Ali Braytee

Kunal Chaturvedi, Ali Braytee, Jun Li et al.

This paper proposes a novel self-supervised based Cut-and-Paste GAN to perform foreground object segmentation and generate realistic composite images without manual annotations. We accomplish this goal by a simple yet effective self-supervised approach coupled with the U-Net based discriminator. The proposed method extends the ability of the standard discriminators to learn not only the global data representations via classification (real/fake) but also learn semantic and structural information through pseudo labels created using the self-supervised task. The proposed method empowers the generator to create meaningful masks by forcing it to learn informative per-pixel as well as global image feedback from the discriminator. Our experiments demonstrate that our proposed method significantly outperforms the state-of-the-art methods on the standard benchmark datasets.

Ali Anaissi, Ali Braytee, Weidong Huang et al.

As dermatological conditions become increasingly common and the availability of dermatologists remains limited, there is a growing need for intelligent tools to support both patients and clinicians in the timely and accurate diagnosis of skin diseases. In this project, we developed a deep learning based model for the classification and diagnosis of skin conditions. By leveraging pretraining on publicly available skin disease image datasets, our model effectively extracted visual features and accurately classified various dermatological cases. Throughout the project, we refined the model architecture, optimized data preprocessing workflows, and applied targeted data augmentation techniques to improve overall performance. The final model, based on the Swin Transformer, achieved a prediction accuracy of 87.71 percent across eight skin lesion classes on the ISIC2019 dataset. These results demonstrate the model's potential as a diagnostic support tool for clinicians and a self assessment aid for patients.

Ali Anaissi, Seid Miad Zandavi, Weidong Huang et al.

Single-cell data analysis has the potential to revolutionize personalized medicine by characterizing disease-associated molecular changes at the single-cell level. Advanced single-cell multimodal assays can now simultaneously measure various molecules (e.g., DNA, RNA, Protein) across hundreds of thousands of individual cells, providing a comprehensive molecular readout. A significant analytical challenge is integrating single-cell measurements across different modalities. Various methods have been developed to address this challenge, but there has been no systematic evaluation of these techniques with different preprocessing strategies. This study examines a general pipeline for single-cell data analysis, which includes normalization, data integration, and dimensionality reduction. The performance of different algorithm combinations often depends on the dataset sizes and characteristics. We evaluate six datasets across diverse modalities, tissues, and organisms using three metrics: Silhouette Coefficient Score, Adjusted Rand Index, and Calinski-Harabasz Index. Our experiments involve combinations of seven normalization methods, four dimensional reduction methods, and five integration methods. The results show that Seurat and Harmony excel in data integration, with Harmony being more time-efficient, especially for large datasets. UMAP is the most compatible dimensionality reduction method with the integration techniques, and the choice of normalization method varies depending on the integration method used.

Ali Anaissi, Ali Braytee, Junaid Akram

We present an advanced approach to medical question-answering (QA) services, using fine-tuned Large Language Models (LLMs) to improve the accuracy and reliability of healthcare information. Our study focuses on optimizing models like LLaMA-2 and Mistral, which have shown great promise in delivering precise, reliable medical answers. By leveraging comprehensive datasets, we applied fine-tuning techniques such as rsDoRA+ and ReRAG. rsDoRA+ enhances model performance through a combination of decomposed model weights, varied learning rates for low-rank matrices, and rank stabilization, leading to improved efficiency. ReRAG, which integrates retrieval on demand and question rewriting, further refines the accuracy of the responses. This approach enables healthcare providers to access fast, dependable information, aiding in more efficient decision-making and fostering greater patient trust. Our work highlights the potential of fine-tuned LLMs to significantly improve the quality and accessibility of medical information services, ultimately contributing to better healthcare outcomes for all.

Hao Feng, Yuanzhe Jia, Ruijia Xu et al.

