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In clinical medicine, precise image segmentation can provide substantial support to clinicians. However, achieving such precision often requires a large amount of finely annotated data, which can be costly. Scribble annotation presents a more efficient alternative, boosting labeling efficiency. However, utilizing such minimal supervision for medical image segmentation training, especially with scribble annotations, poses significant challenges. To address these challenges, we introduce ScribbleVS, a novel framework that leverages scribble annotations. We introduce a Regional Pseudo Labels Diffusion Module to expand the scope of supervision and reduce the impact of noise present in pseudo labels. Additionally, we propose a Dynamic Competitive Selection module for enhanced refinement in selecting pseudo labels. Experiments conducted on the ACDC and MSCMRseg datasets have demonstrated promising results, achieving performance levels that even exceed those of fully supervised methodologies. The codes of this study are available at https://github.com/ortonwang/ScribbleVS.

Semi-supervised learning has received considerable attention for its potential to leverage abundant unlabeled data to enhance model robustness. Pseudo labeling is a widely used strategy in semi supervised learning. However, existing methods often suffer from noise contamination, which can undermine model performance. To tackle this challenge, we introduce a novel Synergy-Guided Regional Supervision of Pseudo Labels (SGRS-Net) framework. Built upon the mean teacher network, we employ a Mix Augmentation module to enhance the unlabeled data. By evaluating the synergy before and after augmentation, we strategically partition the pseudo labels into distinct regions. Additionally, we introduce a Region Loss Evaluation module to assess the loss across each delineated area. Extensive experiments conducted on the LA dataset have demonstrated superior performance over state-of-the-art techniques, underscoring the efficiency and practicality of our framework.

Large language models (LLMs) enhanced with retrieval-augmented generation (RAG) have introduced a new paradigm for web search. However, the limited context awareness of LLMs degrades their performance on RAG tasks. Existing methods to enhance context awareness are often inefficient, incurring time or memory overhead during inference, and many are tailored to specific position embeddings. In this paper, we propose Position-Embedding-Agnostic attention Re-weighting (PEAR), which enhances the context awareness of LLMs with zero inference overhead. Specifically, on a proxy task focused on context copying, we first detect heads which suppress the models' context awareness thereby diminishing RAG performance. To weaken the impact of these heads, we re-weight their outputs with learnable coefficients. The LLM (with frozen parameters) is optimized by adjusting these coefficients to minimize loss on the proxy task. As a result, the coefficients are optimized to values less than one, thereby reducing their tendency to suppress RAG performance. During inference, the optimized coefficients are fixed to re-weight these heads, regardless of the specific task at hand. Our proposed PEAR offers two major advantages over previous approaches: (1) It introduces zero additional inference overhead in terms of memory usage or inference time, while outperforming competitive baselines in accuracy and efficiency across various RAG tasks. (2) It is independent of position embedding algorithms, ensuring broader applicability., Comment: preprint

Recently, mobile AI agents based on VLMs have been gaining increasing attention. These works typically utilize VLM as a foundation, fine-tuning it with instruction-based mobile datasets. However, these VLMs are typically pre-trained on general-domain data, which often results in a lack of fundamental capabilities specific to the mobile domain. Therefore, they may struggle to recognize specific UI elements and understand intra-UI fine-grained information. In addition, the current fine-tuning task focuses on interacting with the most relevant element for the given instruction. These fine-tuned VLMs may still ignore the relationships between UI pages, neglect the roles of elements in page transitions and lack inter-UI understanding. To address issues, we propose a VLM called MobileVLM, which includes two additional pre-training stages to enhance both intra- and inter-UI understanding. We defined four UI-based pre-training tasks, enabling the model to better perceive fine-grained elements and capture page transition actions. To address the lack of mobile pre-training data, we built a large Chinese mobile dataset Mobile3M from scratch, which contains 3 million UI pages, and real-world transition actions, forming a directed graph structure. Experimental results show MobileVLM excels on both our test set and public mobile benchmarks, outperforming existing VLMs.

