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Automatic mitochondrial segmentation enjoys great popularity with the development of deep learning. However, the coarse prediction raised by the presence of regular 3D grids in previous methods regardless of 3D CNN or the vision transformers suggest a possibly sub-optimal feature arrangement. To mitigate this limitation, we attempt to interpret the 3D EM image stacks as a set of interrelated 3D fragments for a better solution. However, it is non-trivial to model the 3D fragments without introducing excessive computational overhead. In this paper, we design a coherent fragment vision transformer (FragViT) combined with affinity learning to manipulate features on 3D fragments yet explore mutual relationships to model fragment-wise context, enjoying locality prior without sacrificing global reception. The proposed FragViT includes a fragment encoder and a hierarchical fragment aggregation module. The fragment encoder is equipped with affinity heads to transform the tokens into fragments with homogeneous semantics, and the multi-layer self-attention is used to explicitly learn inter-fragment relations with long-range dependencies. The hierarchical fragment aggregation module is responsible for hierarchically aggregating fragment-wise prediction back to the final voxel-wise prediction in a progressive manner. Extensive experimental results on the challenging MitoEM, Lucchi, and AC3/AC4 benchmarks demonstrate the effectiveness of the proposed method.

AAAI 2024

Electron Microscopy Images as Set of Fragments for Mitochondrial Segmentation

medical and biological imaging

segmentation

computer vision

technical paper

We are pleased to announce the Thirty-Eighth AAAI Conference on Artificial Intelligence (AAAI-24), which will be held in Vancouver, British Columbia at the Vancouver Convention Centre – West Building from 20-27 February, 2024.

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-24 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and a range of other activities to be announced.

We expect for AAAI-24 to be an in-person conference – one author of all accepted papers will be expected to present work in person unless there are exceptional circumstances that prevent this.<br><br><br><br>

In order to access the AAAI-24 event page you need to register [here](https://aaai.org/aaai-conference/registration/)

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. 

In open-set recognition (OSR), a promising strategy is exploiting pseudo-unknown data outside given K known classes as an additional K+1-th class to explicitly model potential open space. However, treating unknown classes without distinction is unequal for them relative to known classes due to the category-agnostic and scale-agnostic of the unknowns. This inevitably not only disrupts the inherent distributions of unknown classes but also incurs both class-wise and instance-wise imbalances between known and unknown classes. Ideally, the OSR problem should model the whole class space as K+$\infty$, but enumerating all unknowns is impractical. Since the core of OSR is to effectively model the boundaries of known classes, this means just focusing on the unknowns nearing the boundaries of targeted known classes seems sufficient. Thus, as a compromise, we convert the open classes from infinite to K, with a novel concept Target-Aware Universum (TAU) and propose a simple yet effective framework Dual Contrastive Learning with Target-Aware Universum (DCTAU). In details, guided by the targeted known classes, TAU automatically expands the unknown classes from the previous 1 to K, effectively alleviating the distribution disruption and the imbalance issues mentioned above. Then, a novel Dual Contrastive (DC) loss is designed, where all instances irrespective of known or TAU are considered as positives to contrast with their respective negatives. Experimental results indicate DCTAU sets a new state-of-the-art.

All Beings Are Equal in Open Set Recognition | VIDEO

In recent years, spectral graph neural networks, characterized by polynomial filters, have garnered increasing attention and have achieved remarkable performance in tasks such as node classification. These models typically assume that eigenvalues for the normalized Laplacian matrix are distinct from each other, thus expecting a polynomial filter to have a high fitting ability. However, this paper empirically observes that normalized Laplacian matrices frequently possess repeated eigenvalues. Moreover, we theoretically establish that the number of distinguishable eigenvalues plays a pivotal role in determining the expressive power of spectral graph neural networks. In light of this observation, we propose an eigenvalue correction strategy that can free polynomial filters from the constraints of repeated eigenvalue inputs. Concretely, the proposed eigenvalue correction strategy enhances the uniform distribution of eigenvalues, thus mitigating repeated eigenvalues, and improving the fitting capacity and expressive power of polynomial filters. Extensive experimental results on both synthetic and real-world datasets demonstrate the superiority of our method.