Image recognition techniques heavily rely on abundant labeled data, particularly in medical contexts. Addressing the challenges associated with obtaining labeled data has led to the prominence of self-supervised learning and semi-supervised learning, especially in scenarios with limited annotated data. In this paper, we proposed an innovative approach by integrating self-supervised learning into semi-supervised models to enhance medical image recognition. Our methodology commences with pre-training on unlabeled data utilizing the BYOL method. Subsequently, we merge pseudo-labeled and labeled datasets to construct a neural network classifier, refining it through iterative fine-tuning. Experimental results on three different datasets demonstrate that our approach optimally leverages unlabeled data, outperforming existing methods in terms of accuracy for medical image recognition.

Ahmad Hussein, Mukesh Prasad, Ali Braytee

Advancements in high-throughput technologies have led to a shift from traditional hypothesis-driven methodologies to data-driven approaches. Multi-omics refers to the integrative analysis of data derived from multiple 'omes', such as genomics, proteomics, transcriptomics, metabolomics, and microbiomics. This approach enables a comprehensive understanding of biological systems by capturing different layers of biological information. Deep learning methods are increasingly utilized to integrate multi-omics data, offering insights into molecular interactions and enhancing research into complex diseases. However, these models, with their numerous interconnected layers and nonlinear relationships, often function as black boxes, lacking transparency in decision-making processes. To overcome this challenge, explainable artificial intelligence (xAI) methods are crucial for creating transparent models that allow clinicians to interpret and work with complex data more effectively. This review explores how xAI can improve the interpretability of deep learning models in multi-omics research, highlighting its potential to provide clinicians with clear insights, thereby facilitating the effective application of such models in clinical settings.

Cheng Qian, Xianglong Shi, Shanshan Yao et al.

We present a refined approach to biomedical question-answering (QA) services by integrating large language models (LLMs) with Multi-BERT configurations. By enhancing the ability to process and prioritize vast amounts of complex biomedical data, this system aims to support healthcare professionals in delivering better patient outcomes and informed decision-making. Through innovative use of BERT and BioBERT models, combined with a multi-layer perceptron (MLP) layer, we enable more specialized and efficient responses to the growing demands of the healthcare sector. Our approach not only addresses the challenge of overfitting by freezing one BERT model while training another but also improves the overall adaptability of QA services. The use of extensive datasets, such as BioASQ and BioMRC, demonstrates the system's ability to synthesize critical information. This work highlights how advanced language models can make a tangible difference in healthcare, providing reliable and responsive tools for professionals to manage complex information, ultimately serving the broader goal of improved care and data-driven insights.

Ali Anaissi, Yuanzhe Jia, Ali Braytee et al.

This study delves into the application of Generative Adversarial Networks (GANs) within the context of imbalanced datasets. Our primary aim is to enhance the performance and stability of GANs in such datasets. In pursuit of this objective, we introduce a novel network architecture known as Damage GAN, building upon the ContraD GAN framework which seamlessly integrates GANs and contrastive learning. Through the utilization of contrastive learning, the discriminator is trained to develop an unsupervised representation capable of distinguishing all provided samples. Our approach draws inspiration from the straightforward framework for contrastive learning of visual representations (SimCLR), leading to the formulation of a distinctive loss function. We also explore the implementation of self-damaging contrastive learning (SDCLR) to further enhance the optimization of the ContraD GAN model. Comparative evaluations against baseline models including the deep convolutional GAN (DCGAN) and ContraD GAN demonstrate the evident superiority of our proposed model, Damage GAN, in terms of generated image distribution, model stability, and image quality when applied to imbalanced datasets.

Yanjie Wu, Yuhao Ji, Saiho Lee et al.

The complexities of healthcare data, including privacy concerns, imbalanced datasets, and interoperability issues, necessitate innovative machine learning solutions. Swarm Learning (SL), a decentralized alternative to Federated Learning, offers privacy-preserving distributed training, but its reliance on blockchain technology hinders accessibility and scalability. This paper introduces a \textit{Simplified Peer-to-Peer Swarm Learning (P2P-SL) Framework} tailored for resource-constrained environments. By eliminating blockchain dependencies and adopting lightweight peer-to-peer communication, the proposed framework ensures robust model synchronization while maintaining data privacy. Applied to cancer histopathology, the framework integrates optimized pre-trained models, such as TorchXRayVision, enhanced with DenseNet decoders, to improve diagnostic accuracy. Extensive experiments demonstrate the framework's efficacy in handling imbalanced and biased datasets, achieving comparable performance to centralized models while preserving privacy. This study paves the way for democratizing advanced machine learning in healthcare, offering a scalable, accessible, and efficient solution for privacy-sensitive diagnostic applications.

