Computational neuroscience | EPFL Graph Search

Computational neuroscience (also known as theoretical neuroscience or mathematical neuroscience) is a branch of neuroscience which employs mathematical models, computer simulations, theoretical analysis and abstractions of the brain to understand the principles that govern the development, structure, physiology and cognitive abilities of the nervous system. Computational neuroscience employs computational simulations to validate and solve mathematical models, and so can be seen as a sub-field of theoretical neuroscience; however, the two fields are often synonymous. The term mathematical neuroscience is also used sometimes, to stress the quantitative nature of the field. Computational neuroscience focuses on the description of biologically plausible neurons (and neural systems) and their physiology and dynamics, and it is therefore not directly concerned with biologically unrealistic models used in connectionism, control theory, cybernetics, quantitative psychology, machine

A Pipeline Based Approach for Experimental Neuroscience Data Management

Muhammad Asif Jan

The field of neuroscience is witnessing a huge influx of experimental data thanks to the improvements in the data acquisition tools and techniques. Most of this data is being collected by thousands of experimenters located in various institutions around the world. There is also a growing interest in using this experimental data for building biologically realistic computational models of the neuronal systems. One such project i.e. the Blue Brain Project is developing a bottom-up neuronal modeling and simulation framework using experimental data collected at laboratories worldwide. However, to use the experimental data effectively in computational neuroscience research, the data needs to be annotated with metadata such as details of the experimental protocols and conditions, animal subject used etc. Most of the platforms for experimental neuroscience data management operate under the assumption that the primary data has been validated, and properly annotated before it is uploaded to the system. Thus putting the responsibility of validating, and annotating the experimental data with the experimenter conducting the study. Consequently, most experimenters maintain their own data using ad-hoc systems with non-standard metadata schemes; and only upload the final set of data to the data management platform. As a result, the metadata is usually incomplete, and does not always comply with the requirements of the data management platform, negatively impacting the reusability of their data. The current thesis work explored the question of the experimental data management within the context of the Blue Brain Project, and designs a data management pipeline catering for the acquisition, annotation and validation of the experimental data and associated metadata, in order to ensure that the data is usable for the computational modeling purposes. The pipeline enforces a data review process whereby incoming experimental data was made to go through a series of steps, analogous to the scientific review process, systematically improving the quality of the experimental data and associated metadata.

EPFL2011

Biologically plausible unsupervised learning in shallow and deep neural networks

Bernd Albert Illing

The way our brain learns to disentangle complex signals into unambiguous concepts is fascinating but remains largely unknown. There is evidence, however, that hierarchical neural representations play a key role in the cortex. This thesis investigates biologically plausible models of unsupervised learning of hierarchical representations as found in the brain and modern computer vision models. We use computational modeling to address three main questions at the intersection of artificial intelligence (AI) and computational neuroscience.The first question is: What are useful neural representations and when are deep hierarchical representations needed? We approach this point with a systematic study of biologically plausible unsupervised feature learning in a shallow 2-layer networks on digit (MNIST) and object (CIFAR10) classification. Surprisingly, random features support high performance, especially for large hidden layers. When combined with localized receptive fields, random feature networks approach the performance of supervised backpropagation on MNIST, but not on CIFAR10. We suggest that future models of biologically plausible learning should outperform such random feature benchmarks on MNIST, or that such models should be evaluated in different ways.The second question is: How can hierarchical representations be learned with mechanisms supported by neuroscientific evidence? We cover this question by proposing a unifying Hebbian model, inspired by common models of V1 simple and complex cells based on unsupervised sparse coding and temporal invariance learning. In shallow 2-layer networks, our model reproduces learning of simple and complex cell receptive fields, as found in V1. In deeper networks, we stack multiple layers of Hebbian learning but find that it does not yield hierarchical representations of increasing usefulness. From this, we hypothesise that standard Hebbian rules are too constrained to build increasingly useful representations, as observed in higher areas of the visual cortex or deep artificial neural networks.The third question is: Can AI inspire learning models that build deep representations and are still biologically plausible? We address this question by proposing a learning rule that takes inspiration from neuroscience and recent advances in self-supervised deep learning. The proposed rule is Hebbian, i.e. only depends on pre- and post-synaptic neuronal activity, but includes additional local factors, namely predictive dendritic input and widely broadcasted modulation factors. Algorithmically, this rule applies self-supervised contrastive predictive learning to a causal, biological setting using saccades. We find that networks trained with this generalised Hebbian rule build deep hierarchical representations of images, speech and video.We see our modeling as a potential starting point for both, new hypotheses, that can be tested experimentally, and novel AI models that could benefit from added biological realism.

EPFL2021

A Brief History of Simulation Neuroscience

Xue Fan, Henry Markram

Our knowledge of the brain has evolved over millennia in philosophical, experimental and theoretical phases. We suggest that the next phase is simulation neuroscience. The main drivers of simulation neuroscience are big data generated at multiple levels of brain organization and the need to integrate these data to trace the causal chain of interactions within and across all these levels. Simulation neuroscience is currently the only methodology for systematically approaching the multiscale brain. In this review, we attempt to reconstruct the deep historical paths leading to simulation neuroscience, from the first observations of the nerve cell to modern efforts to digitally reconstruct and simulate the brain. Neuroscience began with the identification of the neuron as the fundamental unit of brain structure and function and has evolved towards understanding the role of each cell type in the brain, how brain cells are connected to each other, and how the seemingly infinite networks they form give rise to the vast diversity of brain functions. Neuronal mapping is evolving from subjective descriptions of cell types towards objective classes, subclasses and types. Connectivity mapping is evolving from loose topographic maps between brain regions towards dense anatomical and physiological maps of connections between individual genetically distinct neurons. Functional mapping is evolving from psychological and behavioral stereotypes towards a map of behaviors emerging from structural and functional connectomes. We show how industrialization of neuroscience and the resulting large disconnected datasets are generating demand for integrative neuroscience, how the scale of neuronal and connectivity maps is driving digital atlasing and digital reconstruction to piece together the multiple levels of brain organization, and how the complexity of the interactions between molecules, neurons, microcircuits and brain regions is driving brain simulation to understand the interactions in the multiscale brain.

FRONTIERS MEDIA SA2019