Grid cells in the medial entorhinal cortex (MEC) and place cells in the hippocampus (HC) both form spatial representations. Grid cells fire in triangular grid patterns, while place cells fire at specific locations and respond to contextual cues. How do these interacting systems support not only spatial encoding but also internally driven path planning, such as navigating to locations recalled from cues? Here, we propose a system-level theory of MEC-HC wiring that explains how grid and place cell patterns could be connected to enable cue-triggered goal retrieval, path planning, and reconstruction of sensory experience along planned routes. We suggest that place cells autoassociate sensory inputs with grid cell patterns, allowing sensory cues to trigger recall of goal-location grid patterns. We show analytically that grid-based planning permits shortcuts through unvisited locations and generalizes local transitions to long-range paths. During planning, intermediate grid states trigger place cell pattern completion, reconstructing sensory experiences along the route. Using a single-layer RNN modeling the HC-MEC loop with a planning subnetwork, we demonstrate these effects in both biologically grounded navigation simulations using RatatouGym and visually realistic navigation tasks using Habitat Sim.

Many animals learn cognitive maps of their environment - a simultaneous representation of context, experience, and position. Place cells in the hippocampus, named for their explicit encoding of position, are believed to be a neural substrate of these maps, with place cell "remapping" explaining how this system can represent different contexts. Briefly, place cells alter their firing properties, or "remap", in response to changes in experiential or sensory cues. Substantial sensory changes, produced, e.g., by moving between environments, cause large subpopulations of place cells to change their tuning entirely. While many studies have looked at the physiological basis of remapping, we lack explicit calculations of how the contextual capacity of the place cell system changes as a function of place field firing properties. Here, we propose a geometric approach to understanding population level activity of place cells. Using known firing field statistics, we investigate how changes to place cell firing properties affect the distances between representations of different environments within firing rate space. Using this approach, we find that the number of contexts storable by the hippocampus grows exponentially with the number of place cells, and calculate this exponent for environments of different sizes. We identify a fundamental trade-off between high resolution encoding of position and the number of storable contexts. This trade-off is tuned by place cell width, which might explain the change in firing field scale along the dorsal-ventral axis of the hippocampus. We demonstrate that clustering of place cells near likely points of confusion, such as boundaries, increases the contextual capacity of the place system within our framework and conclude by discussing how our geometric approach could be extended to include other cell types and abstract spaces.

The vertebrate hippocampus is thought to use recurrent connectivity in area CA3 to support episodic memory recall from partial cues. This brain area also contains place cells, whose location-selective firing fields implement maps supporting spatial memory. Here we show that place cells emerge in networks trained to remember temporally continuous sensory episodes. We model CA3 as a recurrent autoencoder that recalls and reconstructs sensory experiences from noisy and partially occluded observations by agents traversing simulated arenas. The agents move in realistic trajectories modeled from rodents and environments are modeled as continuously varying, high-dimensional, sensory experience maps (spatially smoothed Gaussian random fields). Training our autoencoder to accurately pattern-complete and reconstruct sensory experiences with a constraint on total activity causes spatially localized firing fields, i.e., place cells, to emerge in the encoding layer. The emergent place fields reproduce key aspects of hippocampal phenomenology: a) remapping (maintenance of and reversion to distinct learned maps in different environments), implemented via repositioning of experience manifolds in the network’s hidden layer, b) orthogonality of spatial representations in different arenas, c) robust place field emergence in differently shaped rooms, with single units showing multiple place fields in large or complex spaces, and (d) slow representational drift of place fields. We argue that these results arise because continuous traversal of space makes sensory experience temporally continuous. We make testable predictions: a) rapidly changing sensory context will disrupt place fields, b) place fields will form even if recurrent connections are blocked, but reversion to previously learned representations upon remapping will be abolished, c) the dimension of temporally smooth experience sets the dimensionality of place fields, including during virtual navigation of abstract spaces.

Polyp segmentation plays an important role in preventing Colorectal cancer. Although Vision Transformer has been widely introduced in medical image segmentation to compensate the limitations of traditional CNN in modeling global context, its shortcomings in learning the fine-detailed features and the heavy computation cost also hinder its application in challenging polyp segmentation due to the various shapes and sizes of polyps, the low-intensity contrast between polyps and surrounding tissues, and the inherent real-time requirement. In this paper, we propose a multi-scale efficient transformer attention (META) mechanism for fast and high-accuracy polyp segmentation, where efficient transformer blocks are employed to generate multi-scale element-wise attentions for adaptive feature fusion in the famous U-shape encoder-decoder architecture. Specifically, our META mechanism includes two branches to capture multi-scale long-term dependencies, which are implemented via two efficient transformer blocks with different resolutions. The local branch is used to capture a relatively smaller transform attention under a relatively lower resolution, while the global branch is used to capture high-resolution transform attention. The final poly segmentation results are progressively integrated based on the META mechanism in each layer of the decoder. Extensive experiments are conducted on four polyp segmentation datasets (CVC-ClinicDB, Endoscenestill, Kvasir-SEG and ETIS-Larib) to demonstrate its advantages, consistently outperforming different competitors. While using ResNet34 as backbones, it can achieve 85.78% IoU and 92.03% Dice, 88.99% IoU and 93.85% Dice, 86.42% IoU and 91.86% Dice respectively in CVC-ClinicDB, Endoscenestill, and Kvasir-SEG, and a speed of 98 FPS at the input size of$3 \times 512 \times 512$on a NVIDIA GeForce RTX 3090 card. The code is available at https://github.com/szuzzb/META-Unet.Note to Practitioners—Automatic polyp segmentation is a crucial step of polyp recognition and diagnostic of colonoscopy, which usually require both high-accuracy and real-time performance. This article proposes a novel polyp segmentation method, namely META-Unet, by modeling multi-scale attention maps effectively and efficiently based on a novel multi-scale efficient transformer attention (META) mechanism, for faster and higher-accuracy polyp segmentation. We evaluate our META-Unet on four public polyp image segmentation datasets (CVC-ClinicDB, Endoscenestill, Kvasir-SEG and ETIS-Larib). Comprehensive experimental results validate its outstanding performance with a better balance in both accuracy and inference speed. The proposed META mechanism is potentially to be embedded in various deep learning frameworks and facilitates more computer-aided applications in clinical practice.

