Data and Physics driven Deep Learning Models for Fast MRI Reconstruction: Fundamentals and Methodologies

Magnetic Resonance Imaging (MRI) is a pivotal clinical diagnostic tool, yet its extended scanning times often compromise patient comfort and image quality, especially in volumetric, temporal and quantitative scans. This review elucidates recent advances in MRI acceleration via data and physics-driven models, leveraging techniques from algorithm unrolling models, enhancement-based models, and plug-and-play models to emergent full spectrum of generative models. We also explore the synergistic integration of data models with physics-based insights, encompassing the advancements in multi-coil hardware accelerations like parallel imaging and simultaneous multi-slice imaging, and the optimization of sampling patterns. We then focus on domain-specific challenges and opportunities, including image redundancy exploitation, image integrity, evaluation metrics, data heterogeneity, and model generalization. This work also discusses potential solutions and future research directions, emphasizing the role of data harmonization, and federated learning for further improving the general applicability and performance of these methods in MRI reconstruction.

An objective comparison of methods for augmented reality in laparoscopic liver resection by preoperative-to-intraoperative image fusion

Augmented reality for laparoscopic liver resection is a visualisation mode that allows a surgeon to localise tumours and vessels embedded within the liver by projecting them on top of a laparoscopic image. Preoperative 3D models extracted from CT or MRI data are registered to the intraoperative laparoscopic images during this process. In terms of 3D-2D fusion, most of the algorithms make use of anatomical landmarks to guide registration. These landmarks include the liver's inferior ridge, the falciform ligament, and the occluding contours. They are usually marked by hand in both the laparoscopic image and the 3D model, which is time-consuming and may contain errors if done by a non-experienced user. Therefore, there is a need to automate this process so that augmented reality can be used effectively in the operating room. We present the Preoperative-to-Intraoperative Laparoscopic Fusion Challenge (P2ILF), held during the Medical Imaging and Computer Assisted Interventions (MICCAI 2022) conference, which investigates the possibilities of detecting these landmarks automatically and using them in registration. The challenge was divided into two tasks: 1) A 2D and 3D landmark detection task and 2) a 3D-2D registration task. The teams were provided with training data consisting of 167 laparoscopic images and 9 preoperative 3D models from 9 patients, with the corresponding 2D and 3D landmark annotations. A total of 6 teams from 4 countries participated, whose proposed methods were evaluated on 16 images and two preoperative 3D models from two patients. All the teams proposed deep learning-based methods for the 2D and 3D landmark segmentation tasks and differentiable rendering-based methods for the registration task. Based on the experimental outcomes, we propose three key hypotheses that determine current limitations and future directions for research in this domain.

Vivim: a Video Vision Mamba for Medical Video Object Segmentation

Traditional convolutional neural networks have a limited receptive field while transformer-based networks are mediocre in constructing long-term dependency from the perspective of computational complexity. Such the bottleneck poses a significant challenge when processing long video sequences in video analysis tasks. Very recently, the state space models (SSMs) with efficient hardware-aware designs, famous by Mamba, have exhibited impressive achievements in long sequence modeling, which facilitates the development of deep neural networks on many vision tasks. To better capture available cues in video frames, this paper presents a generic Video Vision Mamba-based framework for medical video object segmentation tasks, named Vivim. Our Vivim can effectively compress the long-term spatiotemporal representation into sequences at varying scales by our designed Temporal Mamba Block. Compared to existing video-level Transformer-based methods, our model maintains excellent segmentation results with better speed performance. Extensive experiments on the breast US dataset demonstrate the effectiveness and efficiency of our Vivim. The code for Vivim is available at: https://github.com/scott-yjyang/Vivim.

SegMamba: Long-range Sequential Modeling Mamba For 3D Medical Image Segmentation

The Transformer architecture has shown a remarkable ability in modeling global relationships. However, it poses a significant computational challenge when processing high-dimensional medical images. This hinders its development and widespread adoption in this task. Mamba, as a State Space Model (SSM), recently emerged as a notable manner for long-range dependencies in sequential modeling, excelling in natural language processing filed with its remarkable memory efficiency and computational speed. Inspired by its success, we introduce SegMamba, a novel 3D medical image \textbf{Seg}mentation \textbf{Mamba} model, designed to effectively capture long-range dependencies within whole volume features at every scale. Our SegMamba, in contrast to Transformer-based methods, excels in whole volume feature modeling from a state space model standpoint, maintaining superior processing speed, even with volume features at a resolution of {$64\times 64\times 64$}. Comprehensive experiments on the BraTS2023 dataset demonstrate the effectiveness and efficiency of our SegMamba. The code for SegMamba is available at: https://github.com/ge-xing/SegMamba

SuperCLUE-Math6: Graded Multi-Step Math Reasoning Benchmark for LLMs in Chinese

We introduce SuperCLUE-Math6(SC-Math6), a new benchmark dataset to evaluate the mathematical reasoning abilities of Chinese language models. SC-Math6 is designed as an upgraded Chinese version of the GSM8K dataset with enhanced difficulty, diversity, and application scope. It consists of over 2000 mathematical word problems requiring multi-step reasoning and providing natural language solutions. We propose an innovative scheme to quantify the reasoning capability of large models based on performance over problems with different reasoning steps. Experiments on 12 representative Chinese models demonstrate a clear stratification of reasoning levels, with top models like GPT-4 showing superior performance. SC-Math6 fills the gap in Chinese mathematical reasoning benchmarks and provides a comprehensive testbed to advance the intelligence of Chinese language models.