Ali Anaissi, Junaid Akram, Kunal Chaturvedi et al.

Memes are widely used for humor and cultural commentary, but they are increasingly exploited to spread hateful content. Due to their multimodal nature, hateful memes often evade traditional text-only or image-only detection systems, particularly when they employ subtle or coded references. To address these challenges, we propose a multimodal hate detection framework that integrates key components: OCR to extract embedded text, captioning to describe visual content neutrally, sub-label classification for granular categorization of hateful content, RAG for contextually relevant retrieval, and VQA for iterative analysis of symbolic and contextual cues. This enables the framework to uncover latent signals that simpler pipelines fail to detect. Experimental results on the Facebook Hateful Memes dataset reveal that the proposed framework exceeds the performance of unimodal and conventional multimodal models in both accuracy and AUC-ROC.

Yining Zhao, Ali Braytee, Mukesh Prasad

Medical image captioning via vision-language models has shown promising potential for clinical diagnosis assistance. However, generating contextually relevant descriptions with accurate modality recognition remains challenging. We present DualPrompt-MedCap, a novel dual-prompt enhancement framework that augments Large Vision-Language Models (LVLMs) through two specialized components: (1) a modality-aware prompt derived from a semi-supervised classification model pretrained on medical question-answer pairs, and (2) a question-guided prompt leveraging biomedical language model embeddings. To address the lack of captioning ground truth, we also propose an evaluation framework that jointly considers spatial-semantic relevance and medical narrative quality. Experiments on multiple medical datasets demonstrate that DualPrompt-MedCap outperforms the baseline BLIP-3 by achieving a 22% improvement in modality recognition accuracy while generating more comprehensive and question-aligned descriptions. Our method enables the generation of clinically accurate reports that can serve as medical experts' prior knowledge and automatic annotations for downstream vision-language tasks.

Ahmad Hussein, Mukesh Prasad, Ali Anaissi et al.

Cancer remains one of the leading causes of mortality worldwide, necessitating accurate diagnosis and prognosis. Whole Slide Imaging (WSI) has become an integral part of clinical workflows with advancements in digital pathology. While various studies have utilized WSIs, their extracted features may not fully capture the most relevant pathological information, and their lack of interpretability limits clinical adoption. In this paper, we propose PATH-X, a framework that integrates Vision Transformers (ViT) and Autoencoders with SHAP (Shapley Additive Explanations) to enhance model explainability for patient stratification and risk prediction using WSIs from The Cancer Genome Atlas (TCGA). A representative image slice is selected from each WSI, and numerical feature embeddings are extracted using Google's pre-trained ViT. These features are then compressed via an autoencoder and used for unsupervised clustering and classification tasks. Kaplan-Meier survival analysis is applied to evaluate stratification into two and three risk groups. SHAP is used to identify key contributing features, which are mapped onto histopathological slices to provide spatial context. PATH-X demonstrates strong performance in breast and glioma cancers, where a sufficient number of WSIs enabled robust stratification. However, performance in lung cancer was limited due to data availability, emphasizing the need for larger datasets to enhance model reliability and clinical applicability.

Taoxu Zhao, Meisi Li, Kehao Chen et al.

Multimodal sentiment analysis enhances conventional sentiment analysis, which traditionally relies solely on text, by incorporating information from different modalities such as images, text, and audio. This paper proposes a novel multimodal sentiment analysis architecture that integrates text and image data to provide a more comprehensive understanding of sentiments. For text feature extraction, we utilize BERT, a natural language processing model. For image feature extraction, we employ DINOv2, a vision-transformer-based model. The textual and visual latent features are integrated using proposed fusion techniques, namely the Basic Fusion Model, Self Attention Fusion Model, and Dual Attention Fusion Model. Experiments on three datasets, Memotion 7k dataset, MVSA single dataset, and MVSA multi dataset, demonstrate the viability and practicality of the proposed multimodal architecture.

