MERGE: Multi-faceted Hierarchical Graph-based GNN for Gene Expression Prediction from Whole Slide Histopathology Images

Recent advances in Spatial Transcriptomics (ST) pair histology images with spatially resolved gene expression profiles, enabling predictions of gene expression across different tissue locations based on image patches. This opens up new possibilities for enhancing whole slide image (WSI) prediction tasks with localized gene expression. However, existing methods fail to fully leverage the interactions between different tissue locations, which are crucial for accurate joint prediction. To address this, we introduce MERGE (Multi-faceted hiErarchical gRaph for Gene Expressions), which combines a multi-faceted hierarchical graph construction strategy with graph neural networks (GNN) to improve gene expression predictions from WSIs. By clustering tissue image patches based on both spatial and morphological features, and incorporating intra- and inter-cluster edges, our approach fosters interactions between distant tissue locations during GNN learning. As an additional contribution, we evaluate different data smoothing techniques that are necessary to mitigate artifacts in ST data, often caused by technical imperfections. We advocate for adopting gene-aware smoothing methods that are more biologically justified. Experimental results on gene expression prediction show that our GNN method outperforms state-of-the-art techniques across multiple metrics.

FedAH: Aggregated Head for Personalized Federated Learning

Recently, Federated Learning (FL) has gained popularity for its privacy-preserving and collaborative learning capabilities. Personalized Federated Learning (PFL), building upon FL, aims to address the issue of statistical heterogeneity and achieve personalization. Personalized-head-based PFL is a common and effective PFL method that splits the model into a feature extractor and a head, where the feature extractor is collaboratively trained and shared, while the head is locally trained and not shared. However, retaining the head locally, although achieving personalization, prevents the model from learning global knowledge in the head, thus affecting the performance of the personalized model. To solve this problem, we propose a novel PFL method called Federated Learning with Aggregated Head (FedAH), which initializes the head with an Aggregated Head at each iteration. The key feature of FedAH is to perform element-level aggregation between the local model head and the global model head to introduce global information from the global model head. To evaluate the effectiveness of FedAH, we conduct extensive experiments on five benchmark datasets in the fields of computer vision and natural language processing. FedAH outperforms ten state-of-the-art FL methods in terms of test accuracy by 2.87%. Additionally, FedAH maintains its advantage even in scenarios where some clients drop out unexpectedly. Our code is open-accessed at https://github.com/heyuepeng/FedAH.

RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses challenges due to inherent spatial distortions and modality-specific variations. Existing methods largely rely on direct alignment, which often fails to capture complex cross-modal relationships. To address these limitations, we propose a novel framework that aligns gene and image features using a ranking-based alignment loss, preserving relative similarity across modalities and enabling robust multi-scale alignment. To further enhance the alignment's stability, we employ self-supervised knowledge distillation with a teacher-student network architecture, effectively mitigating disruptions from high dimensionality, sparsity, and noise in gene expression data. Extensive experiments on gene expression prediction and survival analysis demonstrate our framework's effectiveness, showing improved alignment and predictive performance over existing methods and establishing a robust tool for gene-guided image representation learning in digital pathology.

A Multimodal Approach Combining Structural and Cross-domain Textual Guidance for Weakly Supervised OCT Segmentation

Accurate segmentation of Optical Coherence Tomography (OCT) images is crucial for diagnosing and monitoring retinal diseases. However, the labor-intensive nature of pixel-level annotation limits the scalability of supervised learning with large datasets. Weakly Supervised Semantic Segmentation (WSSS) provides a promising alternative by leveraging image-level labels. In this study, we propose a novel WSSS approach that integrates structural guidance with text-driven strategies to generate high-quality pseudo labels, significantly improving segmentation performance. In terms of visual information, our method employs two processing modules that exchange raw image features and structural features from OCT images, guiding the model to identify where lesions are likely to occur. In terms of textual information, we utilize large-scale pretrained models from cross-domain sources to implement label-informed textual guidance and synthetic descriptive integration with two textual processing modules that combine local semantic features with consistent synthetic descriptions. By fusing these visual and textual components within a multimodal framework, our approach enhances lesion localization accuracy. Experimental results on three OCT datasets demonstrate that our method achieves state-of-the-art performance, highlighting its potential to improve diagnostic accuracy and efficiency in medical imaging.

Adversarial Vessel-Unveiling Semi-Supervised Segmentation for Retinopathy of Prematurity Diagnosis

Accurate segmentation of retinal images plays a crucial role in aiding ophthalmologists in diagnosing retinopathy of prematurity (ROP) and assessing its severity. However, due to their underdeveloped, thinner vessels, manual annotation in infant fundus images is very complex, and this presents challenges for fully supervised learning. To address the scarcity of annotations, we propose a semi supervised segmentation framework designed to advance ROP studies without the need for extensive manual vessel annotation. Unlike previous methods that rely solely on limited labeled data, our approach leverages teacher student learning by integrating two powerful components: an uncertainty weighted vessel unveiling module and domain adversarial learning. The vessel unveiling module helps the model effectively reveal obscured and hard to detect vessel structures, while adversarial training aligns feature representations across different domains, ensuring robust and generalizable vessel segmentations. We validate our approach on public datasets (CHASEDB, STARE) and an in-house ROP dataset, demonstrating its superior performance across multiple evaluation metrics. Additionally, we extend the model's utility to a downstream task of ROP multi-stage classification, where vessel masks extracted by our segmentation model improve diagnostic accuracy. The promising results in classification underscore the model's potential for clinical application, particularly in early-stage ROP diagnosis and intervention. Overall, our work offers a scalable solution for leveraging unlabeled data in pediatric ophthalmology, opening new avenues for biomarker discovery and clinical research.

