QuantFormer: Learning to Quantize for Neural Activity Forecasting in Mouse Visual Cortex

Understanding complex animal behaviors hinges on deciphering the neural activity patterns within brain circuits, making the ability to forecast neural activity crucial for developing predictive models of brain dynamics. This capability holds immense value for neuroscience, particularly in applications such as real-time optogenetic interventions. While traditional encoding and decoding methods have been used to map external variables to neural activity and vice versa, they focus on interpreting past data. In contrast, neural forecasting aims to predict future neural activity, presenting a unique and challenging task due to the spatiotemporal sparsity and complex dependencies of neural signals. Existing transformer-based forecasting methods, while effective in many domains, struggle to capture the distinctiveness of neural signals characterized by spatiotemporal sparsity and intricate dependencies. To address this challenge, we here introduce QuantFormer, a transformer-based model specifically designed for forecasting neural activity from two-photon calcium imaging data. Unlike conventional regression-based approaches, QuantFormerreframes the forecasting task as a classification problem via dynamic signal quantization, enabling more effective learning of sparse neural activation patterns. Additionally, QuantFormer tackles the challenge of analyzing multivariate signals from an arbitrary number of neurons by incorporating neuron-specific tokens, allowing scalability across diverse neuronal populations. Trained with unsupervised quantization on the Allen dataset, QuantFormer sets a new benchmark in forecasting mouse visual cortex activity. It demonstrates robust performance and generalization across various stimuli and individuals, paving the way for a foundational model in neural signal prediction.

Self-supervised learning for radio-astronomy source classification: a benchmark

The upcoming Square Kilometer Array (SKA) telescope marks a significant step forward in radio astronomy, presenting new opportunities and challenges for data analysis. Traditional visual models pretrained on optical photography images may not perform optimally on radio interferometry images, which have distinct visual characteristics. Self-Supervised Learning (SSL) offers a promising approach to address this issue, leveraging the abundant unlabeled data in radio astronomy to train neural networks that learn useful representations from radio images. This study explores the application of SSL to radio astronomy, comparing the performance of SSL-trained models with that of traditional models pretrained on natural images, evaluating the importance of data curation for SSL, and assessing the potential benefits of self-supervision to different domain-specific radio astronomy datasets. Our results indicate that, SSL-trained models achieve significant improvements over the baseline in several downstream tasks, especially in the linear evaluation setting; when the entire backbone is fine-tuned, the benefits of SSL are less evident but still outperform pretraining. These findings suggest that SSL can play a valuable role in efficiently enhancing the analysis of radio astronomical data. The trained models and code is available at: \url{https://github.com/dr4thmos/solo-learn-radio}

Evidential Federated Learning for Skin Lesion Image Classification

We introduce FedEvPrompt, a federated learning approach that integrates principles of evidential deep learning, prompt tuning, and knowledge distillation for distributed skin lesion classification. FedEvPrompt leverages two sets of prompts: b-prompts (for low-level basic visual knowledge) and t-prompts (for task-specific knowledge) prepended to frozen pre-trained Vision Transformer (ViT) models trained in an evidential learning framework to maximize class evidences. Crucially, knowledge sharing across federation clients is achieved only through knowledge distillation on attention maps generated by the local ViT models, ensuring enhanced privacy preservation compared to traditional parameter or synthetic image sharing methodologies. FedEvPrompt is optimized within a round-based learning paradigm, where each round involves training local models followed by attention maps sharing with all federation clients. Experimental validation conducted in a real distributed setting, on the ISIC2019 dataset, demonstrates the superior performance of FedEvPrompt against baseline federated learning algorithms and knowledge distillation methods, without sharing model parameters. In conclusion, FedEvPrompt offers a promising approach for federated learning, effectively addressing challenges such as data heterogeneity, imbalance, privacy preservation, and knowledge sharing.

FedRewind: Rewinding Continual Model Exchange for Decentralized Federated Learning

In this paper, we present FedRewind, a novel approach to decentralized federated learning that leverages model exchange among nodes to address the issue of data distribution shift. Drawing inspiration from continual learning (CL) principles and cognitive neuroscience theories for memory retention, FedRewind implements a decentralized routing mechanism where nodes send/receive models to/from other nodes in the federation to address spatial distribution challenges inherent in distributed learning (FL). During local training, federation nodes periodically send their models back (i.e., rewind) to the nodes they received them from for a limited number of iterations. This strategy reduces the distribution shift between nodes' data, leading to enhanced learning and generalization performance. We evaluate our method on multiple benchmarks, demonstrating its superiority over standard decentralized federated learning methods and those enforcing specific routing schemes within the federation. Furthermore, the combination of federated and continual learning concepts enables our method to tackle the more challenging federated continual learning task, with data shifts over both space and time, surpassing existing baselines.

IPMN Risk Assessment under Federated Learning Paradigm

Accurate classification of Intraductal Papillary Mucinous Neoplasms (IPMN) is essential for identifying high-risk cases that require timely intervention. In this study, we develop a federated learning framework for multi-center IPMN classification utilizing a comprehensive pancreas MRI dataset. This dataset includes 653 T1-weighted and 656 T2-weighted MRI images, accompanied by corresponding IPMN risk scores from 7 leading medical institutions, making it the largest and most diverse dataset for IPMN classification to date. We assess the performance of DenseNet-121 in both centralized and federated settings for training on distributed data. Our results demonstrate that the federated learning approach achieves high classification accuracy comparable to centralized learning while ensuring data privacy across institutions. This work marks a significant advancement in collaborative IPMN classification, facilitating secure and high-accuracy model training across multiple centers.

