes like gene regulation, cell differentiation, and DNA replication. YY1-mediated chromatin loop prediction is important to understand diverse types of biological processes which may lead to the development of new therapeutics for neurological disorders and cancers. Existing deep learning predictors are capable to predict YY1-mediated chromatin loops in two different cell lines however, they showed limited performance for the prediction of YY1-mediated loops in the same cell lines and suffer significant performance deterioration in cross cell line setting. To provide computational predictors capable of performing large-scale analyses of YY1-mediated loop prediction across multiple cell lines, this paper presents two novel deep learning predictors. The two proposed predictors make use of Word2vec, one hot encoding for sequence representation and long short-term memory, and a convolution neural network along with a gradient flow strategy similar to DenseNet architectures. Both of the predictors are evaluated on two different benchmark datasets of two cell lines HCT116 and K562. Overall the proposed predictors outperform existing DEEPYY1 predictor with an average maximum margin of 4.65%, 7.45% in terms of AUROC, and accuracy, across both of the datases over the independent test sets and 5.1%, 3.2% over 5-fold validation. In terms of cross-cell evaluation, the proposed predictors boast maximum performance enhancements of up to 9.5% and 27.1% in terms of AUROC over HCT116 and K562 datasets.
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3.
  • Abdipour, Morteza, et al. (creator_code:aut_t)
  • A Design Research Lab—An Integrated Model to Identify Conscious and Unconscious Behavior in the Design Process
  • 2016
  • record:In_t: Advances in Design for Inclusion. - Cham : Springer. - 9783319419619 - 9783319419626
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • To understand how different design solutions affect users, designers traditionally use different evaluation methods that mainly rely on conscious feedback from the users. However, the complexity of human behaviour, where a large part is unconscious, point to a need for an extended tool box addressing the part not accessible to human conscious knowledge. Here, we describe a design research lab where traditional methods are complemented with tools to measure physiological signals influenced by emotional and sympathetic responses. These tools include galvanic skin response (GSR), electrocardiograph (ECG), and electroencephalograph (EEG). Typical sessions with acquired data of conscious and unconscious user reactions are described. The large body of data collected, which also require non-design expertise for interpretation, suggest that a further development towards simplified output data of the unconscious reactions is needed to allow wider use within industrial design work.
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4.
  • Abdipour, Morteza (creator_code:aut_t)
  • User Participatory Design Evaluation and Education through Design Lab
  • 2019
  • swepub:Mat_conferencepaper_t (swepub:level_scientificother_t)abstract
    • This paper presents the possibilities of a design lab that can be used in evaluation processes for different design subjects in design education. Three student projects from different domains are studied to explore how utilizing a design lab for user involvement can affect the design process. The Design Lab is situated at Mid Sweden University and can project images, video and online materials on three walls and provide sound. Different tools to collect data are available, such as video cameras, equipment for psychophysical measurement and software for analysis. The studies show that design students can use the lab to prototype different scenarios or environments as well as to display large subjects at an appropriate scale. The study found that the Design Lab offers possibilities to involve diverse groups of users, such as people with disabilities, the elderly and even dogs, which gave the students the possibility to obtain feedback from the specific users that could provide the most valuable input.
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5.
  • Abdukalikova, Anara, et al. (creator_code:aut_t)
  • Detection of Atrial Fibrillation from Short ECGs : Minimalistic Complexity Analysis for Feature-Based Classifiers
  • 2018
  • record:In_t: Computing in Cardiology 2018. - : IEEE.
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • In order to facilitate data-driven solutions for early detection of atrial fibrillation (AF), the 2017 CinC conference challenge was devoted to automatic AF classification based on short ECG recordings. The proposed solutions concentrated on maximizing the classifiers F 1 score, whereas the complexity of the classifiers was not considered. However, we argue that this must be addressed as complexity places restrictions on the applicability of inexpensive devices for AF monitoring outside hospitals. Therefore, this study investigates the feasibility of complexity reduction by analyzing one of the solutions presented for the challenge.
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6.