Precision breast cancer (BC) risk assessment is crucial for developing individualized screening and prevention. Despite the promising potential of recent mammogram (MG) based deep learning models in predicting BC risk, they mostly overlook the 'time-to-future-event' ordering among patients and exhibit limited explorations into how they track history changes in breast tissue, thereby limiting their clinical application. In this work, we propose a novel method, named OA-BreaCR, to precisely model the ordinal relationship of the time to and between BC events while incorporating longitudinal breast tissue changes in a more explainable manner. We validate our method on public EMBED and inhouse datasets, comparing with existing BC risk prediction and time prediction methods. Our ordinal learning method OA-BreaCR outperforms existing methods in both BC risk and time-to-future-event prediction tasks. Additionally, ordinal heatmap visualizations show the model's attention over time. Our findings underscore the importance of interpretable and precise risk assessment for enhancing BC screening and prevention efforts. The code will be accessible to the public.

Deep neural networks often encounter significant performance drops while facing with domain shifts between training (source) and test (target) data. To address this issue, Test Time Adaptation (TTA) methods have been proposed to adapt pre-trained source model to handle out-of-distribution streaming target data. Although these methods offer some relief, they lack a reliable mechanism for domain shift correction, which can often be erratic in real-world applications. In response, we develop Few-Shot Test Time Adaptation (FS-TTA), a novel and practical setting that utilizes a few-shot support set on top of TTA. Adhering to the principle of few inputs, big gains, FS-TTA reduces blind exploration in unseen target domains. Furthermore, we propose a two-stage framework to tackle FS-TTA, including (i) fine-tuning the pre-trained source model with few-shot support set, along with using feature diversity augmentation module to avoid overfitting, (ii) implementing test time adaptation based on prototype memory bank guidance to produce high quality pseudo-label for model adaptation. Through extensive experiments on three cross-domain classification benchmarks, we demonstrate the superior performance and reliability of our FS-TTA and framework., Comment: 8 pages, 7 figures

The vision-language modeling capability of multi-modal large language models has attracted wide attention from the community. However, in medical domain, radiology report generation using vision-language models still faces significant challenges due to the imbalanced data distribution caused by numerous negated descriptions in radiology reports and issues such as rough alignment between radiology reports and radiography. In this paper, we propose a truthful radiology report generation framework, namely TRRG, based on stage-wise training for cross-modal disease clue injection into large language models. In pre-training stage, During the pre-training phase, contrastive learning is employed to enhance the ability of visual encoder to perceive fine-grained disease details. In fine-tuning stage, the clue injection module we proposed significantly enhances the disease-oriented perception capability of the large language model by effectively incorporating the robust zero-shot disease perception. Finally, through the cross-modal clue interaction module, our model effectively achieves the multi-granular interaction of visual embeddings and an arbitrary number of disease clue embeddings. This significantly enhances the report generation capability and clinical effectiveness of multi-modal large language models in the field of radiology reportgeneration. Experimental results demonstrate that our proposed pre-training and fine-tuning framework achieves state-of-the-art performance in radiology report generation on datasets such as IU-Xray and MIMIC-CXR. Further analysis indicates that our proposed method can effectively enhance the model to perceive diseases and improve its clinical effectiveness.

We introduce DiffSteISR, a pioneering framework for reconstructing real-world stereo images. DiffSteISR utilizes the powerful prior knowledge embedded in pre-trained text-to-image model to efficiently recover the lost texture details in low-resolution stereo images. Specifically, DiffSteISR implements a time-aware stereo cross attention with temperature adapter (TASCATA) to guide the diffusion process, ensuring that the generated left and right views exhibit high texture consistency thereby reducing disparity error between the super-resolved images and the ground truth (GT) images. Additionally, a stereo omni attention control network (SOA ControlNet) is proposed to enhance the consistency of super-resolved images with GT images in the pixel, perceptual, and distribution space. Finally, DiffSteISR incorporates a stereo semantic extractor (SSE) to capture unique viewpoint soft semantic information and shared hard tag semantic information, thereby effectively improving the semantic accuracy and consistency of the generated left and right images. Extensive experimental results demonstrate that DiffSteISR accurately reconstructs natural and precise textures from low-resolution stereo images while maintaining a high consistency of semantic and texture between the left and right views.