Adaptive Aggregation Weights for Federated Segmentation of Pancreas MRI

Federated learning (FL) enables collaborative model training across institutions without sharing sensitive data, making it an attractive solution for medical imaging tasks. However, traditional FL methods, such as Federated Averaging (FedAvg), face difficulties in generalizing across domains due to variations in imaging protocols and patient demographics across institutions. This challenge is particularly evident in pancreas MRI segmentation, where anatomical variability and imaging artifacts significantly impact performance. In this paper, we conduct a comprehensive evaluation of FL algorithms for pancreas MRI segmentation and introduce a novel approach that incorporates adaptive aggregation weights. By dynamically adjusting the contribution of each client during model aggregation, our method accounts for domain-specific differences and improves generalization across heterogeneous datasets. Experimental results demonstrate that our approach enhances segmentation accuracy and reduces the impact of domain shift compared to conventional FL methods while maintaining privacy-preserving capabilities. Significant performance improvements are observed across multiple hospitals (centers).

Large-Scale Multi-Center CT and MRI Segmentation of Pancreas with Deep Learning

Automated volumetric segmentation of the pancreas on cross-sectional imaging is needed for diagnosis and follow-up of pancreatic diseases. While CT-based pancreatic segmentation is more established, MRI-based segmentation methods are understudied, largely due to a lack of publicly available datasets, benchmarking research efforts, and domain-specific deep learning methods. In this retrospective study, we collected a large dataset (767 scans from 499 participants) of T1-weighted (T1W) and T2-weighted (T2W) abdominal MRI series from five centers between March 2004 and November 2022. We also collected CT scans of 1,350 patients from publicly available sources for benchmarking purposes. We developed a new pancreas segmentation method, called PanSegNet, combining the strengths of nnUNet and a Transformer network with a new linear attention module enabling volumetric computation. We tested PanSegNet's accuracy in cross-modality (a total of 2,117 scans) and cross-center settings with Dice and Hausdorff distance (HD95) evaluation metrics. We used Cohen's kappa statistics for intra and inter-rater agreement evaluation and paired t-tests for volume and Dice comparisons, respectively. For segmentation accuracy, we achieved Dice coefficients of 88.3% (std: 7.2%, at case level) with CT, 85.0% (std: 7.9%) with T1W MRI, and 86.3% (std: 6.4%) with T2W MRI. There was a high correlation for pancreas volume prediction with R^2 of 0.91, 0.84, and 0.85 for CT, T1W, and T2W, respectively. We found moderate inter-observer (0.624 and 0.638 for T1W and T2W MRI, respectively) and high intra-observer agreement scores. All MRI data is made available at https://osf.io/kysnj/. Our source code is available at https://github.com/NUBagciLab/PaNSegNet.

Diffexplainer: Towards Cross-modal Global Explanations with Diffusion Models

We present DiffExplainer, a novel framework that, leveraging language-vision models, enables multimodal global explainability. DiffExplainer employs diffusion models conditioned on optimized text prompts, synthesizing images that maximize class outputs and hidden features of a classifier, thus providing a visual tool for explaining decisions. Moreover, the analysis of generated visual descriptions allows for automatic identification of biases and spurious features, as opposed to traditional methods that often rely on manual intervention. The cross-modal transferability of language-vision models also enables the possibility to describe decisions in a more human-interpretable way, i.e., through text. We conduct comprehensive experiments, which include an extensive user study, demonstrating the effectiveness of DiffExplainer on 1) the generation of high-quality images explaining model decisions, surpassing existing activation maximization methods, and 2) the automated identification of biases and spurious features.

SalFoM: Dynamic Saliency Prediction with Video Foundation Models

Recent advancements in video saliency prediction (VSP) have shown promising performance compared to the human visual system, whose emulation is the primary goal of VSP. However, current state-of-the-art models employ spatio-temporal transformers trained on limited amounts of data, hindering generalizability adaptation to downstream tasks. The benefits of vision foundation models present a potential solution to improve the VSP process. However, adapting image foundation models to the video domain presents significant challenges in modeling scene dynamics and capturing temporal information. To address these challenges, and as the first initiative to design a VSP model based on video foundation models, we introduce SalFoM, a novel encoder-decoder video transformer architecture. Our model employs UnMasked Teacher (UMT) as feature extractor and presents a heterogeneous decoder which features a locality-aware spatio-temporal transformer and integrates local and global spatio-temporal information from various perspectives to produce the final saliency map. Our qualitative and quantitative experiments on the challenging VSP benchmark datasets of DHF1K, Hollywood-2 and UCF-Sports demonstrate the superiority of our proposed model in comparison with the state-of-the-art methods.

Selective Attention-based Modulation for Continual Learning

We present SAM, a biologically-plausible selective attention-driven modulation approach to enhance classification models in a continual learning setting. Inspired by neurophysiological evidence that the primary visual cortex does not contribute to object manifold untangling for categorization and that primordial attention biases are still embedded in the modern brain, we propose to employ auxiliary saliency prediction features as a modulation signal to drive and stabilize the learning of a sequence of non-i.i.d. classification tasks. Experimental results confirm that SAM effectively enhances the performance (in some cases up to about twenty percent points) of state-of-the-art continual learning methods, both in class-incremental and task-incremental settings. Moreover, we show that attention-based modulation successfully encourages the learning of features that are more robust to the presence of spurious features and to adversarial attacks than baseline methods. Code is available at: https://github.com/perceivelab/SAM.