Spatial Filtering Pipeline Evaluation of Cortically Coupled Computer Vision System for Rapid Serial Visual Presentation

Rapid Serial Visual Presentation (RSVP) is a paradigm that supports the application of cortically coupled computer vision to rapid image search. In RSVP, images are presented to participants in a rapid serial sequence which can evoke Event-related Potentials (ERPs) detectable in their Electroencephalogram (EEG). The contemporary approach to this problem involves supervised spatial filtering techniques which are applied for the purposes of enhancing the discriminative information in the EEG data. In this paper we make two primary contributions to that field: 1) We propose a novel spatial filtering method which we call the Multiple Time Window LDA Beamformer (MTWLB) method; 2) we provide a comprehensive comparison of nine spatial filtering pipelines using three spatial filtering schemes namely, MTWLB, xDAWN, Common Spatial Pattern (CSP) and three linear classification methods Linear Discriminant Analysis (LDA), Bayesian Linear Regression (BLR) and Logistic Regression (LR). Three pipelines without spatial filtering are used as baseline comparison. The Area Under Curve (AUC) is used as an evaluation metric in this paper. The results reveal that MTWLB and xDAWN spatial filtering techniques enhance the classification performance of the pipeline but CSP does not. The results also support the conclusion that LR can be effective for RSVP based BCI if discriminative features are available

NiftyNet: a deep-learning platform for medical imaging

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this application requires substantial implementation effort. Thus, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. NiftyNet provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on TensorFlow and supports TensorBoard visualization of 2D and 3D images and computational graphs by default. We present 3 illustrative medical image analysis applications built using NiftyNet: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. NiftyNet enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications.Comment: Wenqi Li and Eli Gibson contributed equally to this work. M. Jorge Cardoso and Tom Vercauteren contributed equally to this work. 26 pages, 6 figures; Update includes additional applications, updated author list and formatting for journal submissio

EEG source imaging assists decoding in a face recognition task

EEG based brain state decoding has numerous applications. State of the art decoding is based on processing of the multivariate sensor space signal, however evidence is mounting that EEG source reconstruction can assist decoding. EEG source imaging leads to high-dimensional representations and rather strong a priori information must be invoked. Recent work by Edelman et al. (2016) has demonstrated that introduction of a spatially focal source space representation can improve decoding of motor imagery. In this work we explore the generality of Edelman et al. hypothesis by considering decoding of face recognition. This task concerns the differentiation of brain responses to images of faces and scrambled faces and poses a rather difficult decoding problem at the single trial level. We implement the pipeline using spatially focused features and show that this approach is challenged and source imaging does not lead to an improved decoding. We design a distributed pipeline in which the classifier has access to brain wide features which in turn does lead to a 15% reduction in the error rate using source space features. Hence, our work presents supporting evidence for the hypothesis that source imaging improves decoding

High-throughput Binding Affinity Calculations at Extreme Scales

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or evolutionarily selected during treatment. Key to overcoming this challenge is an understanding of the molecular determinants of drug binding. Using multi-stage pipelines of molecular simulations we can gain insights into the binding free energy and the residence time of a ligand, which can inform both stratified and personal treatment regimes and drug development. To support the scalable, adaptive and automated calculation of the binding free energy on high-performance computing resources, we introduce the High- throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block approach in order to attain both workflow flexibility and performance. We demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage binding affinity calculation pipelines. This permits a rapid time-to-solution that is essentially invariant of the calculation protocol, size of candidate ligands and number of ensemble simulations. As such, HTBAC advances the state of the art of binding affinity calculations and protocols

Evaluation of a Tree-based Pipeline Optimization Tool for Automating Data Science

As the field of data science continues to grow, there will be an ever-increasing demand for tools that make machine learning accessible to non-experts. In this paper, we introduce the concept of tree-based pipeline optimization for automating one of the most tedious parts of machine learning---pipeline design. We implement an open source Tree-based Pipeline Optimization Tool (TPOT) in Python and demonstrate its effectiveness on a series of simulated and real-world benchmark data sets. In particular, we show that TPOT can design machine learning pipelines that provide a significant improvement over a basic machine learning analysis while requiring little to no input nor prior knowledge from the user. We also address the tendency for TPOT to design overly complex pipelines by integrating Pareto optimization, which produces compact pipelines without sacrificing classification accuracy. As such, this work represents an important step toward fully automating machine learning pipeline design.Comment: 8 pages, 5 figures, preprint to appear in GECCO 2016, edits not yet made from reviewer comment