  • Abdulla, Parosh Aziz, et al. (creator_code:aut_t)
  • Bisimulation minimization of tree automata
  • 2006
  • record:In_t: Implementation and Application of Automata. ; , s. 699-713
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • We extend an algorithm by Paige and Tarjan that solves the coarsest stable refinement problem to the domain of trees. The algorithm is used to minimize nondeterministic tree automata (NTA) with respect to bisimulation. We show that our algorithm has an overall complexity of O ((r) over cap log n), where (r) over cap is the maximum rank of any symbol in the input alphabet, m is the total size of the transition table, and n is the number of states.
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7.
  • Abedan Kondori, Farid, 1983-, et al. (creator_code:aut_t)
  • 3D Active Human Motion Estimation for Biomedical Applications
  • 2012
  • record:In_t: World Congress on Medical Physics and Biomedical Engineering May 26-31, 2012, Beijing, China. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783642293047 - 9783642293054 ; , s. 1014-1017
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • Movement disorders forbid many people from enjoying their daily lives. As with other diseases, diagnosis and analysis are key issues in treating such disorders. Computer vision-based motion capture systems are helpful tools for accomplishing this task. However Classical motion tracking systems suffer from several limitations. First they are not cost effective. Second these systems cannot detect minute motions accurately. Finally they are spatially limited to the lab environment where the system is installed. In this project, we propose an innovative solution to solve the above-mentioned issues. Mounting the camera on human body, we build a convenient, low cost motion capture system that can be used by the patient while practicing daily-life activities. We refer to this system as active motion capture, which is not confined to the lab environment. Real-time experiments in our lab revealed the robustness and accuracy of the system.
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8.
  • Abedan Kondori, Farid, et al. (creator_code:aut_t)
  • A Direct Method for 3D Hand Pose Recovery
  • 2014
  • record:In_t: 2014 22ND INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION (ICPR). - : IEEE COMPUTER SOC. - 9781479952083 ; , s. 345-350
  • swepub:Mat_conferencepaper_t (swepub:level_refereed_t)abstract
    • This paper presents a novel approach for performing intuitive 3D gesture-based interaction using depth data acquired by Kinect. Unlike current depth-based systems that focus only on classical gesture recognition problem, we also consider 3D gesture pose estimation for creating immersive gestural interaction. In this paper, we formulate gesture-based interaction system as a combination of two separate problems, gesture recognition and gesture pose estimation. We focus on the second problem and propose a direct method for recovering hand motion parameters. Based on the range images, a new version of optical flow constraint equation is derived, which can be utilized to directly estimate 3D hand motion without any need of imposing other constraints. Our experiments illustrate that the proposed approach performs properly in real-time with high accuracy. As a proof of concept, we demonstrate the system performance in 3D object manipulation. This application is intended to explore the system capabilities in real-time biomedical applications. Eventually, system usability test is conducted to evaluate the learnability, user experience and interaction quality in 3D interaction in comparison to 2D touch-screen interaction.
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9.
  • Abedan Kondori, Farid, 1983-, et al. (creator_code:aut_t)
  • Active human gesture capture for diagnosing and treating movement disorders
  • 2013
  • record:In_t: Proceeding of The Swedish Symposium on Image Analysis (SSBA2013), Gothenburg, Sweden.
  • swepub:Mat_conferencepaper_t (swepub:level_scientificother_t)abstract
    • Movement disorders prevent many people fromenjoying their daily lives. As with other diseases, diagnosisand analysis are key issues in treating such disorders.Computer vision-based motion capture systems are helpfultools for accomplishing this task. However Classical motiontracking systems suffer from several limitations. First theyare not cost effective. Second these systems cannot detectminute motions accurately. Finally they are spatially limitedto the lab environment where the system is installed. In thisproject, we propose an innovative solution to solve the abovementionedissues. Mounting the camera on human body, webuild a convenient, low cost motion capture system that canbe used by the patient in daily-life activities. We refer tothis system as active motion capture, which is not confinedto the lab environment. Real-time experiments in our labrevealed the robustness and accuracy of the system.
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10.
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