Large Language Models (LLMs) have been widely applied in various professional fields. By fine-tuning the models using domain specific question and answer datasets, the professional domain knowledge and Q\&A abilities of these models have significantly improved, for example, medical professional LLMs that use fine-tuning of doctor-patient Q\&A data exhibit extraordinary disease diagnostic abilities. However, we observed that despite improvements in specific domain knowledge, the performance of medical LLM in long-context understanding has significantly declined, especially compared to general language models with similar parameters. The purpose of this study is to investigate the phenomenon of reduced performance in understanding long-context in medical LLM. We designed a series of experiments to conduct open-book professional knowledge exams on all models to evaluate their ability to read long-context. By adjusting the proportion and quantity of general data and medical data in the process of fine-tuning, we can determine the best data composition to optimize the professional model and achieve a balance between long-context performance and specific domain knowledge., Comment: 5 pages, 1 figure. Accepted by the Workshop on Long-Context Foundation Models (LCFM) at ICML 2024

Adversarial learning helps generative models translate MRI from source to target sequence when lacking paired samples. However, implementing MRI synthesis with adversarial learning in clinical settings is challenging due to training instability and mode collapse. To address this issue, we leverage intermediate sequences to estimate the common latent space among multi-sequence MRI, enabling the reconstruction of distinct sequences from the common latent space. We propose a generative model that compresses discrete representations of each sequence to estimate the Gaussian distribution of vector-quantized common (VQC) latent space between multiple sequences. Moreover, we improve the latent space consistency with contrastive learning and increase model stability by domain augmentation. Experiments using BraTS2021 dataset show that our non-adversarial model outperforms other GAN-based methods, and VQC latent space aids our model to achieve (1) anti-interference ability, which can eliminate the effects of noise, bias fields, and artifacts, and (2) solid semantic representation ability, with the potential of one-shot segmentation. Our code is publicly available.

With the remarkable advancements of large language models (LLMs), LLM-based agents have become a research hotspot in human-computer interaction. However, there is a scarcity of benchmarks available for LLM-based mobile agents. Benchmarking these agents generally faces three main challenges: (1) The inefficiency of UI-only operations imposes limitations to task evaluation. (2) Specific instructions within a singular application lack adequacy for assessing the multi-dimensional reasoning and decision-making capacities of LLM mobile agents. (3) Current evaluation metrics are insufficient to accurately assess the process of sequential actions. To this end, we propose Mobile-Bench, a novel benchmark for evaluating the capabilities of LLM-based mobile agents. First, we expand conventional UI operations by incorporating 103 collected APIs to accelerate the efficiency of task completion. Subsequently, we collect evaluation data by combining real user queries with augmentation from LLMs. To better evaluate different levels of planning capabilities for mobile agents, our data is categorized into three distinct groups: SAST, SAMT, and MAMT, reflecting varying levels of task complexity. Mobile-Bench comprises 832 data entries, with more than 200 tasks specifically designed to evaluate multi-APP collaboration scenarios. Furthermore, we introduce a more accurate evaluation metric, named CheckPoint, to assess whether LLM-based mobile agents reach essential points during their planning and reasoning steps.

Ultrasound is widely used in clinical practice due to its affordability, portability, and safety. However, current AI research often overlooks combined disease prediction and tissue segmentation. We propose UniUSNet, a universal framework for ultrasound image classification and segmentation. This model handles various ultrasound types, anatomical positions, and input formats, excelling in both segmentation and classification tasks. Trained on a comprehensive dataset with over 9.7K annotations from 7 distinct anatomical positions, our model matches state-of-the-art performance and surpasses single-dataset and ablated models. Zero-shot and fine-tuning experiments show strong generalization and adaptability with minimal fine-tuning. We plan to expand our dataset and refine the prompting mechanism, with model weights and code available at (https://github.com/Zehui-Lin/UniUSNet)., Comment: Accepted to BIBM 2024

