Topology-Aware Exploration of Circle of Willis for CTA and MRA: Segmentation, Detection, and Classification

The Circle of Willis (CoW) vessels is critical to connecting major circulations of the brain. The topology of the vascular structure is clinical significance to evaluate the risk, severity of the neuro-vascular diseases. The CoW has two representative angiographic imaging modalities, computed tomography angiography (CTA) and magnetic resonance angiography (MRA). TopCow24 provided 125 paired CTA-MRA dataset for the analysis of CoW. To explore both CTA and MRA images in a unified framework to learn the inherent topology of Cow, we construct the universal dataset via independent intensity preprocess, followed by joint resampling and normarlization. Then, we utilize the topology-aware loss to enhance the topology completeness of the CoW and the discrimination between different classes. A complementary topology-aware refinement is further conducted to enhance the connectivity within the same class. Our method was evaluated on all the three tasks and two modalities, achieving competitive results. In the final test phase of TopCow24 Challenge, we achieved the second place in the CTA-Seg-Task, the third palce in the CTA-Box-Task, the first place in the CTA-Edg-Task, the second place in the MRA-Seg-Task, the third palce in the MRA-Box-Task, the second place in the MRA-Edg-Task.

LNQ 2023 challenge: Benchmark of weakly-supervised techniques for mediastinal lymph node quantification

Accurate assessment of lymph node size in 3D CT scans is crucial for cancer staging, therapeutic management, and monitoring treatment response. Existing state-of-the-art segmentation frameworks in medical imaging often rely on fully annotated datasets. However, for lymph node segmentation, these datasets are typically small due to the extensive time and expertise required to annotate the numerous lymph nodes in 3D CT scans. Weakly-supervised learning, which leverages incomplete or noisy annotations, has recently gained interest in the medical imaging community as a potential solution. Despite the variety of weakly-supervised techniques proposed, most have been validated only on private datasets or small publicly available datasets. To address this limitation, the Mediastinal Lymph Node Quantification (LNQ) challenge was organized in conjunction with the 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023). This challenge aimed to advance weakly-supervised segmentation methods by providing a new, partially annotated dataset and a robust evaluation framework. A total of 16 teams from 5 countries submitted predictions to the validation leaderboard, and 6 teams from 3 countries participated in the evaluation phase. The results highlighted both the potential and the current limitations of weakly-supervised approaches. On one hand, weakly-supervised approaches obtained relatively good performance with a median Dice score of $61.0\%$. On the other hand, top-ranked teams, with a median Dice score exceeding $70\%$, boosted their performance by leveraging smaller but fully annotated datasets to combine weak supervision and full supervision. This highlights both the promise of weakly-supervised methods and the ongoing need for high-quality, fully annotated data to achieve higher segmentation performance.

Similarity is Not All You Need: Endowing Retrieval Augmented Generation with Multi Layered Thoughts

In recent years, large language models (LLMs) have made remarkable achievements in various domains. However, the untimeliness and cost of knowledge updates coupled with hallucination issues of LLMs have curtailed their applications in knowledge intensive tasks, where retrieval augmented generation (RAG) can be of help. Nevertheless, existing retrieval augmented models typically use similarity as a bridge between queries and documents and follow a retrieve then read procedure. In this work, we argue that similarity is not always the panacea and totally relying on similarity would sometimes degrade the performance of retrieval augmented generation. To this end, we propose MetRag, a Multi layEred Thoughts enhanced Retrieval Augmented Generation framework. To begin with, beyond existing similarity oriented thought, we embrace a small scale utility model that draws supervision from an LLM for utility oriented thought and further come up with a smarter model by comprehensively combining the similarity and utility oriented thoughts. Furthermore, given the fact that the retrieved document set tends to be huge and using them in isolation makes it difficult to capture the commonalities and characteristics among them, we propose to make an LLM as a task adaptive summarizer to endow retrieval augmented generation with compactness-oriented thought. Finally, with multi layered thoughts from the precedent stages, an LLM is called for knowledge augmented generation. Extensive experiments on knowledge-intensive tasks have demonstrated the superiority of MetRag.

