ICH-SCNet: Intracerebral Hemorrhage Segmentation and Prognosis Classification Network Using CLIP-guided SAM mechanism

Intracerebral hemorrhage (ICH) is the most fatal subtype of stroke and is characterized by a high incidence of disability. Accurate segmentation of the ICH region and prognosis prediction are critically important for developing and refining treatment plans for post-ICH patients. However, existing approaches address these two tasks independently and predominantly focus on imaging data alone, thereby neglecting the intrinsic correlation between the tasks and modalities. This paper introduces a multi-task network, ICH-SCNet, designed for both ICH segmentation and prognosis classification. Specifically, we integrate a SAM-CLIP cross-modal interaction mechanism that combines medical text and segmentation auxiliary information with neuroimaging data to enhance cross-modal feature recognition. Additionally, we develop an effective feature fusion module and a multi-task loss function to improve performance further. Extensive experiments on an ICH dataset reveal that our approach surpasses other state-of-the-art methods. It excels in the overall performance of classification tasks and outperforms competing models in all segmentation task metrics.

LPUWF-LDM: Enhanced Latent Diffusion Model for Precise Late-phase UWF-FA Generation on Limited Dataset

Ultra-Wide-Field Fluorescein Angiography (UWF-FA) enables precise identification of ocular diseases using sodium fluorescein, which can be potentially harmful. Existing research has developed methods to generate UWF-FA from Ultra-Wide-Field Scanning Laser Ophthalmoscopy (UWF-SLO) to reduce the adverse reactions associated with injections. However, these methods have been less effective in producing high-quality late-phase UWF-FA, particularly in lesion areas and fine details. Two primary challenges hinder the generation of high-quality late-phase UWF-FA: the scarcity of paired UWF-SLO and early/late-phase UWF-FA datasets, and the need for realistic generation at lesion sites and potential blood leakage regions. This study introduces an improved latent diffusion model framework to generate high-quality late-phase UWF-FA from limited paired UWF images. To address the challenges as mentioned earlier, our approach employs a module utilizing Cross-temporal Regional Difference Loss, which encourages the model to focus on the differences between early and late phases. Additionally, we introduce a low-frequency enhanced noise strategy in the diffusion forward process to improve the realism of medical images. To further enhance the mapping capability of the variational autoencoder module, especially with limited datasets, we implement a Gated Convolutional Encoder to extract additional information from conditional images. Our Latent Diffusion Model for Ultra-Wide-Field Late-Phase Fluorescein Angiography (LPUWF-LDM) effectively reconstructs fine details in late-phase UWF-FA and achieves state-of-the-art results compared to other existing methods when working with limited datasets. Our source code is available at: https://github.com/Tinysqua/****.

Toward Robust Early Detection of Alzheimer's Disease via an Integrated Multimodal Learning Approach

Alzheimer's Disease (AD) is a complex neurodegenerative disorder marked by memory loss, executive dysfunction, and personality changes. Early diagnosis is challenging due to subtle symptoms and varied presentations, often leading to misdiagnosis with traditional unimodal diagnostic methods due to their limited scope. This study introduces an advanced multimodal classification model that integrates clinical, cognitive, neuroimaging, and EEG data to enhance diagnostic accuracy. The model incorporates a feature tagger with a tabular data coding architecture and utilizes the TimesBlock module to capture intricate temporal patterns in Electroencephalograms (EEG) data. By employing Cross-modal Attention Aggregation module, the model effectively fuses Magnetic Resonance Imaging (MRI) spatial information with EEG temporal data, significantly improving the distinction between AD, Mild Cognitive Impairment, and Normal Cognition. Simultaneously, we have constructed the first AD classification dataset that includes three modalities: EEG, MRI, and tabular data. Our innovative approach aims to facilitate early diagnosis and intervention, potentially slowing the progression of AD. The source code and our private ADMC dataset are available at https://github.com/JustlfC03/MSTNet.