Computed Tomography (CT) is a frequently utilized imaging technology that is employed in the clinical diagnosis of many disorders. However, clinical diagnosis, data storage, and management are posed huge challenges by a huge volume of non-homogeneous CT data in terms of imaging quality. As a result, the quality assessment of CT images is a crucial problem that demands consideration. The history, advancements in research, and current developments in CT image quality assessment (IQA) are examined in this paper. In this review, we collected and researched more than 500 CT-IQA publications published before August 2023. And we provide the visualization analysis of keywords and co-citations in the knowledge graph of these papers. Prospects and obstacles for the continued development of CT-IQA are also covered. At present, significant research branches in the CT-IQA domain include Phantom study, Artificial intelligence deep-learning reconstruction algorithm, Dose reduction opportunity, and Virtual monoenergetic reconstruction. Artificial intelligence (AI)-based CT-IQA also becomes a trend. It increases the accuracy of the CT scanning apparatus, amplifies the impact of the CT system reconstruction algorithm, and creates an effective algorithm for post-processing CT images. AI-based medical IQA offers excellent application opportunities in clinical work. AI can provide uniform quality assessment criteria and more comprehensive guidance amongst various healthcare facilities, and encourage them to identify one another's images. It will help lower the number of unnecessary tests and associated costs, and enhance the quality of medical imaging and assessment efficiency.

Multi-modal image fusion aims to combine information from different modes to create a single image with comprehensive information and detailed textures. However, fusion models based on convolutional neural networks encounter limitations in capturing global image features due to their focus on local convolution operations. Transformer-based models, while excelling in global feature modeling, confront computational challenges stemming from their quadratic complexity. Recently, the Selective Structured State Space Model has exhibited significant potential for long-range dependency modeling with linear complexity, offering a promising avenue to address the aforementioned dilemma. In this paper, we propose FusionMamba, a novel dynamic feature enhancement method for multimodal image fusion with Mamba. Specifically, we devise an improved efficient Mamba model for image fusion, integrating efficient visual state space model with dynamic convolution and channel attention. This refined model not only upholds the performance of Mamba and global modeling capability but also diminishes channel redundancy while enhancing local enhancement capability. Additionally, we devise a dynamic feature fusion module (DFFM) comprising two dynamic feature enhancement modules (DFEM) and a cross modality fusion mamba module (CMFM). The former serves for dynamic texture enhancement and dynamic difference perception, whereas the latter enhances correlation features between modes and suppresses redundant intermodal information. FusionMamba has yielded state-of-the-art (SOTA) performance across various multimodal medical image fusion tasks (CT-MRI, PET-MRI, SPECT-MRI), infrared and visible image fusion task (IR-VIS) and multimodal biomedical image fusion dataset (GFP-PC), which is proved that our model has generalization ability. The code for FusionMamba is available at https://github.com/millieXie/FusionMamba.

Optical-SAR image matching is a fundamental task for image fusion and visual navigation. However, all large-scale open SAR dataset for methods development are collected from single platform, resulting in limited satellite types and spatial resolutions. Since images captured by different sensors vary significantly in both geometric and radiometric appearance, existing methods may fail to match corresponding regions containing the same content. Besides, most of existing datasets have not been categorized based on the characteristics of different scenes. To encourage the design of more general multi-modal image matching methods, we introduce a large-scale Multi-sources,Multi-resolutions, and Multi-scenes dataset for Optical-SAR image matching(3MOS). It consists of 155K optical-SAR image pairs, including SAR data from six commercial satellites, with resolutions ranging from 1.25m to 12.5m. The data has been classified into eight scenes including urban, rural, plains, hills, mountains, water, desert, and frozen earth. Extensively experiments show that none of state-of-the-art methods achieve consistently superior performance across different sources, resolutions and scenes. In addition, the distribution of data has a substantial impact on the matching capability of deep learning models, this proposes the domain adaptation challenge in optical-SAR image matching. Our data and code will be available at:https://github.com/3M-OS/3MOS., Comment: 20pages 17 figures

ChatGPT and other general large language models (LLMs) have achieved remarkable success, but they have also raised concerns about the misuse of AI-generated texts. Existing AI-generated text detection models, such as based on BERT and RoBERTa, are prone to in-domain over-fitting, leading to poor out-of-domain (OOD) detection performance. In this paper, we first collected Chinese text responses generated by human experts and 9 types of LLMs, for which to multiple domains questions, and further created a dataset that mixed human-written sentences and sentences polished by LLMs. We then proposed LLM-Detector, a novel method for both document-level and sentence-level text detection through Instruction Tuning of LLMs. Our method leverages the wealth of knowledge LLMs acquire during pre-training, enabling them to detect the text they generate. Instruction tuning aligns the model's responses with the user's expected text detection tasks. Experimental results show that previous methods struggle with sentence-level AI-generated text detection and OOD detection. In contrast, our proposed method not only significantly outperforms baseline methods in both sentence-level and document-level text detection but also demonstrates strong generalization capabilities. Furthermore, since LLM-Detector is trained based on open-source LLMs, it is easy to customize for deployment., Comment: 17 pages, 13 tables, 7 figures

