computational neuroscientists

Abstract: Animals have a remarkable capacity for autonomy---driven by intrinsic motivation---without external sensory cues or extrinsic objectives, yet the computational mechanisms behind this ability largely remain a mystery. We combine whole-brain recordings in the fruit fly (Drosophila melanogaster), which reveal neural representations of spontaneous exploratory decisions more than 10 seconds in advance, with a neuromechanical digital twin to test whether optimizing intrinsic goals yields realistically embodied artificial agents that quantitatively match fly behavior and internal representations of future volitional action during exploration. Our hierarchical policy selects from a discrete library of low-level motor primitives, consistent with ethological theories of behavioral syllables. We train agents without external reward using 20 intrinsic motivation algorithms spanning curiosity, entropy, and competency methods. The agents are evaluated in a virtual tethered-ball assay modeled on the fly experiment, comparing spontaneous locomotor statistics and internal representations and decoding future turn direction from kinematics and neural activity on the same timescales observed in flies. DIAYN, a hierarchical competency algorithm learning discrete policies that maximize behavioral entropy and the separability of induced sensory observations, achieves the strongest joint behavioral and neural prospective coding performance relative to flies. Its learned policies closely capture individual variability in fly exploration strategies, suggesting that this diversity serves to maximize state-space coverage at the population level. DIAYN's latent activity also closely captures the sum-difference rule for interhemispheric encoding of kinematics in biological flies. These results establish hierarchical, intrinsically motivated agents as a powerful framework for reverse-engineering animal autonomy.

Abstract: Neural network models are increasingly constructed from synapse-resolution connectomes, and the same circuit is now available in reconstructions from other animals and pipelines. We do not know whether such models are dependent on the reconstruction they are built from, and whether connectome differences are biological or measurement errors. We studied the Drosophila head-direction circuit in nine versions: four flies (male CNS, hemibrain, Fly Wire, BANC) and five variants of the same fly varying only by thresholds, proofreading or synapse detection. Using wiring-based correspondences validated by anatomical labels, we place all differences on one scale. A change of synapse detection within one fly changed the circuit more than halfway to the smallest inter-fly difference on four distances; proofreading differences were smaller but depended on the metric, and left and right halves of one fly differed no more than a random half. Networks trained on each wiring to hold a cued heading developed near-perfect ring attractors, but their error increased from below 1 degree to 10-28 degrees when all weights changed by 1%. Training on each wiring did not transfer to any other connectome, including other versions of the same fly; refitting thirty cell-type gains, we repaired filtering-level differences but remaining error depended on wiring distance. Training with noise lowered precision and enhanced transfer. Imaging data indicate compasses drift smoothly and do not break; they function despite differences comparable to those of this study.Therefore, connectome-constrained models need to reflect the reconstruction they stem from and the robustness normal circuits exhibit and models lack.

Abstract: Understanding when neural networks learn interpretable representations is central to mechanistic interpretability. We study this through identifiability: when can supervised learning recover the true latent variables underlying the data? We introduce two data generating processes distinguished by their causal direction where either labels cause latents (generative) or latents cause labels (discriminative). When the representation has at least as many dimensions as the latent space, we prove that the optimal encoders are linear in the latents. Conversely, when dimensions are insufficient, identifiability generically fails and encoders become nonlinear. We then show that additional constraints yield recovery of individual latent variables, not just linear mixtures. In the generative setting, non-negative activations and energy efficiency force each neuron to encode exactly one latent, providing a precise account of selective grandmother cell-like responses. In the discriminative setting, when latents are sparse and the true measurement matrix satisfies the spark condition, the learned encoder inherits compressed sensing structure, enabling sparse dictionary learning to perfectly recover individual latents. This constitutes, to our knowledge, the first identifiability result for undercomplete nonlinear independent component analysis. Our framework unifies nonlinear ICA, compressed sensing, and neural network interpretability, delineating exactly when representations transition from nonlinear distortions to linear representations and, under additional constraints or steps, to clean, axis-aligned codes. Theoretical predictions are validated on synthetic benchmarks and on activations drawn from vision models, large language models, and macaque inferotemporal cortex.

