A Text Mining Pipeline Using Active and Deep Learning Aimed at Curating Information in Computational Neuroscience

The curation of neuroscience entities is crucial to ongoing efforts in neuroinformatics and computational neuroscience, such as those being deployed in the context of continuing large-scale brain modelling projects. However, manually sifting through thousands of articles for new information about modelled entities is a painstaking and low-reward task. Text mining can be used to help a curator extract relevant information from this literature in a systematic way. We propose the application of text mining methods for the neuroscience literature. Specifically, two computational neuroscientists annotated a corpus of entities pertinent to neuroscience using active learning techniques to enable swift, targeted annotation. We then trained machine learning models to recognise the entities that have been identified. The entities covered are Neuron Types, Brain Regions, Experimental Values, Units, Ion Currents, Channels, and Conductances and Model organisms. We tested a traditional rule-based approach, a conditional random field and a model using deep learning named entity recognition, finding that the deep learning model was superior. Our final results show that we can detect a range of named entities of interest to the neuroscientist with a macro average precision, recall and F1 score of 0.866, 0.817 and 0.837 respectively. The contributions of this work are as follows: 1) We provide a set of Named Entity Recognition (NER) tools that are capable of detecting neuroscience entities with performance above or similar to prior work. 2) We propose a methodology for training NER tools for neuroscience that requires very little training data to get strong performance. This can be adapted for any sub-domain within neuroscience. 3) We provide a small corpus with annotations for multiple entity types, as well as annotation guidelines to help others reproduce our experiments.

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data

Shailesh Appukuttan, Luca Leonardo Bologna, Szabolcs Kali, Carmen Alina Lupascu, Rosanna Migliore, Eilif Benjamin Muller, Armando Romani, Sàra Sàray, Werner Alfons Hilda Van Geit

Anatomically and biophysically detailed data-driven neuronal models have become widely used tools for understanding and predicting the behavior and function of neurons. Due to the increasing availability of experimental data from anatomical and electrophysiological measurements as well as the growing number of computational and software tools that enable accurate neuronal modeling, there are now a large number of different models of many cell types available in the literature. These models were usually built to capture a few important or interesting properties of the given neuron type, and it is often unknown how they would behave outside their original context. In addition, there is currently no simple way of quantitatively comparing different models regarding how closely they match specific experimental observations. This limits the evaluation, re-use and further development of the existing models. Further, the development of new models could also be significantly facilitated by the ability to rapidly test the behavior of model candidates against the relevant collection of experimental data. We address these problems for the representative case of the CA1 pyramidal cell of the rat hippocampus by developing an open-source Python test suite, which makes it possible to automatically and systematically test multiple properties of models by making quantitative comparisons between the models and electrophysiological data. The tests cover various aspects of somatic behavior, and signal propagation and integration in apical dendrites. To demonstrate the utility of our approach, we applied our tests to compare the behavior of several different rat hippocampal CA1 pyramidal cell models from the ModelDB database against electrophysiological data available in the literature, and evaluated how well these models match experimental observations in different domains. We also show how we employed the test suite to aid the development of models within the European Human Brain Project (HBP), and describe the integration of the tests into the validation framework developed in the HBP, with the aim of facilitating more reproducible and transparent model building in the neuroscience community. Author summary Anatomically and biophysically detailed neuronal models are useful tools in neuroscience because they allow the prediction of the behavior and the function of the studied cell type under circumstances that are hard to investigate experimentally. However, most detailed biophysical models have been built to capture a few selected properties of the real neuron, and it is often unknown how they would behave under different circumstances, or whether they can be used to successfully answer different scientific questions. To help the modeling community develop better neural models, and to make the process of model building more reproducible and transparent, we developed a test suite that enables the comparison of the behavior of models of neurons in the rat hippocampus and their evaluation against experimental data. Applying our tests to several models available in the literature enabled us to assess and compare how precisely each of these models is able to match various electrophysiological properties of the real neurons. We also use the test suite in the model development workflow of the European Human Brain Project to aid the construction of better models of hippocampal neurons and networks.

PUBLIC LIBRARY SCIENCE2021

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

Theory of representation learning in cortical neural networks

Carlos Stein Naves de Brito

Our brain continuously self-organizes to construct and maintain an internal representation of the world based on the information arriving through sensory stimuli. Remarkably, cortical areas related to different sensory modalities appear to share the same functional unit, the neuron, and develop through the same learning mechanism, synaptic plasticity. It motivates the conjecture of a unifying theory to explain cortical representational learning across sensory modalities. In this thesis we present theories and computational models of learning and optimization in neural networks, postulating functional properties of synaptic plasticity that support the apparent universal learning capacity of cortical networks. In the past decades, a variety of theories and models have been proposed to describe receptive field formation in sensory areas. They include normative models such as sparse coding, and bottom-up models such as spike-timing dependent plasticity. We bring together candidate explanations by demonstrating that in fact a single principle is sufficient to explain receptive field development. First, we show that many representative models of sensory development are in fact implementing variations of a common principle: nonlinear Hebbian learning. Second, we reveal that nonlinear Hebbian learning is sufficient for receptive field formation through sensory inputs. A surprising result is that our findings are independent of specific details, and allow for robust predictions of the learned receptive fields. Thus nonlinear Hebbian learning and natural statistics can account for many aspects of receptive field formation across models and sensory modalities. The Hebbian learning theory substantiates that synaptic plasticity can be interpreted as an optimization procedure, implementing stochastic gradient descent. In stochastic gradient descent inputs arrive sequentially, as in sensory streams. However, individual data samples have very little information about the correct learning signal, and it becomes a fundamental problem to know how many samples are required for reliable synaptic changes. Through estimation theory, we develop a novel adaptive learning rate model, that adapts the magnitude of synaptic changes based on the statistics of the learning signal, enabling an optimal use of data samples. Our model has a simple implementation and demonstrates improved learning speed, making this a promising candidate for large artificial neural network applications. The model also makes predictions on how cortical plasticity may modulate synaptic plasticity for optimal learning. The optimal sampling size for reliable learning allows us to estimate optimal learning times for a given model. We apply this theory to derive analytical bounds on times for the optimization of synaptic connections. First, we show this optimization problem to have exponentially many saddle-nodes, which lead to small gradients and slow learning. Second, we show that the number of input synapses to a neuron modulates the magnitude of the initial gradient, determining the duration of learning. Our final result reveals that the learning duration increases supra-linearly with the number of synapses, suggesting an effective limit on synaptic connections and receptive field sizes in developing neural networks.

EPFL2016