Ethical Reflections of Human Brain Research and Smart Information Systems

open access journalThis case study explores ethical issues that relate to the use of Smart Infor-mation Systems (SIS) in human brain research. The case study is based on the Human Brain Project (HBP), which is a European Union funded project. The project uses SIS to build a research infrastructure aimed at the advancement of neuroscience, medicine and computing. The case study was conducted to assess how the HBP recognises and deal with ethical concerns relating to the use of SIS in human brain research. To under-stand some of the ethical implications of using SIS in human brain research, data was collected through a document review and three semi-structured interviews with partic-ipants from the HBP. Results from the case study indicate that the main ethical concerns with the use of SIS in human brain research include privacy and confidentiality, the security of personal data, discrimination that arises from bias and access to the SIS and their outcomes. Furthermore, there is an issue with the transparency of the processes that are involved in human brain research. In response to these issues, the HBP has put in place different mechanisms to ensure responsible research and innovation through a dedicated pro-gram. The paper provides lessons for the responsible implementation of SIS in research, including human brain research and extends some of the mechanisms that could be employed by researchers and developers of SIS for research in addressing such issues

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

NullHop: A Flexible Convolutional Neural Network Accelerator Based on Sparse Representations of Feature Maps

Convolutional neural networks (CNNs) have become the dominant neural network architecture for solving many state-of-the-art (SOA) visual processing tasks. Even though Graphical Processing Units (GPUs) are most often used in training and deploying CNNs, their power efficiency is less than 10 GOp/s/W for single-frame runtime inference. We propose a flexible and efficient CNN accelerator architecture called NullHop that implements SOA CNNs useful for low-power and low-latency application scenarios. NullHop exploits the sparsity of neuron activations in CNNs to accelerate the computation and reduce memory requirements. The flexible architecture allows high utilization of available computing resources across kernel sizes ranging from 1x1 to 7x7. NullHop can process up to 128 input and 128 output feature maps per layer in a single pass. We implemented the proposed architecture on a Xilinx Zynq FPGA platform and present results showing how our implementation reduces external memory transfers and compute time in five different CNNs ranging from small ones up to the widely known large VGG16 and VGG19 CNNs. Post-synthesis simulations using Mentor Modelsim in a 28nm process with a clock frequency of 500 MHz show that the VGG19 network achieves over 450 GOp/s. By exploiting sparsity, NullHop achieves an efficiency of 368%, maintains over 98% utilization of the MAC units, and achieves a power efficiency of over 3TOp/s/W in a core area of 6.3mm$^2$. As further proof of NullHop's usability, we interfaced its FPGA implementation with a neuromorphic event camera for real time interactive demonstrations

Beyond Research Ethics: Dialogues in Neuro-ICT Research

open access articleThe increasing use of information and communication technologies (ICTs) to help facilitate neuroscience adds a new level of complexity to the question of how ethical issues of such research can be identified and addressed. Current research ethics practice, based on ethics reviews by institutional review boards (IRB) and underpinned by ethical principlism, has been widely criticized. In this article, we develop an alternative way of approaching ethics in neuro-ICT research, based on discourse ethics, which implements Responsible Research and Innovation (RRI) through dialogues. We draw on our work in Ethics Support, using the Human Brain Project (HBP) as empirical evidence of the viability of this approach

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

Towards structured sharing of raw and derived neuroimaging data across existing resources

Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery

The Resource Identification Initiative: A cultural shift in publishing

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as What other studies used resource X? To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources

Linking brain structure, activity and cognitive function through computation

Understanding the human brain is a “Grand Challenge” for 21st century research. Computational approaches enable large and complex datasets to be addressed efficiently, supported by artificial neural networks, modeling and simulation. Dynamic generative multiscale models, which enable the investigation of causation across scales and are guided by principles and theories of brain function, are instrumental for linking brain structure and function. An example of a resource enabling such an integrated approach to neuroscientific discovery is the BigBrain, which spatially anchors tissue models and data across different scales and ensures that multiscale models are supported by the data, making the bridge to both basic neuroscience and medicine. Research at the intersection of neuroscience, computing and robotics has the potential to advance neuro-inspired technologies by taking advantage of a growing body of insights into perception, plasticity and learning. To render data, tools and methods, theories, basic principles and concepts interoperable, the Human Brain Project (HBP) has launched EBRAINS, a digital neuroscience research infrastructure, which brings together a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating insights and perspectives for societal benefits

pypet: A Python Toolkit for Data Management of Parameter Explorations

pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.DFG, 103586207, GRK 1589: Verarbeitung sensorischer Informationen in neuronalen Systeme