Abstract: Mandlebrot's coastline paradox reframes measurement as a joint property of an object and its ruler. Here we ask how observational resolution shapes the apparent structure of neural computation. We introduce a scale-indexed decomposition that separates the predictive information captured by direct dependencies from the residual outside that model family. Exact constructions show that projection can convert higher-order dependence into pairwise structure. Projection can increase the direct fraction of surviving information even as total predictive information decreases. A schematic branch-to-soma cascade grounds these effects in local coincidence detection, saturating integration and somatic mixing. Resolving organized nonlinear subunits improves approximation and raises effective representational rank. In a nested hierarchy, these gains occur without increasing information about the target. This distinction separates information availability from access by a restricted readout. A point-neuron or direct population model therefore establishes an effective description at a specified scale. It does not uniquely identify the finer computation that generated the observed relation. Which resolution is adequate depends on the observable and perturbation of interest.

Abstract: Bridging the structural gap between biological brains and artificial neural networks presents a pathway to altered computational dynamics. This paper introduces a Reservoir Computing framework that replaces random networks with biologically realistic modularity by applying the Weighted Stochastic Block Model (WSBM) to Echo State Networks (ESNs). This topological parameterization constructs reservoirs reflecting latent functional sub-circuits. Furthermore, the integration of Input Dynamical Similarity Analysis (InputDSA) provides a mechanism to isolate and compare how structural priors modulate intrinsic recurrent dynamics versus external inputs. By evaluating these architectures, we establish that structural diversity does not necessarily predicts behavioral diversity across the selected network subset. Furthermore, our demixed analysis confirms Anna Karenina principle of dynamics, demonstrating that environmental constraints enforce dynamical convergence in successful agents, while failing networks degenerate into idiosyncratic trajectories.

Abstract: Connectome-constrained neural networks make biological components directly accessible to intervention, but their mechanistic conclusions can still depend on the comparison model, intervention, circuit representation and trained solution. We stress-test these dependencies in flyvis, a \emph{Drosophila} motion-vision model, using its 50-model ensemble, task-matched causal CNN controls and replicated interventions. At the level of model behaviour, three-level reverse-phi reversal in flyvis is strongly period- and velocity-dependent and also appears in task-matched CNNs; neither family reproduces the fly's stationary-sawtooth response. Adversarial direction reversal requires a perturbation bound of 0.21--0.27 times stimulus contrast in flyvis versus 0.13--0.25 in CNNs, but the gap over a parameter-matched CNN largely closes for larger CNNs. At the level of mechanism, matching attribution to the intervention matters: for held-out-mean replacement, first-order edge attribution patching reaches pooled AUROC 0.970 and Spearman 0.872, versus 0.933 and 0.126 when its zero-aligned score is evaluated against the same ground truth. Circuit conclusions also vary with representation and ensemble member. Greedy cell-type sets meet a model-relative T4/T5 tuning criterion in 25 of 50 models, while T4/T5 output silencing reduces the tested optic-flow behaviour to at most two of eight clips in 40. In six models where the cell-type search first succeeds, the corresponding connection sets can be pruned to 13--31 added classes; under an additional two-sided response-amplitude check, only two of those six first-success cell-type sets still meet the tuning threshold. These results support a narrower use of connectome-constrained models: they make mechanistic hypotheses directly testable, but the resulting claims must be scoped to the model family, intervention, representation and trained solution.

Abstract: Neural representations can encode more features than they have dimensions, a phenomenon known as superposition. We study the dimension needed to compute Boolean gates from such representations. For a single threshold layer with a Gaussian random dictionary and uniformly random sparse Boolean inputs, we derive sharp dimension thresholds under two error criteria. A vanishing expected error count can require more dimensions than correctness of every output with high probability. Shared reads explain the gap: rare realizations can produce many errors at once. The expected-count threshold has ball geometry, while joint reliability has box geometry when a gate is evaluated on every feature tuple. Optimizing shared readout weights and biases gives explicit thresholds for conjunction, disjunction, and majority. For pairwise conjunction, the analysis also describes the transition near the threshold, in agreement with exact simulations.

Abstract: Neurons of the brain exhibit a rich repertoire of electrophysiology dynamics with the same repeated stimulus eliciting very different voltage responses from the same cell. One common approach in biophysically detailed models is to capture this variability through ensembles of deterministic parametrizations, at a cost of hundreds of thousands of CPU hours. Existing machine learning surrogates inherit the same limitation, where a stimulus is mapped to a single voltage response. We address this challenge by learning a conditional generative model for single-neuron electrophysiology, using flow matching with a velocity field conditioned on the input current. On biophysically detailed models of two human cortical interneuron types, the generated responses closely reproduce the electrophysiological feature distributions, spike-time structure, and excitability profiles, even matching the experimental recordings from the corresponding human cortical neurons. Near the firing threshold, firing and non-firing responses coexist at the same stimulus amplitude, and at high amplitudes, ensembles may split into low- and high-firing modes near depolarization block. We show that our model recovers both modes in each case, while a neural operator baseline suppresses spiking near threshold and blurs the gap between modes at depolarization block.