Despite the potential benefits of data augmentation for mitigating the data insufficiency, traditional augmentation methods primarily rely on the prior intra-domain knowledge. On the other hand, advanced generative adversarial networks (GANs) generate inter-domain samples with limited variety. These previous methods make limited contributions to describing the decision boundaries for binary classification. In this paper, we propose a distance guided GAN (DisGAN) which controls the variation degrees of generated samples in the hyperplane space. Specifically, we instantiate the idea of DisGAN by combining two ways. The first way is vertical distance GAN (VerDisGAN) where the inter-domain generation is conditioned on the vertical distances. The second way is horizontal distance GAN (HorDisGAN) where the intra-domain generation is conditioned on the horizontal distances. Furthermore, VerDisGAN can produce the class-specific regions by mapping the source images to the hyperplane. Experimental results show that DisGAN consistently outperforms the GAN-based augmentation methods with explainable binary classification. The proposed method can apply to different classification architectures and has potential to extend to multi-class classification., Comment: 12 pages, 8 figures. This work has been submitted to the IEEE TNNLS for possible publication. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media

Existing research has demonstrated that refining large language models (LLMs) through the utilization of machine-generated instruction-following data empowers these models to exhibit impressive zero-shot capabilities for novel tasks, without requiring human-authored instructions. In this paper, we systematically investigate, preprocess, and integrate three Chinese instruction-following datasets with the aim of enhancing the Chinese conversational capabilities of Mixtral-8x7B sparse Mixture-of-Experts model. Through instruction fine-tuning on this carefully processed dataset, we successfully construct the Mixtral-8x7B sparse Mixture-of-Experts model named "Aurora." To assess the performance of Aurora, we utilize three widely recognized benchmark tests: C-Eval, MMLU, and CMMLU. Empirical studies validate the effectiveness of instruction fine-tuning applied to Mixtral-8x7B sparse Mixture-of-Experts model. This work is pioneering in the execution of instruction fine-tuning on a sparse expert-mixed model, marking a significant breakthrough in enhancing the capabilities of this model architecture. Our code, data and model are publicly available at https://github.com/WangRongsheng/Aurora, Comment: 10 pages, 2 figures

Although current data augmentation methods are successful to alleviate the data insufficiency, conventional augmentation are primarily intra-domain while advanced generative adversarial networks (GANs) generate images remaining uncertain, particularly in small-scale datasets. In this paper, we propose a parameterized GAN (ParaGAN) that effectively controls the changes of synthetic samples among domains and highlights the attention regions for downstream classification. Specifically, ParaGAN incorporates projection distance parameters in cyclic projection and projects the source images to the decision boundary to obtain the class-difference maps. Our experiments show that ParaGAN can consistently outperform the existing augmentation methods with explainable classification on two small-scale medical datasets., Comment: 5 pages, 4 figures. This work has been submitted to the IEEE ICASSP for possible publication

Supervised learning algorithms based on Convolutional Neural Networks have become the benchmark for medical image segmentation tasks, but their effectiveness heavily relies on a large amount of labeled data. However, annotating medical image datasets is a laborious and time-consuming process. Inspired by semi-supervised algorithms that use both labeled and unlabeled data for training, we propose the PLGDF framework, which builds upon the mean teacher network for segmenting medical images with less annotation. We propose a novel pseudo-label utilization scheme, which combines labeled and unlabeled data to augment the dataset effectively. Additionally, we enforce the consistency between different scales in the decoder module of the segmentation network and propose a loss function suitable for evaluating the consistency. Moreover, we incorporate a sharpening operation on the predicted results, further enhancing the accuracy of the segmentation. Extensive experiments on three publicly available datasets demonstrate that the PLGDF framework can largely improve performance by incorporating the unlabeled data. Meanwhile, our framework yields superior performance compared to six state-of-the-art semi-supervised learning methods. The codes of this study are available at https://github.com/ortonwang/PLGDF.

