Rapid spatial cognition in mice, with and without neocortex and hippocampus
Jieyu ZhengiD, Rogério GuimarãesiD, Zeynep TuraniD, Anwesha DasiD, Jennifer Yuan-Shih HuiD, Katelyn Sadorf, Pietro PeronaiD, Markus MeisteriD
Abstract
Rapid learning, memory, and generalization are often attributed to the neocortex and hippocampus. We examined these cognitive abilities in mice navigating a reconfigurable 3D labyrinth. Naive wildtype mice solved a complex route within a few rewards, generalized to similar problems, and learned to favor a decision far removed from reward experience, all within a few hours. Computational modeling suggests that much of the learning occurs even before the first occurrence of reward, as the animal builds a model of the environment. Mutant mice lacking neocortex and hippocampus retain all these cognitive abilities, and remember the task over multiple weeks. Their main deficit is a delay of the learning curve from inefficient exploration. In a few hours of exposure to the task, the subcortical brain has little opportunity to reorganize in response to the challenge. We conclude that rapid spatial learning in mice does not strictly require circuits of the hippocampus or neocortex.
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In-depth summary
Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 2 (29 Sept 2026) · CC BY 4.0
Naive mice learn a 9-turn route in a reconfigurable 3D maze within about 20 rewards; mutants lacking neocortex and hippocampus also learn, remember and generalize, though early exploration is inefficient.
Few-shot learning, credit assignment, retention and transfer have mostly been studied each in its own task and are by default interpreted through hippocampus and neocortex. The work measures them together in one reconfigurable, graph-defined maze over a few hours, and tests whether they persist in mice that developed without both structures.
Key results
ShownNaive wildtype mice learned a 9-hole path maze, with a four-way choice at each hole, within about 20 rewards, improving in three phases. Part of the learning, a bias against re-crossing the hole just passed, was acquired before the first reward.
25 mice on Mask A: reward intervals fell to ~0.11 of the starting value; traverse 22 took ~0.2 of the initial duration while running speed rose only ~1.5×. First-traverse corridor error rate was 0.26 vs 0.44 for a memoryless random walker; estimated forward bias rose from ~0.35 to ~0.6, crossing the walker's 0.5 roughly one quarter into the first journey. · 2.2 Rapid learning of a 9-turn maze in three…; 3.1 Rapid rule learning and generalization; 5.7.1 First-order Markov model with forward bias
SuggestedMice lacking neocortex and hippocampus (Emx1-Cre conditional Pals1 knockouts) learned the 9-hole maze, retained it across weeks and transferred experience to new masks. Their deficit centred on slow, repetitive exploration before reward discovery, and fewer reached the learning criterion.
9 of 16 acortical mice learned Mask A; 4 learners vs 27 controls needed ~2.4× as long for four rewards, with D0 ~2.6× and comparable late duration and learning rate. Across genotypes, median traverse duration in later sessions was ~0.4 of Day 1, and stayed below Day 1 even after gaps approaching 60 days. New 9-turn masks: D0 ~0.3, E0 ~0.7 of first maze. Mask D: 5 of 13 acortical vs 8 of 8 siblings learned. · 2.5 Acortical mice rapidly learned the maze…; 2.6 Acortical mice retained maze solutions over…; 2.7 Acortical mice generalized in new mazes
SuggestedIn a cyclic maze of two densely interconnected subgraphs joined by a bottleneck corridor (Mask D), mice learned to favour the bottleneck at its gateway within 1-3 rewards, separately for each direction. Choices inside the subgraphs stayed largely unbiased and routes never settled.
6 of 7 mice obtained rewards; traverses improved ~5× over the first 20. Gateway bottleneck choice (chance 0.2) rose within ~3 rewards outbound and was above chance on the first homebound journey; off-path choices stayed near 1/3 chance for most start corridors, with no trend across rewards. Graph error rates fell only to ~0.7 of initial. First reward followed the bottleneck decision by tens of seconds to minutes. · 2.4 Rapid credit assignment to a remote decision…; 3.2 Rapid learning of remote decisions; 5.6.6 Directional transitions in the Mask D maze
ShownWildtype mice retained Mask A overnight and brought experience to new 9-turn mazes. Transfer lowered both starting and late values of duration and turn error while learning rates stayed similar to Day 1, and an advantage from the familiar turn sequence was short-lived.
