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Bakermans, J. J. W.

Publications and source records attributed to Bakermans, J. J. W..

4 recordsLinked to original sources

Augmenting the Bayesian Brain with learned and reusable world-model components for flexible cognition

The Bayesian Brain hypothesis assumes that cognition relies on internal generative models of the world, yet existing implementations remain constrained by pre-specified, task-specific generative structures and computationally heavy iterative inference schemes. Here, we introduce modular neural state-space models as a scalable realization of the Bayesian Brain, replacing fixed generative structures and pre-specified inference rules with learned world-model components and amortized neural updates. This framework preserves the core commitment to explaining observations through hidden causes while making inference learned and reusable rather than pre-specified and task-specific. Our modular implementation of these models affords learned components to be seamlessly recombined and stacked across superficially different tasks that share similar latent dynamics. Such computational reuse supports zero-shot generalization and predicts selective correlations of inference parameters between tasks. We confirm these key predictions in human behavior, identifying learned and reusable world-model components as a candidate computational principle for flexible cognition.

neuroscience↗

A hierarchical coordinate system for sequence memory in human entorhinal cortex.

The entorhinal cortex (EC) supports a coordinate system for spatial memories, organised in a hierarchy along the EC dorso-ventral axis. Recent theories suggest that a similar coordinate system could scaffold non-spatial memories. Here we show that an abstract hierarchical coordinate system supports arbitrary sequence memories in the human medial temporal lobe (MTL). In single-unit recordings from MTL, we find abstract, coordinate-like coding in a simple sequential memory task. In fMRI we find that abstract coordinate representations are arranged hierarchically along the entorhinal cortex, mirroring the anatomical gradient of grid cells in the rodent EC but now for non-spatial sequences. We replicate this finding in an independent cohort of participants. These data suggest that memories are scaffolded on a hierarchical coordinate system aligned to preserved anatomy across domains and species.

neuroscience↗

Constructing future behaviour in the hippocampal formation through composition and replay

Hippocampus is critical for memory, imagination and constructive reasoning. However, recent models have suggested that its neuronal responses can be well explained by graphs, or state-spaces, that model the transitions between experiences. Here we use simulations and hippocampal recordings to reconcile these views. We show that if state-spaces are constructed compositionally from existing building blocks, or primitives, hippocampal responses can be interpreted as compositional memories, binding these primitives together. Critically, this enables agents to behave optimally in novel environments with no new learning, inferring behaviour directly from the composition. We predict a role for hippocampal replay in building and consolidating these compositional memories. Importantly, due to their compositional nature, replay can construct states the agent has never experienced - effectively building memories of the future. We test these predictions in two datasets by showing that replay events from newly discovered landmarks induce and strengthen new remote firing fields. These memories, built in replay, are compositional. When the landmark is moved, replay builds a new firing field at the same vector to the new location. Together, these findings provide a framework for reasoning about compositional memories, and demonstrate that such memories are formed in hippocampal replay.

neuroscience↗

Pausing controls branching between productive and non-productive pathways during initial transcription

Transcription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. Recently, initial RNA synthesis by the bacterial RNA polymerase (RNAP) has been shown to be interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Here, we employed single-molecule FRET and biochemical analysis to disentangle the pausing-related pathways of bacterial initial transcription. We present further evidence that region {sigma}3.2 constitutes a barrier after the initial transcribing complex synthesizes a 6-nt RNA (ITC6), halting transcription. We also show that the paused ITC6 state acts as a checkpoint that directs RNAP, in an NTP-dependent manner, to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway that blocks transcription initiation. Our results show that abortive RNA release and DNA unscrunching are not as tightly coupled as previously thought.

biophysics↗