While supervised learning has achieved remarkable success, obtaining large-scale labeled datasets in biomedical imaging is often impractical due to high costs and the time-consuming annotations required from radiologists. Semi-supervised learning emerges as an effective strategy to overcome this limitation by leveraging useful information from unlabeled datasets. In this paper, we present a novel semi-supervised learning method, Dual-Decoder Consistency via Pseudo-Labels Guided Data Augmentation (DCPA), for medical image segmentation. We devise a consistency regularization to promote consistent representations during the training process. Specifically, we use distinct decoders for student and teacher networks while maintain the same encoder. Moreover, to learn from unlabeled data, we create pseudo-labels generated by the teacher networks and augment the training data with the pseudo-labels. Both techniques contribute to enhancing the performance of the proposed method. The method is evaluated on three representative medical image segmentation datasets. Comprehensive comparisons with state-of-the-art semi-supervised medical image segmentation methods were conducted under typical scenarios, utilizing 10% and 20% labeled data, as well as in the extreme scenario of only 5% labeled data. The experimental results consistently demonstrate the superior performance of our method compared to other methods across the three semi-supervised settings. The source code is publicly available at https://github.com/BinYCn/DCPA.git.

General large language models (LLMs) such as ChatGPT have shown remarkable success. However, such LLMs have not been widely adopted for medical purposes, due to poor accuracy and inability to provide medical advice. We propose IvyGPT, an LLM based on LLaMA that is trained and fine-tuned with high-quality medical question-answer (QA) instances and Reinforcement Learning from Human Feedback (RLHF). After supervised fine-tuning, IvyGPT has good multi-turn conversation capabilities, but it cannot perform like a doctor in other aspects, such as comprehensive diagnosis. Through RLHF, IvyGPT can output richer diagnosis and treatment answers that are closer to human. In the training, we used QLoRA to train 33 billion parameters on a small number of NVIDIA A100 (80GB) GPUs. Experimental results show that IvyGPT has outperformed other medical GPT models., Comment: 5 pages, 3 figures

Asymmetry is a crucial characteristic of bilateral mammograms (Bi-MG) when abnormalities are developing. It is widely utilized by radiologists for diagnosis. The question of 'what the symmetrical Bi-MG would look like when the asymmetrical abnormalities have been removed ?' has not yet received strong attention in the development of algorithms on mammograms. Addressing this question could provide valuable insights into mammographic anatomy and aid in diagnostic interpretation. Hence, we propose a novel framework, DisAsymNet, which utilizes asymmetrical abnormality transformer guided self-adversarial learning for disentangling abnormalities and symmetric Bi-MG. At the same time, our proposed method is partially guided by randomly synthesized abnormalities. We conduct experiments on three public and one in-house dataset, and demonstrate that our method outperforms existing methods in abnormality classification, segmentation, and localization tasks. Additionally, reconstructed normal mammograms can provide insights toward better interpretable visual cues for clinical diagnosis. The code will be accessible to the public.

Magnetic resonance imaging (MRI) is the most sensitive technique for breast cancer detection among current clinical imaging modalities. Contrast-enhanced MRI (CE-MRI) provides superior differentiation between tumors and invaded healthy tissue, and has become an indispensable technique in the detection and evaluation of cancer. However, the use of gadolinium-based contrast agents (GBCA) to obtain CE-MRI may be associated with nephrogenic systemic fibrosis and may lead to bioaccumulation in the brain, posing a potential risk to human health. Moreover, and likely more important, the use of gadolinium-based contrast agents requires the cannulation of a vein, and the injection of the contrast media which is cumbersome and places a burden on the patient. To reduce the use of contrast agents, diffusion-weighted imaging (DWI) is emerging as a key imaging technique, although currently usually complementing breast CE-MRI. In this study, we develop a multi-sequence fusion network to synthesize CE-MRI based on T1-weighted MRI and DWIs. DWIs with different b-values are fused to efficiently utilize the difference features of DWIs. Rather than proposing a pure data-driven approach, we invent a multi-sequence attention module to obtain refined feature maps, and leverage hierarchical representation information fused at different scales while utilizing the contributions from different sequences from a model-driven approach by introducing the weighted difference module. The results show that the multi-b-value DWI-based fusion model can potentially be used to synthesize CE-MRI, thus theoretically reducing or avoiding the use of GBCA, thereby minimizing the burden to patients. Our code is available at \url{https://github.com/Netherlands-Cancer-Institute/CE-MRI}., Comment: This paper has been accepted by MICCAI 2023

