14,648 research outputs found

    Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template

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    Motivation: Complex diseases induce perturbations to interaction and regulation networks in living systems, resulting in dynamic equilibrium states that differ for different diseases and also normal states. Thus identifying gene expression patterns corresponding to different equilibrium states is of great benefit to the diagnosis and treatment of complex diseases. However, it remains a major challenge to deal with the high dimensionality and small size of available complex disease gene expression datasets currently used for discovering gene expression patterns. Results: Here we present a phase-only correlation (POC) based classification method for recognizing the type of complex diseases. First, a virtual sample template is constructed for each subclass by averaging all samples of each subclass in a training dataset. Then the label of a test sample is determined by measuring the similarity between the test sample and each template. This novel method can detect the similarity of overall patterns emerged from the differentially expressed genes or proteins while ignoring small mismatches. Conclusions: The experimental results obtained on seven publicly available complex disease datasets including microarray and protein array data demonstrate that the proposed POC-based disease classification method is effective and robust for diagnosing complex diseases with regard to the number of initially selected features, and its recognition accuracy is better than or comparable to other state-of-the-art machine learning methods. In addition, the proposed method does not require parameter tuning and data scaling, which can effectively reduce the occurrence of over-fitting and bias

    Fused mechanomyography and inertial measurement for human-robot interface

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    Human-Machine Interfaces (HMI) are the technology through which we interact with the ever-increasing quantity of smart devices surrounding us. The fundamental goal of an HMI is to facilitate robot control through uniting a human operator as the supervisor with a machine as the task executor. Sensors, actuators, and onboard intelligence have not reached the point where robotic manipulators may function with complete autonomy and therefore some form of HMI is still necessary in unstructured environments. These may include environments where direct human action is undesirable or infeasible, and situations where a robot must assist and/or interface with people. Contemporary literature has introduced concepts such as body-worn mechanical devices, instrumented gloves, inertial or electromagnetic motion tracking sensors on the arms, head, or legs, electroencephalographic (EEG) brain activity sensors, electromyographic (EMG) muscular activity sensors and camera-based (vision) interfaces to recognize hand gestures and/or track arm motions for assessment of operator intent and generation of robotic control signals. While these developments offer a wealth of future potential their utility has been largely restricted to laboratory demonstrations in controlled environments due to issues such as lack of portability and robustness and an inability to extract operator intent for both arm and hand motion. Wearable physiological sensors hold particular promise for capture of human intent/command. EMG-based gesture recognition systems in particular have received significant attention in recent literature. As wearable pervasive devices, they offer benefits over camera or physical input systems in that they neither inhibit the user physically nor constrain the user to a location where the sensors are deployed. Despite these benefits, EMG alone has yet to demonstrate the capacity to recognize both gross movement (e.g. arm motion) and finer grasping (e.g. hand movement). As such, many researchers have proposed fusing muscle activity (EMG) and motion tracking e.g. (inertial measurement) to combine arm motion and grasp intent as HMI input for manipulator control. However, such work has arguably reached a plateau since EMG suffers from interference from environmental factors which cause signal degradation over time, demands an electrical connection with the skin, and has not demonstrated the capacity to function out of controlled environments for long periods of time. This thesis proposes a new form of gesture-based interface utilising a novel combination of inertial measurement units (IMUs) and mechanomyography sensors (MMGs). The modular system permits numerous configurations of IMU to derive body kinematics in real-time and uses this to convert arm movements into control signals. Additionally, bands containing six mechanomyography sensors were used to observe muscular contractions in the forearm which are generated using specific hand motions. This combination of continuous and discrete control signals allows a large variety of smart devices to be controlled. Several methods of pattern recognition were implemented to provide accurate decoding of the mechanomyographic information, including Linear Discriminant Analysis and Support Vector Machines. Based on these techniques, accuracies of 94.5% and 94.6% respectively were achieved for 12 gesture classification. In real-time tests, accuracies of 95.6% were achieved in 5 gesture classification. It has previously been noted that MMG sensors are susceptible to motion induced interference. The thesis also established that arm pose also changes the measured signal. This thesis introduces a new method of fusing of IMU and MMG to provide a classification that is robust to both of these sources of interference. Additionally, an improvement in orientation estimation, and a new orientation estimation algorithm are proposed. These improvements to the robustness of the system provide the first solution that is able to reliably track both motion and muscle activity for extended periods of time for HMI outside a clinical environment. Application in robot teleoperation in both real-world and virtual environments were explored. With multiple degrees of freedom, robot teleoperation provides an ideal test platform for HMI devices, since it requires a combination of continuous and discrete control signals. The field of prosthetics also represents a unique challenge for HMI applications. In an ideal situation, the sensor suite should be capable of detecting the muscular activity in the residual limb which is naturally indicative of intent to perform a specific hand pose and trigger this post in the prosthetic device. Dynamic environmental conditions within a socket such as skin impedance have delayed the translation of gesture control systems into prosthetic devices, however mechanomyography sensors are unaffected by such issues. There is huge potential for a system like this to be utilised as a controller as ubiquitous computing systems become more prevalent, and as the desire for a simple, universal interface increases. Such systems have the potential to impact significantly on the quality of life of prosthetic users and others.Open Acces