Improving Expressive Power of Spectral Graph Neural Networks with Eigenvalue Correction

Spinal curvature estimation is important to the diagnosis and treatment of the scoliosis. Existing methods face several issues such as the need of expensive annotations on the vertebral landmarks and being sensitive to the image quality. It is challenging to achieve robust estimation and obtain interpretable results, especially for low-quality images which are blurry and hazy. In this paper, we propose B-Spine, a novel deep learning pipeline to learn B-spline curve representation of the spine and estimate the Cobb angles for spinal curvature estimation from low-quality X-ray images. Given a low-quality input, a novel SegRefine network which employs the unpaired image-to- image translation is proposed to generate a high quality spine mask from the initial segmentation result. Next, a novel mask-based B-spline prediction model is proposed to predict the B-spline curve for the spine centerline. Finally, the Cobb angles are estimated by a hybrid approach which combines the curve slope analysis and a curve-based regression model. We conduct quantitative and qualitative comparisons with the representative and SOTA learning-based methods on the public AASCE2019 dataset and our new proposed Anonymous dataset which contains more challenging low-quality images. The superior performance on both datasets shows our method can achieve both robustness and interpretability for spinal curvature estimation.

B-spine: Learning B-spline Curve Representation for Robust and Interpretable Spinal Curvature Estimation

Electronic health records (EHRs) have become the foundation of machine learning applications in healthcare, while the utility of real patient records is often limited by privacy and security concerns. Synthetic EHR generation provides an additional perspective to compensate for this limitation. Most existing methods synthesize new records based on real EHR data, without consideration of different types of events in EHR data, which cannot control the event combinations in line with medical common sense. In this paper, we propose MSIC,  a Multi-visit health Status Inference model for Collaborative EHR synthesis to address these limitations. First, we formulate the synthetic EHR generation process as a probabilistic graphical model and tightly connect different types of events by modeling the latent health states. Then, we derive a health state inference method tailored for the multi-visit scenario to effectively utilize previous records to synthesize current and future records. Furthermore, we propose to generate medical reports to add textual descriptions for each medical event,  providing broader applications for synthesized EHR data. For generating different paragraphs in each visit, we incorporate a multi-generator deliberation framework to collaborate the message passing of multiple generators and employ a two-phase decoding strategy to generate high-quality reports. Our extensive experiments on the widely used benchmarks, MIMIC-III and MIMIC-IV, demonstrate that \model advances state-of-the-art results on the quality of synthetic data while maintaining low privacy risks.

Collaborative Synthesis of Patient Records through Multi-Visit Health State Inference

Link prediction is a fundamental task in network analysis, with the objective of predicting missing or potential links. While existing studies have mainly concentrated on single networks, it is worth noting that numerous real-world networks exhibit interconnectedness. For example, individuals often register on various social media platforms to access diverse services, such as chatting, tweeting, blogging, and rating movies. These platforms share a subset of users and are termed multilayer networks. The interlayer links in such networks hold valuable information that provides more comprehensive insights into the network structure. To effectively exploit this complementary information and enhance link prediction in the target network, we propose a novel cross-network embedding method. This method aims to represent different networks in a shared latent space, preserving proximity within single networks as well as consistency across multilayer networks. Specifically, nodes can aggregate messages from aligned nodes in other layers. Extensive experiments conducted on real-world datasets demonstrate the superior performance of our proposed method for link prediction in multilayer networks.

Link Prediction in Multilayer Networks via Cross-Network Embedding | VIDEO

In biochemical modeling, some foundational systems can exhibit sudden and profound behavioral shifts, such as the cellular signaling pathway models, in which the physiological responses promptly react to environmental changes, resulting in steep changes in their dynamic model trajectories. These steep changes are one of the major challenges in biochemical modeling governed by nonlinear differential equations. One promising way to tackle this challenge is converting the input data from the time domain to the frequency domain through Fourier Neural Operators, which enhances the ability to analyze data periodicity and regularity. However, the effectiveness of these Fourier based methods diminishes in scenarios with complex abrupt switches. To address this limitation, an innovative Multiscale Attention Wavelet Neural Operator (MAWNO) method is proposed in this paper, which comprehensively combines the attention mechanism with the versatile wavelet transforms to effectively capture these abrupt switches. Specifically, the wavelet transform scrutinizes data across multiple scales to extract the characteristics of abrupt signals into wavelet coefficients, while the self-attention mechanism is adeptly introduced to enhance the wavelet coefficients in high-frequency signals that can better characterize the abrupt switches. Experimental results substantiate MAWNO’s supremacy in terms of accuracy on three classical biochemical models featuring periodic and steep trajectories. https://github.com/SUDERS/MAWNO.

