Adapting to time: Why nature may have evolved a diverse set of neurons.

Brains have evolved diverse neurons with varying morphologies and dynamics that impact temporal information processing. In contrast, most neural network models use homogeneous units that vary only in spatial parameters (weights and biases). To explore the importance of temporal parameters, we trained spiking neural networks on tasks with varying temporal complexity, holding different parameter subsets constant.

Clarifying status of DNNs as models of human vision.

On several key issues we agree with the commentators. Perhaps most importantly, everyone seems to agree that psychology has an important role to play in building better models of human vision, and (most) everyone agrees (including us) that deep neural networks (DNNs) will play an important role in modelling human vision going forward. But there are also disagreements about what models are for, how DNN-human correspondences should be evaluated, the value of alternative modelling approaches, and impact of marketing hype in the literature.

Accurate staging of chick embryonic tissues via deep learning of salient features.

Recent work shows that the developmental potential of progenitor cells in the HH10 chick brain changes rapidly, accompanied by subtle changes in morphology. This demands increased temporal resolution for studies of the brain at this stage, necessitating precise and unbiased staging. Here, we investigated whether we could train a deep convolutional neural network to sub-stage HH10 chick brains using a small dataset of 151 expertly labelled images.

The role of capacity constraints in Convolutional Neural Networks for learning random versus natural data.

Convolutional neural networks (CNNs) are often described as promising models of human vision, yet they show many differences from human abilities. We focus on a superhuman capacity of top-performing CNNs, namely, their ability to learn very large datasets of random patterns. We verify that human learning on such tasks is extremely limited, even with few stimuli.

Deep problems with neural network models of human vision.

Deep neural networks (DNNs) have had extraordinary successes in classifying photographic images of objects and are often described as the best models of biological vision. This conclusion is largely based on three sets of findings: (1) DNNs are more accurate than any other model in classifying images taken from various datasets, (2) DNNs do the best job in predicting the pattern of human errors in classifying objects taken from various behavioral datasets, and (3) DNNs do the best job in predicting brain signals in response to images taken from various brain datasets (e.g.

Biological convolutions improve DNN robustness to noise and generalisation.

Deep Convolutional Neural Networks (DNNs) have achieved superhuman accuracy on standard image classification benchmarks. Their success has reignited significant interest in their use as models of the primate visual system, bolstered by claims of their architectural and representational similarities. However, closer scrutiny of these models suggests that they rely on various forms of shortcut learning to achieve their impressive performance, such as using texture rather than shape information.

Estimating disease prevalence in large datasets using genetic risk scores.

Clinical classification is essential for estimating disease prevalence but is difficult, often requiring complex investigations. The widespread availability of population level genetic data makes novel genetic stratification techniques a highly attractive alternative. We propose a generalizable mathematical framework for determining disease prevalence within a cohort using genetic risk scores.

Vangl2 promotes the formation of long cytonemes to enable distant Wnt/β-catenin signaling.

Wnt signaling regulates cell proliferation and cell differentiation as well as migration and polarity during development. However, it is still unclear how the Wnt ligand distribution is precisely controlled to fulfil these functions. Here, we show that the planar cell polarity protein Vangl2 regulates the distribution of Wnt by cytonemes.

Ten simple rules for writing Dockerfiles for reproducible data science.

Computational science has been greatly improved by the use of containers for packaging software and data dependencies. In a scholarly context, the main drivers for using these containers are transparency and support of reproducibility; in turn, a workflow's reproducibility can be greatly affected by the choices that are made with respect to building containers. In many cases, the build process for the container's image is created from instructions provided in a Dockerfile format.

Additive Combination of Spectra Reflected from Porous Silicon and Carbon/Porous Silicon Rugate Filters to Improve Vapor Selectivity.

Selectivity remains a challenge for rapid optical vapor sensing via light reflected from porous silicon photonic crystals. This work highlights a method to increase optical vapor selectivity of porous silicon rugate filters by analyzing additive spectra from two rugate filter substrates with different functionalities, an oxidized and carbonized surface. Individually, both porous silicon rugate filters demonstrated sensitivity but not selectivity toward the vapor analytes.

Hiding a plane with a pixel: examining shape-bias in CNNs and the benefit of building in biological constraints.

When deep convolutional neural networks (CNNs) are trained "end-to-end" on raw data, some of the feature detectors they develop in their early layers resemble the representations found in early visual cortex. This result has been used to draw parallels between deep learning systems and human visual perception. In this study, we show that when CNNs are trained end-to-end they learn to classify images based on whatever feature is predictive of a category within the dataset.

Optogenetics in Silicon: A Neural Processor for Predicting Optically Active Neural Networks.

We present a reconfigurable neural processor for real-time simulation and prediction of opto-neural behaviour. We combined a detailed Hodgkin-Huxley CA3 neuron integrated with a four-state Channelrhodopsin-2 (ChR2) model into reconfigurable silicon hardware. Our architecture consists of a Field Programmable Gated Array (FPGA) with a custom-built computing data-path, a separate data management system and a memory approach based router.

PyRhO: A Multiscale Optogenetics Simulation Platform.

Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO.

Computational modeling of the neural representation of object shape in the primate ventral visual system.

Neurons in successive stages of the primate ventral visual pathway encode the spatial structure of visual objects. In this paper, we investigate through computer simulation how these cell firing properties may develop through unsupervised visually-guided learning. Individual neurons in the model are shown to exploit statistical regularity and temporal continuity of the visual inputs during training to learn firing properties that are similar to neurons in V4 and TEO.

STDP in lateral connections creates category-based perceptual cycles for invariance learning with multiple stimuli.

Learning to recognise objects and faces is an important and challenging problem tackled by the primate ventral visual system. One major difficulty lies in recognising an object despite profound differences in the retinal images it projects, due to changes in view, scale, position and other identity-preserving transformations. Several models of the ventral visual system have been successful in coping with these issues, but have typically been privileged by exposure to only one object at a time.

How lateral connections and spiking dynamics may separate multiple objects moving together.

Over successive stages, the ventral visual system of the primate brain develops neurons that respond selectively to particular objects or faces with translation, size and view invariance. The powerful neural representations found in Inferotemporal cortex form a remarkably rapid and robust basis for object recognition which belies the difficulties faced by the system when learning in natural visual environments. A central issue in understanding the process of biological object recognition is how these neurons learn to form separate representations of objects from complex visual scenes composed of multiple objects.

A self-organizing model of the visual development of hand-centred representations.

We show how hand-centred visual representations could develop in the primate posterior parietal and premotor cortices during visually guided learning in a self-organizing neural network model. The model incorporates trace learning in the feed-forward synaptic connections between successive neuronal layers. Trace learning encourages neurons to learn to respond to input images that tend to occur close together in time.

Transformation-invariant visual representations in self-organizing spiking neural networks.

The ventral visual pathway achieves object and face recognition by building transformation-invariant representations from elementary visual features. In previous computer simulation studies with rate-coded neural networks, the development of transformation-invariant representations has been demonstrated using either of two biologically plausible learning mechanisms, Trace learning and Continuous Transformation (CT) learning. However, it has not previously been investigated how transformation-invariant representations may be learned in a more biologically accurate spiking neural network.