In recent years, deep learning has become a breakthrough technique in assisting medical image diagnosis. Supervised learning using convolutional neural networks (CNN) provides state-of-the-art performance and has served as a benchmark for various medical image segmentation and classification. However, supervised learning deeply relies on large-scale annotated data, which is expensive, time-consuming, and even impractical to acquire in medical imaging applications. Active Learning (AL) methods have been widely applied in natural image classification tasks to reduce annotation costs by selecting more valuable examples from the unlabeled data pool. However, their application in medical image segmentation tasks is limited, and there is currently no effective and universal AL-based method specifically designed for 3D medical image segmentation. To address this limitation, we propose an AL-based method that can be simultaneously applied to 2D medical image classification, segmentation, and 3D medical image segmentation tasks. We extensively validated our proposed active learning method on three publicly available and challenging medical image datasets, Kvasir Dataset, COVID-19 Infection Segmentation Dataset, and BraTS2019 Dataset. The experimental results demonstrate that our PCDAL can achieve significantly improved performance with fewer annotations in 2D classification and segmentation and 3D segmentation tasks. The codes of this study are available at https://github.com/ortonwang/PCDAL.

Magnetic resonance images (MRI) acquired with low through-plane resolution compromise time and cost. The poor resolution in one orientation is insufficient to meet the requirement of high resolution for early diagnosis of brain disease and morphometric study. The common Single image super-resolution (SISR) solutions face two main challenges: (1) local detailed and global anatomical structural information combination; and (2) large-scale restoration when applied for reconstructing thick-slice MRI into high-resolution (HR) iso-tropic data. To address these problems, we propose a novel two-stage network for brain MRI SR named TransMRSR based on the convolutional blocks to extract local information and transformer blocks to capture long-range dependencies. TransMRSR consists of three modules: the shallow local feature extraction, the deep non-local feature capture, and the HR image reconstruction. We perform a generative task to encapsulate diverse priors into a generative network (GAN), which is the decoder sub-module of the deep non-local feature capture part, in the first stage. The pre-trained GAN is used for the second stage of SR task. We further eliminate the potential latent space shift caused by the two-stage training strategy through the self-distilled truncation trick. The extensive experiments show that our method achieves superior performance to other SSIR methods on both public and private datasets. Code is released at https://github.com/goddesshs/TransMRSR.git ., Comment: 2023 CGI

Recently, Users Generated Content (UGC) videos becomes ubiquitous in our daily lives. However, due to the limitations of photographic equipments and techniques, UGC videos often contain various degradations, in which one of the most visually unfavorable effects is the underexposure. Therefore, corresponding video enhancement algorithms such as Low-Light Video Enhancement (LLVE) have been proposed to deal with the specific degradation. However, different from video enhancement algorithms, almost all existing Video Quality Assessment (VQA) models are built generally rather than specifically, which measure the quality of a video from a comprehensive perspective. To the best of our knowledge, there is no VQA model specially designed for videos enhanced by LLVE algorithms. To this end, we first construct a Low-Light Video Enhancement Quality Assessment (LLVE-QA) dataset in which 254 original low-light videos are collected and then enhanced by leveraging 8 LLVE algorithms to obtain 2,060 videos in total. Moreover, we propose a quality assessment model specialized in LLVE, named Light-VQA. More concretely, since the brightness and noise have the most impact on low-light enhanced VQA, we handcraft corresponding features and integrate them with deep-learning-based semantic features as the overall spatial information. As for temporal information, in addition to deep-learning-based motion features, we also investigate the handcrafted brightness consistency among video frames, and the overall temporal information is their concatenation. Subsequently, spatial and temporal information is fused to obtain the quality-aware representation of a video. Extensive experimental results show that our Light-VQA achieves the best performance against the current State-Of-The-Art (SOTA) on LLVE-QA and public dataset. Dataset and Codes can be found at https://github.com/wenzhouyidu/Light-VQA.