TopoTxR: A topology-guided deep convolutional network for breast parenchyma learning on DCE-MRIs

Characterization of breast parenchyma in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a challenging task owing to the complexity of underlying tissue structures. Existing quantitative approaches, like radiomics and deep learning models, lack explicit quantification of intricate and subtle parenchymal structures, including fibroglandular tissue. To address this, we propose a novel topological approach that explicitly extracts multi-scale topological structures to better approximate breast parenchymal structures, and then incorporates these structures into a deep-learning-based prediction model via an attention mechanism. Our topology-informed deep learning model, \emph{TopoTxR}, leverages topology to provide enhanced insights into tissues critical for disease pathophysiology and treatment response. We empirically validate \emph{TopoTxR} using the VICTRE phantom breast dataset, showing that the topological structures extracted by our model effectively approximate the breast parenchymal structures. We further demonstrate \emph{TopoTxR}'s efficacy in predicting response to neoadjuvant chemotherapy. Our qualitative and quantitative analyses suggest differential topological behavior of breast tissue in treatment-na\"ive imaging, in patients who respond favorably to therapy as achieving pathological complete response (pCR) versus those who do not. In a comparative analysis with several baselines on the publicly available I-SPY 1 dataset (N=161, including 47 patients with pCR and 114 without) and the Rutgers proprietary dataset (N=120, with 69 patients achieving pCR and 51 not), \emph{TopoTxR} demonstrates a notable improvement, achieving a 2.6\% increase in accuracy and a 4.6\% enhancement in AUC compared to the state-of-the-art method.

MultiPull: Detailing Signed Distance Functions by Pulling Multi-Level Queries at Multi-Step

Reconstructing a continuous surface from a raw 3D point cloud is a challenging task. Recent methods usually train neural networks to overfit on single point clouds to infer signed distance functions (SDFs). However, neural networks tend to smooth local details due to the lack of ground truth signed distances or normals, which limits the performance of overfitting-based methods in reconstruction tasks. To resolve this issue, we propose a novel method, named MultiPull, to learn multi-scale implicit fields from raw point clouds by optimizing accurate SDFs from coarse to fine. We achieve this by mapping 3D query points into a set of frequency features, which makes it possible to leverage multi-level features during optimization. Meanwhile, we introduce optimization constraints from the perspective of spatial distance and normal consistency, which play a key role in point cloud reconstruction based on multi-scale optimization strategies. Our experiments on widely used object and scene benchmarks demonstrate that our method outperforms the state-of-the-art methods in surface reconstruction.

NYC-Event-VPR: A Large-Scale High-Resolution Event-Based Visual Place Recognition Dataset in Dense Urban Environments

Visual place recognition (VPR) enables autonomous robots to identify previously visited locations, which contributes to tasks like simultaneous localization and mapping (SLAM). VPR faces challenges such as accurate image neighbor retrieval and appearance change in scenery. Event cameras, also known as dynamic vision sensors, are a new sensor modality for VPR and offer a promising solution to the challenges with their unique attributes: high temporal resolution (1MHz clock), ultra-low latency (in {\mu}s), and high dynamic range (>120dB). These attributes make event cameras less susceptible to motion blur and more robust in variable lighting conditions, making them suitable for addressing VPR challenges. However, the scarcity of event-based VPR datasets, partly due to the novelty and cost of event cameras, hampers their adoption. To fill this data gap, our paper introduces the NYC-Event-VPR dataset to the robotics and computer vision communities, featuring the Prophesee IMX636 HD event sensor (1280x720 resolution), combined with RGB camera and GPS module. It encompasses over 13 hours of geotagged event data, spanning 260 kilometers across New York City, covering diverse lighting and weather conditions, day/night scenarios, and multiple visits to various locations. Furthermore, our paper employs three frameworks to conduct generalization performance assessments, promoting innovation in event-based VPR and its integration into robotics applications.

Inferring Neural Signed Distance Functions by Overfitting on Single Noisy Point Clouds through Finetuning Data-Driven based Priors

It is important to estimate an accurate signed distance function (SDF) from a point cloud in many computer vision applications. The latest methods learn neural SDFs using either a data-driven based or an overfitting-based strategy. However, these two kinds of methods are with either poor generalization or slow convergence, which limits their capability under challenging scenarios like highly noisy point clouds. To resolve this issue, we propose a method to promote pros of both data-driven based and overfitting-based methods for better generalization, faster inference, and higher accuracy in learning neural SDFs. We introduce a novel statistical reasoning algorithm in local regions which is able to finetune data-driven based priors without signed distance supervision, clean point cloud, or point normals. This helps our method start with a good initialization, and converge to a minimum in a much faster way. Our numerical and visual comparisons with the state-of-the-art methods show our superiority over these methods in surface reconstruction and point cloud denoising on widely used shape and scene benchmarks. The code is available at https://github.com/chenchao15/LocalN2NM.

TopoDiffusionNet: A Topology-aware Diffusion Model

Diffusion models excel at creating visually impressive images but often struggle to generate images with a specified topology. The Betti number, which represents the number of structures in an image, is a fundamental measure in topology. Yet, diffusion models fail to satisfy even this basic constraint. This limitation restricts their utility in applications requiring exact control, like robotics and environmental modeling. To address this, we propose TopoDiffusionNet (TDN), a novel approach that enforces diffusion models to maintain the desired topology. We leverage tools from topological data analysis, particularly persistent homology, to extract the topological structures within an image. We then design a topology-based objective function to guide the denoising process, preserving intended structures while suppressing noisy ones. Our experiments across four datasets demonstrate significant improvements in topological accuracy. TDN is the first to integrate topology with diffusion models, opening new avenues of research in this area.