An important problem in systems neuroscience is to identify the latent dynamics underlying neural population activity. Here we address this problem by introducing a low-dimensional nonlinear model for latent neural population dynamics using neural ordinary differential equations (neural ODEs), with noisy sensory inputs and Poisson spike train outputs. We refer to this as the Poisson Latent Neural Differential Equations (PLNDE) model. We apply the PLNDE framework to a variety of synthetic datasets, and show that it accurately infers the phase portraits and fixed points of nonlinear systems augmented to produce spike train data, including the FitzHugh-Nagumo oscillator, a 3-dimensional nonlinear spiral, and a nonlinear sensory decision-making model with attractor dynamics. Our model significantly outperforms existing methods at inferring single-trial neural firing rates and the corresponding latent trajectories that generated them, especially in the regime where the spike counts and number of trials are low. We then apply our model to multi-region neural population recordings from medial frontal cortex of rats performing an auditory decision-making task. Our model provides a general, interpretable framework for investigating the neural mechanisms of decision-making and other cognitive computations through the lens of dynamical systems.

Organ transplantation is often the last resort for treating end-stage illnesses, but managing transplant wait-lists is challenging because of organ scarcity and the complexity of assessing donor-recipient compatibility. In this paper, we develop a data-driven model for (real-time) organ allocation using observational data for transplant outcomes. Our model integrates a queuing-theoretic framework with unsupervised learning to cluster the organs into ``organ types'', and then construct priority queues (associated with each organ type) wherein incoming patients are assigned. To reason about organ allocations, the model uses synthetic controls to infer a patient's survival outcomes under counterfactual allocations to the different organ types– the model is trained end-to-end to optimise the trade-off between patient waiting time and expected survival time. The usage of synthetic controls enable patient-level interpretations of allocation decisions that can be presented and understood by clinicians. We test our model on multiple data sets, and show that it outperforms other organ-allocation policies in terms of added life-years, and death count. Furthermore, we introduce a novel organ-allocation simulator to accurately test new policies.

CNNs and computational models of biological vision share some fundamental principles, which opened new avenues of research. However, fruitful cross-field research is hampered by conventional CNN architectures being based on spatially and depthwise discrete representations, which cannot accommodate certain aspects of biological complexity such as continuously varying receptive field sizes and dynamics of neuronal responses. Here we propose deep continuous networks (DCNs), which combine spatially continuous filters, with the continuous depth framework of neural ODEs. This allows us to learn the spatial support of the filters during training, as well as model the continuous evolution of feature maps, linking DCNs closely to biological models. We show that DCNs are versatile and highly applicable to standard image classification and reconstruction problems, where they improve parameter and data efficiency, and allow for meta-parametrization. We illustrate the biological plausibility of the scale distributions learned by DCNs and explore their performance in a neuroscientifically inspired pattern completion task. Finally, we investigate an efficient implementation of DCNs by changing input contrast.

In this paper, we propose a conceptually simple but very effective attention module for Convolutional Neural Networks (ConvNets). In contrast to existing channel-wise and spatial-wise attention modules, our module instead infers 3-D attention weights for the feature map in a layer without adding parameters to the original networks. Specifically, we base on some well-known neuroscience theories and propose to optimize an energy function to find the importance of each neuron. We further derive a fast closed-form solution for the energy function, and show that the solution can be implemented in less than ten lines of code. Another advantage of the module is that most of the operators are selected based on the solution to the defined energy function, avoiding too many efforts for structure tuning. Quantitative evaluations on various visual tasks demonstrate that the proposed module is flexible and effective to improve the representation ability of many ConvNets. Our code is available at Pytorch-SimAM.

Sufficient dimension reduction (SDR) methods are a family of supervised methods for dimensionality reduction that seek to reduce dimensionality while preserving information about a target variable of interest. However, existing SDR methods typically require more observations than the number of dimensions ($N > p$). To overcome this limitation, we propose Class-conditional Factor Analytic Dimensions (CFAD), a model-based dimensionality reduction method for high-dimensional, small-sample data. We show that CFAD substantially outperforms existing SDR methods in the small-sample regime, and can be extended to incorporate prior information such as smoothness in the projection axes. We demonstrate the effectiveness of CFAD with an application to functional magnetic resonance imaging (fMRI) measurements during visual object recognition and working memory tasks, where it outperforms existing SDR and a variety of other dimensionality-reduction methods.

Robustness to variations in lighting conditions is a key objective for any deep vision system. To this end, our paper extends the receptive field of convolutional neural networks with two residual components, ubiquitous in the visual processing system of vertebrates: On-center and off-center pathways, with an excitatory center and inhibitory surround; OOCS for short. The On-center pathway is excited by the presence of a light stimulus in its center, but not in its surround, whereas the Off-center pathway is excited by the absence of a light stimulus in its center, but not in its surround. We design OOCS pathways via a difference of Gaussians, with their variance computed analytically from the size of the receptive fields. OOCS pathways complement each other in their response to light stimuli, ensuring this way a strong edge-detection capability, and as a result an accurate and robust inference under challenging lighting conditions. We provide extensive empirical evidence showing that networks supplied with OOCS pathways gain accuracy and illumination-robustness from the novel edge representation, compared to other baselines.

For machine agents to successfully interact with humans in real-world settings, they will need to develop an understanding of human mental life. Intuitive psychology, the ability to reason about hidden mental variables that drive observable actions, comes naturally to people: even pre-verbal infants can tell agents from objects, expecting agents to act efficiently to achieve goals given constraints. Despite recent interest in machine agents that reason about other agents, it is not clear if such agents learn or hold the core psychology principles that drive human reasoning. Inspired by cognitive development studies on intuitive psychology, we present a benchmark consisting of a large dataset of procedurally generated 3D animations, AGENT (Action, Goal, Efficiency, coNstraint, uTility), structured around four scenarios (goal preferences, action efficiency, unobserved constraints, and cost-reward trade-offs) that probe key concepts of core intuitive psychology. We validate AGENT with human-ratings, propose an evaluation protocol emphasizing generalization, and compare two strong baselines built on Bayesian inverse planning and a Theory of Mind neural network. Our results suggest that to pass the designed tests of core intuitive psychology at human levels, a model must acquire or have built-in representations of how agents plan, combining utility computations and core knowledge of objects and physics.