Texture plays an important role in cartoon illustrations to display object materials and enrich visual experiences. Unfortunately, manually designing and drawing an appropriate texture is not easy even for proficient artists, let alone novice or amateur people. While there exist tons of textures on the Internet, it is not easy to pick an appropriate one using traditional text-based search engines. Although several texture pickers have been proposed, they still require the users to browse the textures by themselves, which is still labor-intensive and time-consuming. In this article, an automatic texture recommendation system is proposed for recommending multiple textures to replace a set of user-specified regions in a cartoon illustration with visually pleasant look. Two measurements, the suitability measurement and the style-consistency measurement, are proposed to make sure that the recommended textures are suitable for cartoon illustration and at the same time mutually consistent in style. The suitability is measured based on the synthesizability, cartoonity, and region fitness of textures. The style-consistency is predicted using a learning-based solution since it is subjective to judge whether two textures are consistent in style. An optimization problem is formulated and solved via the genetic algorithm. Our method is validated on various cartoon illustrations, and convincing results are obtained.

Deep learning models have achieved remarkable success in multi-type nuclei segmentation. These models are mostly trained at once with the full annotation of all types of nuclei available, while lack the ability of continually learning new classes due to the problem of catastrophic forgetting. In this paper, we study the practical and important class-incremental continual learning problem, where the model is incrementally updated to new classes without accessing to previous data. We propose a novel continual nuclei segmentation method, to avoid forgetting knowledge of old classes and facilitate the learning of new classes, by achieving feature-level knowledge distillation with prototype-wise relation distillation and contrastive learning. Concretely, prototype-wise relation distillation imposes constraints on the inter-class relation similarity, encouraging the encoder to extract similar class distribution for old classes in the feature space. Prototype-wise contrastive learning with a hard sampling strategy enhances the intra-class compactness and inter-class separability of features, improving the performance on both old and new classes. Experiments on two multi-type nuclei segmentation benchmarks, i.e., MoNuSAC and CoNSeP, demonstrate the effectiveness of our method with superior performance over many competitive methods. Codes are available at https://github.com/zzw-szu/CoNuSeg.

Most state-of-the-art deep networks proposed for biomedical image segmentation are developed based on U-Net. While remarkable success has been achieved, its inherent limitations hinder it from yielding more precise segmentation. First, its receptive field is limited due to the fixed kernel size, which prevents the network from modeling global context information. Second, when spatial information captured by shallower layer is directly transmitted to higher layers by skip connections, the process inevitably introduces noise and irrelevant information to feature maps and blurs their semantic meanings. In this article, we propose a novel segmentation network equipped with a new context prior guidance (CPG) module to overcome these limitations for biomedical image segmentation, namely context prior guidance network (CPG-Net). Specifically, we first extract a set of context priors under the supervision of a coarse segmentation and then employ these context priors to model the global context information and bridge the spatial-semantic gap between high-level features and low-level features. The CPG module contains two major components: context prior representation (CPR) and semantic complement flow (SCF). CPR is used to extract pixels belonging to the same objects and hence produce more discriminative features to distinguish different objects. We further introduce deep semantic information for each CPR by the SCF mechanism to compensate the semantic information diluted during the decoding. We extensively evaluate the proposed CPG-Net on three famous biomedical image segmentation tasks with diverse imaging modalities and semantic environments. Experimental results demonstrate the effectiveness of our network, consistently outperforming state-of-the-art segmentation networks in all the three tasks. Codes are available at https://github.com/zzw-szu/CPGNet .

We study the semi-supervised learning problem, using a few labeled data and a large amount of unlabeled data to train the network, by developing a cross-patch dense contrastive learning framework, to segment cellular nuclei in histopathologic images. This task is motivated by the expensive burden on collecting labeled data for histopathologic image segmentation tasks. The key idea of our method is to align features of teacher and student networks, sampled from cross-image in both patch- and pixel-levels, for enforcing the intra-class compactness and inter-class separability of features that as we shown is helpful for extracting valuable knowledge from unlabeled data. We also design a novel optimization framework that combines consistency regularization and entropy minimization techniques, showing good property in eviction of gradient vanishing. We assess the proposed method on two publicly available datasets, and obtain positive results on extensive experiments, outperforming the state-of-the-art methods. Codes are available at https://github.com/zzw-szu/CDCL.