TC-KANRecon: High-Quality and Accelerated MRI Reconstruction via Adaptive KAN Mechanisms and Intelligent Feature Scaling

Magnetic Resonance Imaging (MRI) has become essential in clinical diagnosis due to its high resolution and multiple contrast mechanisms. However, the relatively long acquisition time limits its broader application. To address this issue, this study presents an innovative conditional guided diffusion model, named as TC-KANRecon, which incorporates the Multi-Free U-KAN (MF-UKAN) module and a dynamic clipping strategy. TC-KANRecon model aims to accelerate the MRI reconstruction process through deep learning methods while maintaining the quality of the reconstructed images. The MF-UKAN module can effectively balance the tradeoff between image denoising and structure preservation. Specifically, it presents the multi-head attention mechanisms and scalar modulation factors, which significantly enhances the model's robustness and structure preservation capabilities in complex noise environments. Moreover, the dynamic clipping strategy in TC-KANRecon adjusts the cropping interval according to the sampling steps, thereby mitigating image detail loss typically caused by traditional cropping methods and enriching the visual features of the images. Furthermore, the MC-Model module incorporates full-sampling k-space information, realizing efficient fusion of conditional information, enhancing the model's ability to process complex data, and improving the realism and detail richness of reconstructed images. Experimental results demonstrate that the proposed method outperforms other MRI reconstruction methods in both qualitative and quantitative evaluations. Notably, TC-KANRecon method exhibits excellent reconstruction results when processing high-noise, low-sampling-rate MRI data. Our source code is available at https://github.com/lcbkmm/TC-KANRecon.

GFE-Mamba: Mamba-based AD Multi-modal Progression Assessment via Generative Feature Extraction from MCI

Alzheimer's Disease (AD) is an irreversible neurodegenerative disorder that often progresses from Mild Cognitive Impairment (MCI), leading to memory loss and significantly impacting patients' lives. Clinical trials indicate that early targeted interventions for MCI patients can potentially slow or halt the development and progression of AD. Previous research has shown that accurate medical classification requires the inclusion of extensive multimodal data, such as assessment scales and various neuroimaging techniques like Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET). However, consistently tracking the diagnosis of the same individual over time and simultaneously collecting multimodal data poses significant challenges. To address this issue, we introduce GFE-Mamba, a classifier based on Generative Feature Extraction (GFE). This classifier effectively integrates data from assessment scales, MRI, and PET, enabling deeper multimodal fusion. It efficiently extracts both long and short sequence information and incorporates additional information beyond the pixel space. This approach not only improves classification accuracy but also enhances the interpretability and stability of the model. We constructed datasets of over 3000 samples based on the Alzheimer's Disease Neuroimaging Initiative (ADNI) for a two-step training process. Our experimental results demonstrate that the GFE-Mamba model is effective in predicting the conversion from MCI to AD and outperforms several state-of-the-art methods. Our source code and ADNI dataset processing code are available at https://github.com/Tinysqua/GFE-Mamba.

stEnTrans: Transformer-based deep learning for spatial transcriptomics enhancement

The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while retaining spatial information. However, current popular spatial transcriptomics techniques either have shallow sequencing depth or low resolution. We present stEnTrans, a deep learning method based on Transformer architecture that provides comprehensive predictions for gene expression in unmeasured areas or unexpectedly lost areas and enhances gene expression in original and inputed spots. Utilizing a self-supervised learning approach, stEnTrans establishes proxy tasks on gene expression profile without requiring additional data, mining intrinsic features of the tissues as supervisory information. We evaluate stEnTrans on six datasets and the results indicate superior performance in enhancing spots resolution and predicting gene expression in unmeasured areas compared to other deep learning and traditional interpolation methods. Additionally, Our method also can help the discovery of spatial patterns in Spatial Transcriptomics and enrich to more biologically significant pathways. Our source code is available at https://github.com/shuailinxue/stEnTrans.

Multimodal contrastive learning for spatial gene expression prediction using histology images

In recent years, the advent of spatial transcriptomics (ST) technology has unlocked unprecedented opportunities for delving into the complexities of gene expression patterns within intricate biological systems. Despite its transformative potential, the prohibitive cost of ST technology remains a significant barrier to its widespread adoption in large-scale studies. An alternative, more cost-effective strategy involves employing artificial intelligence to predict gene expression levels using readily accessible whole-slide images (WSIs) stained with Hematoxylin and Eosin (H\&E). However, existing methods have yet to fully capitalize on multimodal information provided by H&E images and ST data with spatial location. In this paper, we propose \textbf{mclSTExp}, a multimodal contrastive learning with Transformer and Densenet-121 encoder for Spatial Transcriptomics Expression prediction. We conceptualize each spot as a "word", integrating its intrinsic features with spatial context through the self-attention mechanism of a Transformer encoder. This integration is further enriched by incorporating image features via contrastive learning, thereby enhancing the predictive capability of our model. Our extensive evaluation of \textbf{mclSTExp} on two breast cancer datasets and a skin squamous cell carcinoma dataset demonstrates its superior performance in predicting spatial gene expression. Moreover, mclSTExp has shown promise in interpreting cancer-specific overexpressed genes, elucidating immune-related genes, and identifying specialized spatial domains annotated by pathologists. Our source code is available at https://github.com/shizhiceng/mclSTExp.