Magnetic resonance imaging (MRI) is highly sensitive for lesion detection in the breasts. Sequences obtained with different settings can capture the specific characteristics of lesions. Such multi-parameter MRI information has been shown to improve radiologist performance in lesion classification, as well as improving the performance of artificial intelligence models in various tasks. However, obtaining multi-parameter MRI makes the examination costly in both financial and time perspectives, and there may be safety concerns for special populations, thus making acquisition of the full spectrum of MRI sequences less durable. In this study, different than naive input fusion or feature concatenation from existing MRI parameters, a novel $\textbf{I}$ntegrated MRI $\textbf{M}$ulti-$\textbf{P}$arameter reinf$\textbf{O}$rcement fusion generato$\textbf{R}$ wi$\textbf{T}$h $\textbf{A}$tte$\textbf{NT}$ion Network (IMPORTANT-Net) is developed to generate missing parameters. First, the parameter reconstruction module is used to encode and restore the existing MRI parameters to obtain the corresponding latent representation information at any scale level. Then the multi-parameter fusion with attention module enables the interaction of the encoded information from different parameters through a set of algorithmic strategies, and applies different weights to the information through the attention mechanism after information fusion to obtain refined representation information. Finally, a reinforcement fusion scheme embedded in a $V^{-}$-shape generation module is used to combine the hierarchical representations to generate the missing MRI parameter. Results showed that our IMPORTANT-Net is capable of generating missing MRI parameters and outperforms comparable state-of-the-art networks. Our code is available at https://github.com/Netherlands-Cancer-Institute/MRI_IMPORTANT_NET.

Multi-sequence MRIs can be necessary for reliable diagnosis in clinical practice due to the complimentary information within sequences. However, redundant information exists across sequences, which interferes with mining efficient representations by modern machine learning or deep learning models. To handle various clinical scenarios, we propose a sequence-to-sequence generation framework (Seq2Seq) for imaging-differentiation representation learning. In this study, not only do we propose arbitrary 3D/4D sequence generation within one model to generate any specified target sequence, but also we are able to rank the importance of each sequence based on a new metric estimating the difficulty of a sequence being generated. Furthermore, we also exploit the generation inability of the model to extract regions that contain unique information for each sequence. We conduct extensive experiments using three datasets including a toy dataset of 20,000 simulated subjects, a brain MRI dataset of 1,251 subjects, and a breast MRI dataset of 2,101 subjects, to demonstrate that (1) our proposed Seq2Seq is efficient and lightweight for complex clinical datasets and can achieve excellent image quality; (2) top-ranking sequences can be used to replace complete sequences with non-inferior performance; (3) combining MRI with our imaging-differentiation map leads to better performance in clinical tasks such as glioblastoma MGMT promoter methylation status prediction and breast cancer pathological complete response status prediction. Our code is available at https://github.com/fiy2W/mri_seq2seq.

We introduce LYSTO, the Lymphocyte Assessment Hackathon, which was held in conjunction with the MICCAI 2019 Conference in Shenzen (China). The competition required participants to automatically assess the number of lymphocytes, in particular T-cells, in histopathological images of colon, breast, and prostate cancer stained with CD3 and CD8 immunohistochemistry. Differently from other challenges setup in medical image analysis, LYSTO participants were solely given a few hours to address this problem. In this paper, we describe the goal and the multi-phase organization of the hackathon; we describe the proposed methods and the on-site results. Additionally, we present post-competition results where we show how the presented methods perform on an independent set of lung cancer slides, which was not part of the initial competition, as well as a comparison on lymphocyte assessment between presented methods and a panel of pathologists. We show that some of the participants were capable to achieve pathologist-level performance at lymphocyte assessment. After the hackathon, LYSTO was left as a lightweight plug-and-play benchmark dataset on grand-challenge website, together with an automatic evaluation platform. LYSTO has supported a number of research in lymphocyte assessment in oncology. LYSTO will be a long-lasting educational challenge for deep learning and digital pathology, it is available at https://lysto.grand-challenge.org/., Comment: will be sumitted to IEEE-JBHI