Multiscale Attention Wavelet Neural Operator for Capturing Steep Trajectories in Biochemical Systems

Numerous techniques excel in brain tumor segmentation using multi-modal magnetic resonance imaging (MRI) sequences, delivering exceptional results. However, the prevalent absence of modalities in clinical scenarios hampers performance. Current approaches frequently resort to zero maps as substitutes for missing modalities, inadvertently introducing feature bias and redundant computations. To address these issues, we present the Token Merging transFormer (TMFormer) for robust brain tumor segmentation with missing modalities. TMFormer tackles these challenges by extracting and merging accessible modalities into more compact token sequences. The architecture comprises two core components: the Uni-modal Token Merging Block (UMB) and the Multi-modal Token Merging Block (MMB). The UMB enhances individual modality representation by adaptively consolidating spatially redundant tokens within and outside tumor-related regions, thereby refining token sequences for augmented representational capacity. Meanwhile, the MMB mitigates multi-modal feature fusion bias, exclusively leveraging tokens from present modalities and merging them into a unified multi-modal representation to accommodate varying modality combinations. Extensive experimental results on the BraTS 2018 and 2020 datasets demonstrate the superiority and efficacy of TMFormer compared to state-of-the-art methods when dealing with missing modalities.

TMFormer: Token Merging Transformer for Brain Tumor Segmentation with Missing Modalities

Multi-modal image segmentation is one of the core issues in computer vision. The main challenge lies in integrating common information between modalities while retaining specific patterns for each modality. Existing methods typically perform full fine-tuning on RGB-based pre-trained parameters to inherit the powerful representation of the foundation model. Although effective, such paradigm is not optimal due to weak transferability and scarce downstream data. Inspired by the recent success of prompt learning in language models, we propose the Grouping Prompt Tuning Framework (GoPT), which introduces explicit semantic grouping to learn modal-related prompts, adapting the frozen pre-trained foundation model to various downstream multi-modal segmentation tasks. Specifically, a class-aware uni-modal prompter is designed to balance intra- and inter-modal semantic propagation by grouping modality-specific class tokens, thereby improving the adaptability of spatial information. Furthermore, an alignment-induced cross-modal prompter is introduced to aggregate class-aware representations and share prompt parameters among different modalities to assist in modeling common statistics. Extensive experiments show the superiority of our GoPT, which achieves SOTA performance on various downstream multi-modal image segmentation tasks by training only < 1% model parameters.

Prompting Multi-Modal Image Segmentation with Semantic Grouping

Recent advancements in deep learning have greatly improved the efficiency of auxiliary medical diagnostics. However, concerns over patient privacy and data annotation costs restrict the viability of centralized training models. In response, federated semi-supervised learning has garnered substantial attention from medical institutions. However, it faces challenges arising from knowledge discrepancies among local clients and class imbalance in non-independent and identically distributed data. Existing methods like class balance adaptation for addressing class imbalance often overlook low-confidence yet valuable rare samples in unlabeled data and may compromise client privacy. To address these issues, we propose a novel framework with class awareness balance and dual teacher distillation called FedCD. FedCD introduces a global-local framework to balance and purify global and local knowledge. Additionally, we introduce a novel class awareness balance module to effectively explore potential rare classes and encourage balanced learning in unlabeled clients. Importantly, our approach prioritizes privacy protection by only exchanging network parameters during communication. Experimental results on two medical datasets under various settings demonstrate the effectiveness of FedCD. The code is available at https://github.com/YunzZ-Liu/FedCD.

FedCD: Federated Semi-supervised Learning with Class Awareness Balance via Dual Teachers

Image Quality Assessment (IQA) has long been a research hotspot in the field of image processing, especially No-Reference Image Quality Assessment (NR-IQA). Due to the powerful feature extraction ability, existing Convolution Neural Network (CNN) and Transformers based NR-IQA methods have achieved considerable progress. However, they still exhibit limited capability when facing unknown authentic distortion database. To further improve NR-IQA performance, in this paper, a novel supervised contrastive learning (SCL) and Transformer-based NR-IQA model SaTQA is proposed. We first train a model on a large-scale synthetic dataset by SCL (no image subjective score is required) to extract degradation features of images with various distortion types and levels. To further extract distortion information from images, we propose a backbone network incorporating the Multi-Stream Block (MSB) by combining the CNN inductive bias and Transformer long-term dependence modeling capability. Finally, we propose the Patch Attention Block (PAB) to obtain the final distorted image quality score by fusing the degradation features learned from contrastive learning with the perceptual distortion information extracted by the backbone network. Experimental results on seven standard IQA datasets show that SaTQA outperforms the state-of-the-art methods for both synthetic and authentic datasets.

Electron Microscopy Images as Set of Fragments for Mitochondrial Segmentation

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Electron Microscopy Images as Set of Fragments for Mitochondrial Segmentation

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All Beings Are Equal in Open Set Recognition | VIDEO

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