Dense Vision Transformer Compression with Few Samples

Few-shot model compression aims to compress a large model into a more compact one with only a tiny training set (even without labels). Block-level pruning has recently emerged as a leading technique in achieving high accuracy and low latency in few-shot CNN compression. But, few-shot compression for Vision Transformers (ViT) remains largely unexplored, which presents a new challenge. In particular, the issue of sparse compression exists in traditional CNN few-shot methods, which can only produce very few compressed models of different model sizes. This paper proposes a novel framework for few-shot ViT compression named DC-ViT. Instead of dropping the entire block, DC-ViT selectively eliminates the attention module while retaining and reusing portions of the MLP module. DC-ViT enables dense compression, which outputs numerous compressed models that densely populate the range of model complexity. DC-ViT outperforms state-of-the-art few-shot compression methods by a significant margin of 10 percentage points, along with lower latency in the compression of ViT and its variants.

DiffuLT: How to Make Diffusion Model Useful for Long-tail Recognition

This paper proposes a new pipeline for long-tail (LT) recognition. Instead of re-weighting or re-sampling, we utilize the long-tailed dataset itself to generate a balanced proxy that can be optimized through cross-entropy (CE). Specifically, a randomly initialized diffusion model, trained exclusively on the long-tailed dataset, is employed to synthesize new samples for underrepresented classes. Then, we utilize the inherent information in the original dataset to filter out harmful samples and keep the useful ones. Our strategy, Diffusion model for Long-Tail recognition (DiffuLT), represents a pioneering utilization of generative models in long-tail recognition. DiffuLT achieves state-of-the-art results on CIFAR10-LT, CIFAR100-LT, and ImageNet-LT, surpassing the best competitors with non-trivial margins. Abundant ablations make our pipeline interpretable, too. The whole generation pipeline is done without any external data or pre-trained model weights, making it highly generalizable to real-world long-tailed settings.

M2-Encoder: Advancing Bilingual Image-Text Understanding by Large-scale Efficient Pretraining

Vision-language foundation models like CLIP have revolutionized the field of artificial intelligence. Nevertheless, VLM models supporting multi-language, e.g., in both Chinese and English, have lagged due to the relative scarcity of large-scale pretraining datasets. Toward this end, we introduce a comprehensive bilingual (Chinese-English) dataset BM-6B with over 6 billion image-text pairs, aimed at enhancing multimodal foundation models to well understand images in both languages. To handle such a scale of dataset, we propose a novel grouped aggregation approach for image-text contrastive loss computation, which reduces the communication overhead and GPU memory demands significantly, facilitating a 60% increase in training speed. We pretrain a series of bilingual image-text foundation models with an enhanced fine-grained understanding ability on BM-6B, the resulting models, dubbed as $M^2$-Encoders (pronounced "M-Square"), set new benchmarks in both languages for multimodal retrieval and classification tasks. Notably, Our largest $M^2$-Encoder-10B model has achieved top-1 accuracies of 88.5% on ImageNet and 80.7% on ImageNet-CN under a zero-shot classification setting, surpassing previously reported SoTA methods by 2.2% and 21.1%, respectively. The $M^2$-Encoder series represents one of the most comprehensive bilingual image-text foundation models to date, so we are making it available to the research community for further exploration and development.

Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challenge

Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway trees remains prohibitively time-consuming. While significant efforts have been made towards enhancing airway modelling, current public-available datasets concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023' (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for prognosis, a strong airway-derived biomarker (Hazard ratio>1.5, p<0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.