Xing Zi, Jinghao Xiao, Yunxiao Shi et al.

Visual Question Answering (VQA) in remote sensing (RS) is pivotal for interpreting Earth observation data. However, existing RS VQA datasets are constrained by limitations in annotation richness, question diversity, and the assessment of specific reasoning capabilities. This paper introduces RSVLM-QA dataset, a new large-scale, content-rich VQA dataset for the RS domain. RSVLM-QA is constructed by integrating data from several prominent RS segmentation and detection datasets: WHU, LoveDA, INRIA, and iSAID. We employ an innovative dual-track annotation generation pipeline. Firstly, we leverage Large Language Models (LLMs), specifically GPT-4.1, with meticulously designed prompts to automatically generate a suite of detailed annotations including image captions, spatial relations, and semantic tags, alongside complex caption-based VQA pairs. Secondly, to address the challenging task of object counting in RS imagery, we have developed a specialized automated process that extracts object counts directly from the original segmentation data; GPT-4.1 then formulates natural language answers from these counts, which are paired with preset question templates to create counting QA pairs. RSVLM-QA comprises 13,820 images and 162,373 VQA pairs, featuring extensive annotations and diverse question types. We provide a detailed statistical analysis of the dataset and a comparison with existing RS VQA benchmarks, highlighting the superior depth and breadth of RSVLM-QA's annotations. Furthermore, we conduct benchmark experiments on Six mainstream Vision Language Models (VLMs), demonstrating that RSVLM-QA effectively evaluates and challenges the understanding and reasoning abilities of current VLMs in the RS domain. We believe RSVLM-QA will serve as a pivotal resource for the RS VQA and VLM research communities, poised to catalyze advancements in the field.

Xing Zi, Tengjun Ni, Xianjing Fan et al.

Accurate and automated captioning of aerial imagery is crucial for applications like environmental monitoring, urban planning, and disaster management. However, this task remains challenging due to complex spatial semantics and domain variability. To address these issues, we introduce \textbf{AeroLite}, a lightweight, tag-guided captioning framework designed to equip small-scale language models (1--3B parameters) with robust and interpretable captioning capabilities specifically for remote sensing images. \textbf{AeroLite} leverages GPT-4o to generate a large-scale, semantically rich pseudo-caption dataset by integrating multiple remote sensing benchmarks, including DLRSD, iSAID, LoveDA, WHU, and RSSCN7. To explicitly capture key semantic elements such as orientation and land-use types, AeroLite employs natural language processing techniques to extract relevant semantic tags. These tags are then learned by a dedicated multi-label CLIP encoder, ensuring precise semantic predictions. To effectively fuse visual and semantic information, we propose a novel bridging multilayer perceptron (MLP) architecture, aligning semantic tags with visual embeddings while maintaining minimal computational overhead. AeroLite's flexible design also enables seamless integration with various pretrained large language models. We adopt a two-stage LoRA-based training approach: the initial stage leverages our pseudo-caption dataset to capture broad remote sensing semantics, followed by fine-tuning on smaller, curated datasets like UCM and Sydney Captions to refine domain-specific alignment. Experimental evaluations demonstrate that AeroLite surpasses significantly larger models (e.g., 13B parameters) in standard captioning metrics, including BLEU and METEOR, while maintaining substantially lower computational costs.

Yuxin Miao, Xinyuan Yang, Hongda Fan et al.

Gastric cancer is one of the most commonly diagnosed cancers and has a high mortality rate. Due to limited medical resources, developing machine learning models for gastric cancer recognition provides an efficient solution for medical institutions. However, such models typically require large sample sizes for training and testing, which can challenge patient privacy. Federated learning offers an effective alternative by enabling model training across multiple institutions without sharing sensitive patient data. This paper addresses the limited sample size of publicly available gastric cancer data with a modified data processing method. This paper introduces FedSAF, a novel federated learning algorithm designed to improve the performance of existing methods, particularly in non-independent and identically distributed (non-IID) data scenarios. FedSAF incorporates attention-based message passing and the Fisher Information Matrix to enhance model accuracy, while a model splitting function reduces computation and transmission costs. Hyperparameter tuning and ablation studies demonstrate the effectiveness of this new algorithm, showing improvements in test accuracy on gastric cancer datasets, with FedSAF outperforming existing federated learning methods like FedAMP, FedAvg, and FedProx. The framework's robustness and generalization ability were further validated across additional datasets (SEED, BOT, FashionMNIST, and CIFAR-10), achieving high performance in diverse environments.

