Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs, perturbational data is required. However, most GRN discovery methods only operate on observational data. Recent advances in neural network-based causal discovery methods have significantly improved causal discovery, including handling interventional data, improvements in performance and scalability. However, applying state-of-the-art (SOTA) causal discovery methods in biology poses challenges, such as noisy data and a large number of samples. Thus, adapting the causal discovery methods is necessary to handle these challenges. In this paper, we introduce DiscoGen, a neural network-based GRN discovery method that can denoise gene expression measurements and handle interventional data. We demonstrate that our model outperforms SOTA neural network-based causal discovery methods.

With a view to bridging the gap between deep learning and symbolic AI, we present a novel end-to-end neural network architecture that learns to form propositional representations with an explicitly relational structure from raw pixel data. In order to evaluate and analyse the architecture, we introduce a family of simple visual relational reasoning tasks of varying complexity. We show that the proposed architecture, when pre-trained on a curriculum of such tasks, learns to generate reusable representations that better facilitate subsequent learning on previously unseen tasks when compared to a number of baseline architectures. The workings of a successfully trained model are visualised to shed some light on how the architecture functions.

Is coding a relevant metaphor for building AI? A commentary on "Is coding a relevant metaphor for the brain?", by Romain Brette Abstract Brette contends that the neural coding metaphor is an invalid basis for theories of what the brain does (Brette, 2019). Here, we argue that it is an insufficient guide for building an artificial intelligence (AI) that learns to accomplish short-and long-term goals in a complex, changing environment. The goal of neuroscience is to explain how the brain enables intelligent behaviour, while the goal of agent-based AI is to build agents that behave intelligently. Neuroscience, Brette attests, has suffered from an exaggerated (and technically inaccurate) concern for the codes transmitted by particular parts of the brain.

We present Spectral Inference Networks, a framework for learning eigenfunctions of linear operators by stochastic optimization. Spectral Inference Networks generalize Slow Feature Analysis to generic symmetric operators, and are closely related to Variational Monte Carlo methods from computational physics. As such, they can be a powerful tool for unsupervised representation learning from video or pairs of data. We derive a training algorithm for Spectral Inference Networks that addresses the bias in the gradients due to finite batch size and allows for online learning of multiple eigenfunctions. We show results of training Spectral Inference Networks on problems in quantum mechanics and feature learning for videos on synthetic datasets as well as the Arcade Learning Environment. Our results demonstrate that Spectral Inference Networks accurately recover eigenfunctions of linear operators, can discover interpretable representations from video and find meaningful subgoals in reinforcement learning environments.

How do neural networks learn to represent information? Here, we address this question by assuming that neural networks seek to generate an optimal population representation for a fixed linear decoder. We define a loss function for the quality of the population read-out and derive the dynamical equations for both neurons and synapses from the requirement to minimize this loss. The dynamical equations yield a network of integrate-and-fire neurons undergoing Hebbian plasticity. We show that, through learning, initially regular and highly correlated spike trains evolve towards Poisson-distributed and independent spike trains with much lower firing rates. The learning rule drives the network into an asynchronous, balanced regime where all inputs to the network are represented optimally for the given decoder. We show that the network dynamics and synaptic plasticity jointly balance the excitation and inhibition received by each unit as tightly as possible and, in doing so, minimize the prediction error between the inputs and the decoded outputs. In turn, spikes are only signalled whenever this prediction error exceeds a certain value, thereby implementing a predictive coding scheme. Our work suggests that several of the features reported in cortical networks, such as the high trial-to-trial variability, the balance between excitation and inhibition, and spike-timing dependent plasticity, are simply signatures of an efficient, spike-based code.