PnPNet: Pull-and-Push Networks for Volumetric Segmentation with Boundary Confusion

Precise boundary segmentation of volumetric images is a critical task for image-guided diagnosis and computer-assisted intervention, especially for boundary confusion in clinical practice. However, U-shape networks cannot effectively resolve this challenge due to the lack of boundary shape constraints. Besides, existing methods of refining boundaries overemphasize the slender structure, which results in the overfitting phenomenon due to networks' limited abilities to model tiny objects. In this paper, we reconceptualize the mechanism of boundary generation by encompassing the interaction dynamics with adjacent regions. Moreover, we propose a unified network termed PnPNet to model shape characteristics of the confused boundary region. Core ingredients of PnPNet contain the pushing and pulling branches. Specifically, based on diffusion theory, we devise the semantic difference module (SDM) from the pushing branch to squeeze the boundary region. Explicit and implicit differential information inside SDM significantly boost representation abilities for inter-class boundaries. Additionally, motivated by the K-means algorithm, the class clustering module (CCM) from the pulling branch is introduced to stretch the intersected boundary region. Thus, pushing and pulling branches will shrink and enlarge the boundary uncertainty respectively. They furnish two adversarial forces to promote models to output a more precise delineation of boundaries. We carry out experiments on three challenging public datasets and one in-house dataset, containing three types of boundary confusion in model predictions. Experimental results demonstrate the superiority of PnPNet over other segmentation networks, especially on evaluation metrics of HD and ASSD. Besides, pushing and pulling branches can serve as plug-and-play modules to enhance classic U-shape baseline models. Codes are available.

Implicit Shape Modeling for Anatomical Structure Refinement of Volumetric Medical Images

Shape modeling of volumetric medical images is a critical task for quantitative analysis and surgical plans in computer-aided diagnosis. To relieve the burden of expert clinicians, the reconstructed shapes are widely acquired from deep learning models, e.g. Convolutional Neural Networks (CNNs), followed by marching cube algorithm. However, automatically obtaining reconstructed shapes can not always achieve perfect results due to the limited resolution of images and lack of shape prior constraints. In this paper, we design a unified framework for the refinement of medical image segmentation on top of an implicit neural network. Specifically, To learn a sharable shape prior from different instances within the same category in the training phase, the physical information of volumetric medical images are firstly utilized to construct the Physical-Informed Continuous Coordinate Transform (PICCT). PICCT transforms the input data in an aligned manner fed into the implicit shape modeling. To better learn shape representation, we introduce implicit shape constraints on top of the signed distance function (SDF) into the implicit shape modeling of both instances and latent template. For the inference phase, a template interaction module (TIM) is proposed to refine initial results produced by CNNs via deforming deep implicit templates with latent codes. Experimental results on three datasets demonstrated the superiority of our approach in shape refinement. The Chamfer Distance/Earth Mover's Distance achieved by the proposed method are 0.232/0.087 on the Liver dataset, 0.128/0.069 on the Pancreas dataset, and 0.417/0.100 on the Lung Lobe dataset.

Rethinking Memory and Communication Cost for Efficient Large Language Model Training

As model sizes and training datasets continue to increase, large-scale model training frameworks reduce memory consumption by various sharding techniques. However, the huge communication overhead reduces the training efficiency, especially in public cloud environments with varying network bandwidths. In this paper, we rethink the impact of memory consumption and communication overhead on the training speed of large language model, and propose a memory-communication balanced \underline{Pa}rtial \underline{R}edundancy \underline{O}ptimizer (PaRO). PaRO reduces the amount and frequency of inter-group communication by grouping GPU clusters and introducing minor intra-group memory redundancy, thereby improving the training efficiency of the model. Additionally, we propose a Hierarchical Overlapping Ring (HO-Ring) communication topology to enhance communication efficiency between nodes or across switches in large model training. Our experiments demonstrate that the HO-Ring algorithm improves communication efficiency by 32.6\% compared to the traditional Ring algorithm. Compared to the baseline ZeRO, PaRO significantly improves training throughput by 1.2x-2.6x and achieves a near-linear scalability. Therefore, the PaRO strategy provides more fine-grained options for the trade-off between memory consumption and communication overhead in different training scenarios.