Day 2.1 Mask A vs Day 1 (8 mice): D0 ~0.3, E0 ~0.5, Dlate ~0.4, Elate ~0.6. Days 2.2-2.4: D0 ~0.6, E0 ~0.7, Dlate ~0.7 and Elate ~0.6 of Day 1, with similar learning rates; first-traverse corridor error in a new maze ~0.6 of Day 1. On Day 2.1, Mask B (Mask A's turn sequence) vs Mask C gave D0 ~0.6, an advantage gone by Days 2.2-2.4. · 2.3 Overnight memory and generalization to new…; Figure legends
SuggestedIn simulations on the Mask D graph, a model-based circuit that learns a map from unrewarded exploration (Endotaxis) reproduced one-shot bottleneck preference, whereas tabular TD(0) Q-learning propagated value slowly. On Mask A, mouse errors also contradicted model-free predictions.
Before reward both agents match the memoryless walker (bottleneck choice 0.2); after one reward Endotaxis is perfect, while Q-learning (20 agents) lags, depending on self-play routes. On one mouse's first two journeys, Endotaxis learned adjacency from sorties, then signalled the bottleneck above control corridors. In early outbound Mask A traverses, mouse turn errors were lower at holes farthest from reward. · 2.8 Candidate algorithms for few-shot spatial…; 3.2 Rapid learning of remote decisions; 5.7.2 The Endotaxis Model; 5.7.3 Model-free Reinforcement Learning
Methods, data and reproducibility
Mice alternated between two water ports through an 11×11 two-layer maze in darkness, its connectivity set by a swappable hole mask; DeepLabCut tracks were scored for traverse duration and turn, corridor and tile errors and fit with exponential learning curves. Wildtype mice were compared with Pals1 conditional knockouts (Emx1-Cre) lacking neocortex and hippocampus, and with Q-learning and Endotaxis simulations.
- C57BL/6J wildtype mice (Jackson Laboratory Strain 000664), experimentally naive adults aged 61-106 days · mouse · n = 47
- Acortical mice: homozygous Pals1 loxp/loxp; Emx1-Cre+ conditional knockouts (Emx1-Cre line Jackson Strain 005628) lacking neocortex and hippocampus · mouse · n = 18
- Cre-negative sibling controls from the mutant colony · mouse · n = 9
- Behavioural sessions analysed across all animals (33 male, 41 female) · mouse · n = 208 sessions from 74 animals
- Wildtype cohort for Day 1 Mask A and the two-day path-graph experiment (Masks A, B, C) · mouse · n = 25 mice
- Wildtype cohort given Mask D as first complex mask after Mask O training · mouse · n = 7 mice (6 obtained rewards)
- Tray-swap landmark test with a clean copy of Mask A · mouse · n = 8 mice
- Structural MRI and retrograde HSV-hEF1-mCherry tracing from superior colliculus in acortical and wildtype mice · mouse
- Methods & tools
- Manhattan Maze (custom reconfigurable two-layer maze), DeepLabCut 2.2rc3 / 3.0.0rc14, Sanworks Bpod State Machine r2.s, MATLAB, scipy.optimize.curve_fit, Endotaxis model, Tabular TD(0) Q-learning, FlyCapture / SpinView (Teledyne FLIR), Transnetyx genotyping, HSV-hEF1-mCherry retrograde tracing, 3D gradient-echo MRI, Allen Institute Mouse Brain Reference Atlas
- Data & accessions
- https://github.com/Jieyusz/Zheng_2026_Manhattan
- Software & environment
- DeepLabCut 2.2rc3 and 3.0.0rc14; scipy.optimize.curve_fit for curve fits; Bpod State Machine r2.s driven by a MATLAB script. No requirement files, containers or other package versions are stated.
- Reproducibility gaps
- Shared data are processed trajectories; raw videos are not stated to be available. Further information for reanalysis comes from the lead contact on request. Robustness of Endotaxis results to parameter choice is reported as data not shown.
Limitations (6)
- The fully enclosed two-layer maze rules out wired neural recording, so the study is behavioural only; the authors propose open-top or wireless-recording versions for future work. · stated by the authors
- The sensory basis of the learning remains unresolved, particularly in the mutants, which retain no primary sensory or motor cortex apart from piriform cortex. · stated by the authors
- The mutant brain is developmentally rewired (e.g. altered dLGN and retinal projections), so it is not a normal brain minus cortex; subtler roles of hippocampus and neocortex would need targeted, reversible silencing during learning. · stated by the authors
- Endotaxis is presented as one possible mechanism, not a unique one; its parameters were chosen to illustrate qualitative behaviour rather than fitted to the mouse data. · stated by the authors
- Acortical conclusions rest on few animals selected by a 20-reward criterion (4 learners for Mask A curves, 5 for Mask D), some trained with human assistance or an intermediate Mask E, so they describe the subset that got past exploration rather than the whole line. · noted in this summary
- The wildtype credit-assignment result on Mask D comes from a single cohort of 6 mice. · noted in this summary
Who should read:Read this if you study rodent spatial learning, latent learning or credit assignment, or want a reconfigurable graph-structured maze for testing few-shot learning algorithms against mouse behaviour.
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