MCRPL: A Pretrain, Prompt & Fine-tune Paradigm for Non-overlapping Many-to-one Cross-domain Recommendation

Cross-domain Recommendation (CR) is the task that tends to improve the recommendations in the sparse target domain by leveraging the information from other rich domains. Existing methods of cross-domain recommendation mainly focus on overlapping scenarios by assuming users are totally or partially overlapped, which are taken as bridges to connect different domains. However, this assumption does not always hold since it is illegal to leak users' identity information to other domains. Conducting Non-overlapping MCR (NMCR) is challenging since 1) The absence of overlapping information prevents us from directly aligning different domains, and this situation may get worse in the MCR scenario. 2) The distribution between source and target domains makes it difficult for us to learn common information across domains. To overcome the above challenges, we focus on NMCR, and devise MCRPL as our solution. To address Challenge 1, we first learn shared domain-agnostic and domain-dependent prompts, and pre-train them in the pre-training stage. To address Challenge 2, we further update the domain-dependent prompts with other parameters kept fixed to transfer the domain knowledge to the target domain. We conduct experiments on five real-world domains, and the results show the advance of our MCRPL method compared with several recent SOTA baselines.

A unified multichannel far-field speech recognition system: combining neural beamforming with attention based end-to-end model

Far-field speech recognition is a challenging task that conventionally uses signal processing beamforming to attack noise and interference problem. But the performance has been found usually limited due to heavy reliance on environmental assumption. In this paper, we propose a unified multichannel far-field speech recognition system that combines the neural beamforming and transformer-based Listen, Spell, Attend (LAS) speech recognition system, which extends the end-to-end speech recognition system further to include speech enhancement. Such framework is then jointly trained to optimize the final objective of interest. Specifically, factored complex linear projection (fCLP) has been adopted to form the neural beamforming. Several pooling strategies to combine look directions are then compared in order to find the optimal approach. Moreover, information of the source direction is also integrated in the beamforming to explore the usefulness of source direction as a prior, which is usually available especially in multi-modality scenario. Experiments on different microphone array geometry are conducted to evaluate the robustness against spacing variance of microphone array. Large in-house databases are used to evaluate the effectiveness of the proposed framework and the proposed method achieve 19.26\% improvement when compared with a strong baseline.

EPA: Neural Collapse Inspired Robust Out-of-Distribution Detector

Out-of-distribution (OOD) detection plays a crucial role in ensuring the security of neural networks. Existing works have leveraged the fact that In-distribution (ID) samples form a subspace in the feature space, achieving state-of-the-art (SOTA) performance. However, the comprehensive characteristics of the ID subspace still leave under-explored. Recently, the discovery of Neural Collapse ($\mathcal{NC}$) sheds light on novel properties of the ID subspace. Leveraging insight from $\mathcal{NC}$, we observe that the Principal Angle between the features and the ID feature subspace forms a superior representation for measuring the likelihood of OOD. Building upon this observation, we propose a novel $\mathcal{NC}$-inspired OOD scoring function, named Entropy-enhanced Principal Angle (EPA), which integrates both the global characteristic of the ID subspace and its inner property. We experimentally compare EPA with various SOTA approaches, validating its superior performance and robustness across different network architectures and OOD datasets.

Towards Flexible, Scalable, and Adaptive Multi-Modal Conditioned Face Synthesis

Recent progress in multi-modal conditioned face synthesis has enabled the creation of visually striking and accurately aligned facial images. Yet, current methods still face issues with scalability, limited flexibility, and a one-size-fits-all approach to control strength, not accounting for the differing levels of conditional entropy, a measure of unpredictability in data given some condition, across modalities. To address these challenges, we introduce a novel uni-modal training approach with modal surrogates, coupled with an entropy-aware modal-adaptive modulation, to support flexible, scalable, and scalable multi-modal conditioned face synthesis network. Our uni-modal training with modal surrogate that only leverage uni-modal data, use modal surrogate to decorate condition with modal-specific characteristic and serve as linker for inter-modal collaboration , fully learns each modality control in face synthesis process as well as inter-modal collaboration. The entropy-aware modal-adaptive modulation finely adjust diffusion noise according to modal-specific characteristics and given conditions, enabling well-informed step along denoising trajectory and ultimately leading to synthesis results of high fidelity and quality. Our framework improves multi-modal face synthesis under various conditions, surpassing current methods in image quality and fidelity, as demonstrated by our thorough experimental results.

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.