SCKansformer: Fine-Grained Classification of Bone Marrow Cells via Kansformer Backbone and Hierarchical Attention Mechanisms

The incidence and mortality rates of malignant tumors, such as acute leukemia, have risen significantly. Clinically, hospitals rely on cytological examination of peripheral blood and bone marrow smears to diagnose malignant tumors, with accurate blood cell counting being crucial. Existing automated methods face challenges such as low feature expression capability, poor interpretability, and redundant feature extraction when processing high-dimensional microimage data. We propose a novel fine-grained classification model, SCKansformer, for bone marrow blood cells, which addresses these challenges and enhances classification accuracy and efficiency. The model integrates the Kansformer Encoder, SCConv Encoder, and Global-Local Attention Encoder. The Kansformer Encoder replaces the traditional MLP layer with the KAN, improving nonlinear feature representation and interpretability. The SCConv Encoder, with its Spatial and Channel Reconstruction Units, enhances feature representation and reduces redundancy. The Global-Local Attention Encoder combines Multi-head Self-Attention with a Local Part module to capture both global and local features. We validated our model using the Bone Marrow Blood Cell Fine-Grained Classification Dataset (BMCD-FGCD), comprising over 10,000 samples and nearly 40 classifications, developed with a partner hospital. Comparative experiments on our private dataset, as well as the publicly available PBC and ALL-IDB datasets, demonstrate that SCKansformer outperforms both typical and advanced microcell classification methods across all datasets. Our source code and private BMCD-FGCD dataset are available at https://github.com/JustlfC03/SCKansformer.

UWAFA-GAN: Ultra-Wide-Angle Fluorescein Angiography Transformation via Multi-scale Generation and Registration Enhancement

Fundus photography, in combination with the ultra-wide-angle fundus (UWF) techniques, becomes an indispensable diagnostic tool in clinical settings by offering a more comprehensive view of the retina. Nonetheless, UWF fluorescein angiography (UWF-FA) necessitates the administration of a fluorescent dye via injection into the patient's hand or elbow unlike UWF scanning laser ophthalmoscopy (UWF-SLO). To mitigate potential adverse effects associated with injections, researchers have proposed the development of cross-modality medical image generation algorithms capable of converting UWF-SLO images into their UWF-FA counterparts. Current image generation techniques applied to fundus photography encounter difficulties in producing high-resolution retinal images, particularly in capturing minute vascular lesions. To address these issues, we introduce a novel conditional generative adversarial network (UWAFA-GAN) to synthesize UWF-FA from UWF-SLO. This approach employs multi-scale generators and an attention transmit module to efficiently extract both global structures and local lesions. Additionally, to counteract the image blurriness issue that arises from training with misaligned data, a registration module is integrated within this framework. Our method performs non-trivially on inception scores and details generation. Clinical user studies further indicate that the UWF-FA images generated by UWAFA-GAN are clinically comparable to authentic images in terms of diagnostic reliability. Empirical evaluations on our proprietary UWF image datasets elucidate that UWAFA-GAN outperforms extant methodologies. The code is accessible at https://github.com/Tinysqua/UWAFA-GAN.

ConsistencyDet: A Robust Object Detector with a Denoising Paradigm of Consistency Model

Object detection, a quintessential task in the realm of perceptual computing, can be tackled using a generative methodology. In the present study, we introduce a novel framework designed to articulate object detection as a denoising diffusion process, which operates on the perturbed bounding boxes of annotated entities. This framework, termed ConsistencyDet, leverages an innovative denoising concept known as the Consistency Model. The hallmark of this model is its self-consistency feature, which empowers the model to map distorted information from any temporal stage back to its pristine state, thereby realizing a "one-step denoising" mechanism. Such an attribute markedly elevates the operational efficiency of the model, setting it apart from the conventional Diffusion Model. Throughout the training phase, ConsistencyDet initiates the diffusion sequence with noise-infused boxes derived from the ground-truth annotations and conditions the model to perform the denoising task. Subsequently, in the inference stage, the model employs a denoising sampling strategy that commences with bounding boxes randomly sampled from a normal distribution. Through iterative refinement, the model transforms an assortment of arbitrarily generated boxes into definitive detections. Comprehensive evaluations employing standard benchmarks, such as MS-COCO and LVIS, corroborate that ConsistencyDet surpasses other leading-edge detectors in performance metrics. Our code is available at https://github.com/Tankowa/ConsistencyDet.