Abstract: By making use of partial information decomposition, we analyse information transmission through a local processor which receives two streams of integrated inputs. We revise previously stated conditions for contextual modulation that are based on the components of partial information decomposition, and introduce a condition for the presence of signal integration. Exact results are obtained for information-theoretic measures and the components of partial information decomposition using the Ibroja method. A general class of activation functions is considered along with a particular divisive normalisation transfer function. These results are applied with several activation functions, of additive, multiplicative, subtractive and divisive forms, with graphical illustration, and the conditions for modulation and integration are tested in each case. The revised information-theoretic conditions are also applied to noisy data obtained from a realistic simulation of a model layer 5b pyramidal cell in three distinct regimes defined by experimental design and characterised by the values of the input basal and apical amplitudes. Evidence for driving basal input with modulating apical input, driving apical input with modulating basal input, and of apical-basal signal integration is presented.

Abstract: Representations are routinely used across machine learning, psychology, and neuroscience to draw inferences about the computations of biological and artificial systems. Such inferences presume a meaningful link between representational geometry and the computation being performed. For artificial neural networks, however, the extent to which function constrains representation remains unclear. One key obstacle is that these networks admit parameter symmetries: changes in parameterization that preserve function exactly while reshaping representational geometry. Here, we show that a broad class of parameter symmetries acts on representations through just three primitive feature transformations: addition, duplication, and scaling. This feature-level characterization yields a closed-form decomposition of representational geometry into essential and auxiliary components, which makes precise how degeneracy in representational geometry can grow with overparameterization even when function is held fixed. Finally, we show that implementation-level selection rules can resolve this degeneracy, yielding identifiable geometries in which features are weighted according to their contributions to the network's function. Together, our results delineate when representations can support inferences about computation, and when they cannot.

Abstract: Recovering hidden transport mechanisms from sparse spatiotemporal observations is a fundamental inverse problem in scientific machine learning. In brain tracer imaging, dynamic contrast-enhanced MRI (DCE-MRI) provides time-resolved measurements of tracer concentration, while the underlying velocity and source mechanisms governing tracer propagation remain unobserved. We formulate this problem as physics-informed latent-state inference, in which the transport field itself is the primary object of inference rather than an auxiliary variable used only to reconstruct observed densities. We propose Physics-Informed Neural Optimal Mass Transport (PI-NOMT), a framework that represents density, velocity, and source as continuous neural fields and combines a continuous neural density teacher, recursive differentiable advection--diffusion--source rollout, unbalanced optimal-transport regularization, and governing-equation supervision. Physical laws act as structural priors that constrain the space of admissible transport mechanisms, while observed tracer dynamics provide evidence for estimating the latent transport state. We evaluate PI-NOMT on a synthetic benchmark with known ground-truth transport and on DCE-MRI sequences from nine control rats. On the synthetic benchmark, PI-NOMT accurately recovers the prescribed velocity field, including its magnitude, direction, and integrated trajectories, rather than merely reconstructing endpoint densities. Across the nine rat datasets, the framework yields sub-percent local endpoint error, consistent physical speed scales, and low post-training PDE and incompressibility residuals. These results support physics-informed latent-state inference as a general framework for recovering hidden transport mechanisms from observed dynamic scalar fields.

Abstract: The aim of this work is to examine the connectomes of Caenorhabditis elegans through a computational lens using the reservoir computing framework. Connectomes are mappings of biological neural networks; C. elegans is the first organism for which physical connectomes covering the whole nervous system have been published. The connectomes of C. elegans used in this paper have been derived at different ages of the organism and are based on three different ways of measuring inter-cellular connections. They have, with minimal preprocessing, been implemented as reservoirs in the form of echo state networks, which are recurrent neural networks. In reservoir computing, the reservoir itself is not trained, rather the output of the reservoir is passed to a comparatively small read-out module in which training takes place. Training and testing is conducted in different neuro-inspired tasks, with the aim of using these tasks as a benchmark for the connectomes. This process has been repeated with different configurations of the reservoir and equally sized but randomized null models have been used for comparison. The results show that the biological wiring and a bio-informed configuration of input and output nodes of the reservoirs do not necessarily lead to better performance. Contrarily, the randomized null models are often outperforming the original connectomes on the chosen benchmarks. At the same time it becomes clear that the results depend a lot on the configuration of the reservoir and the way the connectome has been derived from the organism. Connectomes from different ages may produce varying outcome, without a clear trend becoming visible.