Xing Zi, Kairui Jin, Xian Tao et al.

Pixel-level segmentation is essential in remote sensing, where foundational vision models like CLIP and Segment Anything Model(SAM) have demonstrated significant capabilities in zero-shot segmentation tasks. Despite their advances, challenges specific to remote sensing remain substantial. Firstly, The SAM without clear prompt constraints, often generates redundant masks, and making post-processing more complex. Secondly, the CLIP model, mainly designed for global feature alignment in foundational models, often overlooks local objects crucial to remote sensing. This oversight leads to inaccurate recognition or misplaced focus in multi-target remote sensing imagery. Thirdly, both models have not been pre-trained on multi-scale aerial views, increasing the likelihood of detection failures. To tackle these challenges, we introduce the innovative VTPSeg pipeline, utilizing the strengths of Grounding DINO, CLIP, and SAM for enhanced open-vocabulary image segmentation. The Grounding DINO+(GD+) module generates initial candidate bounding boxes, while the CLIP Filter++(CLIP++) module uses a combination of visual and textual prompts to refine and filter out irrelevant object bounding boxes, ensuring that only pertinent objects are considered. Subsequently, these refined bounding boxes serve as specific prompts for the FastSAM model, which executes precise segmentation. Our VTPSeg is validated by experimental and ablation study results on five popular remote sensing image segmentation datasets.

Yuchong Yao, Xiaohui Wangr, Yuanbang Ma et al.

Class imbalance occurs in many real-world applications, including image classification, where the number of images in each class differs significantly. With imbalanced data, the generative adversarial networks (GANs) leans to majority class samples. The two recent methods, Balancing GAN (BAGAN) and improved BAGAN (BAGAN-GP), are proposed as an augmentation tool to handle this problem and restore the balance to the data. The former pre-trains the autoencoder weights in an unsupervised manner. However, it is unstable when the images from different categories have similar features. The latter is improved based on BAGAN by facilitating supervised autoencoder training, but the pre-training is biased towards the majority classes. In this work, we propose a novel Conditional Variational Autoencoder with Balanced Pre-training for Generative Adversarial Networks (CAPGAN) as an augmentation tool to generate realistic synthetic images. In particular, we utilize a conditional convolutional variational autoencoder with supervised and balanced pre-training for the GAN initialization and training with gradient penalty. Our proposed method presents a superior performance of other state-of-the-art methods on the highly imbalanced version of MNIST, Fashion-MNIST, CIFAR-10, and two medical imaging datasets. Our method can synthesize high-quality minority samples in terms of Fréchet inception distance, structural similarity index measure and perceptual quality.

Ali Braytee, Wei Liu

Multi-label learning handles instances associated with multiple class labels. The original label space is a logical matrix with entries from the Boolean domain $\in \left \{ 0,1 \right \}$. Logical labels are not able to show the relative importance of each semantic label to the instances. The vast majority of existing methods map the input features to the label space using linear projections with taking into consideration the label dependencies using logical label matrix. However, the discriminative features are learned using one-way projection from the feature representation of an instance into a logical label space. Given that there is no manifold in the learning space of logical labels, which limits the potential of learned models. In this work, inspired from a real-world example in image annotation to reconstruct an image from the label importance and feature weights. We propose a novel method in multi-label learning to learn the projection matrix from the feature space to semantic label space and projects it back to the original feature space using encoder-decoder deep learning architecture. The key intuition which guides our method is that the discriminative features are identified due to map the features back and forth using two linear projections. To the best of our knowledge, this is one of the first attempts to study the ability to reconstruct the original features from the label manifold in multi-label learning. We show that the learned projection matrix identifies a subset of discriminative features across multiple semantic labels. Extensive experiments on real-world datasets show the superiority of the proposed method.