    Human-Centric Machine Vision

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    Recently, the algorithms for the processing of the visual information have greatly evolved, providing efficient and effective solutions to cope with the variability and the complexity of real-world environments. These achievements yield to the development of Machine Vision systems that overcome the typical industrial applications, where the environments are controlled and the tasks are very specific, towards the use of innovative solutions to face with everyday needs of people. The Human-Centric Machine Vision can help to solve the problems raised by the needs of our society, e.g. security and safety, health care, medical imaging, and human machine interface. In such applications it is necessary to handle changing, unpredictable and complex situations, and to take care of the presence of humans

    Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems

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    A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains elusive. One of the reasons is that proteins are not acting alone, but are specifically interacting with other proteins and biomolecules, forming intricate interaction networks that are essential for the majority of cell processes and pathological conditions. Thus, characterizing such interaction networks is an important step in understanding how information flows from gene to phenotype. Indeed, structural characterization of protein–protein interactions at atomic resolution has many applications in biomedicine, from diagnosis and vaccine design, to drug discovery. However, despite the advances of experimental structural determination, the number of interactions for which there is available structural data is still very small. In this context, a complementary approach is computational modeling of protein interactions by docking, which is usually composed of two major phases: (i) sampling of the possible binding modes between the interacting molecules and (ii) scoring for the identification of the correct orientations. In addition, prediction of interface and hot-spot residues is very useful in order to guide and interpret mutagenesis experiments, as well as to understand functional and mechanistic aspects of the interaction. Computational docking is already being applied to specific biomedical problems within the context of personalized medicine, for instance, helping to interpret pathological mutations involved in protein–protein interactions, or providing modeled structural data for drug discovery targeting protein–protein interactions.Spanish Ministry of Economy grant number BIO2016-79960-R; D.B.B. is supported by a predoctoral fellowship from CONACyT; M.R. is supported by an FPI fellowship from the Severo Ochoa program. We are grateful to the Joint BSC-CRG-IRB Programme in Computational Biology.Peer ReviewedPostprint (author's final draft

    Eye-tracking assistive technologies for individuals with amyotrophic lateral sclerosis

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    Amyotrophic lateral sclerosis, also known as ALS, is a progressive nervous system disorder that affects nerve cells in the brain and spinal cord, resulting in the loss of muscle control. For individuals with ALS, where mobility is limited to the movement of the eyes, the use of eye-tracking-based applications can be applied to achieve some basic tasks with certain digital interfaces. This paper presents a review of existing eye-tracking software and hardware through which eye-tracking their application is sketched as an assistive technology to cope with ALS. Eye-tracking also provides a suitable alternative as control of game elements. Furthermore, artificial intelligence has been utilized to improve eye-tracking technology with significant improvement in calibration and accuracy. Gaps in literature are highlighted in the study to offer a direction for future research

    Low vision assistance with mobile devices

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    Low vision affects many people, both young and old. Low vision conditions can range from near- and far-sightedness to conditions such as blind spots and tunnel vision. With the growing popularity of mobile devices such as smartphones, there is large opportunity for use of these multipurpose devices to provide low vision assistance. Furthermore, Google\u27s Android operating system provides a robust environment for applications in various fields, including low vision assistance. The objective of this thesis research is to develop a system for low vision assistance that displays important information at the preferred location of the user\u27s visual field. To that end, a first release of a prototype blind spot/tunnel vision assistance system was created and demonstrated on an Android smartphone. Various algorithms for face detection and face tracking were implemented on the Android platform and their performance was assessed with regards to metrics such as throughput and battery usage. Specifically, Viola-Jones, Support Vector Machines, and a color-based method from Pai et al were used for face detection. Template matching, CAMShift, and Lucas-Kanade methods were used for face tracking. It was found that face detection and tracking could be successfully executed within acceptable bounds of time and battery usage, and in some cases performed faster than it would take a comparable cloud-based system for offloading algorithm usage to complete execution

    11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

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