Muhammad Waqas

Yousef Alhwaiti, Muhammad Ishaq, Muhammad Hameed Siddiqi et al.

The tomato is one of the most important fruits on earth. It plays an important and useful role in the agricultural production of any country. This research propose a novel smart technique for early detection of late blight diseases in tomatoes. This work improve the dataset with an increase in images from the field (the Plant Village dataset) and proposed a hybrid algorithm composed of support vector machines (SVM) and histogram-oriented gradients (HOG) for real-time detection of late blight tomato disease. To propose a HOG-based SVM model for early detection of late blight tomato leaf disease. To check the performance of the proposed model in terms of MSE, accuracy, precision, and recall as compared to Decision Tree and KNN. The integration of advanced technology in agriculture has the potential to revolutionize the industry, making it more efficient, sustainable, and profitable. This research work on the early detection of tomato diseases contributes to the growing importance of smart farming, the need for climate-smart agriculture, the rising need to more efficiently utilize natural resources, and the demand for higher crop yields. The proposed hybrid algorithm of SVM and HOG has significant potential for the early detection of late blight disease in tomato plants. The performance of the proposed model against decision tree and KNN algorithms and the results may assist in selecting the best algorithm for future applications. The research work can help farmers make data-driven decisions to optimize crop yield and quality while also reducing the environmental impact of farming practices.

Muhammad Waqas, Muhammad Ashraf, Muhammad Zakwan

Modulation classification is an essential step of signal processing and has been regularly applied in the field of tele-communication. Since variations of frequency with respect to time remains a vital distinction among radio signals having different modulation formats, these variations can be used for feature extraction by converting 1-D radio signals into frequency domain. In this paper, we propose a scheme for Automatic Modulation Classification (AMC) using modern architectures of Convolutional Neural Networks (CNN), through generating spectrum images of eleven different modulation types. Additionally, we perform resolution transformation of spectrograms that results up to 99.61% of computational load reduction and 8x faster conversion from the received I/Q data. This proposed AMC is implemented on CPU and GPU, to recognize digital as well as analogue signal modulation schemes on signals. The performance is evaluated on existing CNN models including SqueezeNet, Resnet-50, InceptionResnet-V2, Inception-V3, VGG-16 and Densenet-201. Best results of 91.2% are achieved in presence of AWGN and other noise impairments in the signals, stating that the transformed spectrogram-based AMC has good classification accuracy as the spectral features are highly discriminant, and CNN based models have capability to extract these high-dimensional features. The spectrograms were created under different SNRs ranging from 5 to 30db with a step size of 5db to observe the experimental results at various SNR levels. The proposed methodology is efficient to be applied in wireless communication networks for real-time applications.

Amgad Muneer, Muhammad Waqas, Maliazurina B Saad et al.

Cancer research is increasingly driven by the integration of diverse data modalities, spanning from genomics and proteomics to imaging and clinical factors. However, extracting actionable insights from these vast and heterogeneous datasets remains a key challenge. The rise of foundation models (FMs) -- large deep-learning models pretrained on extensive amounts of data serving as a backbone for a wide range of downstream tasks -- offers new avenues for discovering biomarkers, improving diagnosis, and personalizing treatment. This paper presents a comprehensive review of widely adopted integration strategies of multimodal data to assist advance the computational approaches for data-driven discoveries in oncology. We examine emerging trends in machine learning (ML) and deep learning (DL), including methodological frameworks, validation protocols, and open-source resources targeting cancer subtype classification, biomarker discovery, treatment guidance, and outcome prediction. This study also comprehensively covers the shift from traditional ML to FMs for multimodal integration. We present a holistic view of recent FMs advancements and challenges faced during the integration of multi-omics with advanced imaging data. We identify the state-of-the-art FMs, publicly available multi-modal repositories, and advanced tools and methods for data integration. We argue that current state-of-the-art integrative methods provide the essential groundwork for developing the next generation of large-scale, pre-trained models poised to further revolutionize oncology. To the best of our knowledge, this is the first review to systematically map the transition from conventional ML to advanced FM for multimodal data integration in oncology, while also framing these developments as foundational for the forthcoming era of large-scale AI models in cancer research.

Amgad Muneer, Kai Zhang, Ibraheem Hamdi et al.

Foundation models (FMs) are driving a prominent shift in artificial intelligence across different domains, including biomedical imaging. These models are designed to move beyond narrow pattern recognition towards emulating sophisticated clinical reasoning, understanding complex spatial relationships, and integrating multimodal data with unprecedented flexibility. However, a critical gap exists between this potential and the current reality, where the clinical evaluation and deployment of FMs are hampered by significant challenges. Herein, we critically assess the current state-of-the-art, analyzing hype by examining the core capabilities and limitations of FMs in the biomedical domain. We also provide a taxonomy of reasoning, ranging from emulated sequential logic and spatial understanding to the integration of explicit symbolic knowledge, to evaluate whether these models exhibit genuine cognition or merely mimic surface-level patterns. We argue that a critical frontier lies beyond statistical correlation, in the pursuit of causal inference, which is essential for building robust models that understand cause and effect. Furthermore, we discuss the paramount issues in deployment stemming from trustworthiness, bias, and safety, dissecting the challenges of algorithmic bias, data bias and privacy, and model hallucinations. We also draw attention to the need for more inclusive, rigorous, and clinically relevant validation frameworks to ensure their safe and ethical application. We conclude that while the vision of autonomous AI-doctors remains distant, the immediate reality is the emergence of powerful technology and assistive tools that would benefit clinical practice. The future of FMs in biomedical imaging hinges not on scale alone, but on developing hybrid, causally aware, and verifiably safe systems that augment, rather than replace, human expertise.

Anas Zafar, Muhammad Waqas, Amgad Muneer et al.

Low-dose CT (LDCT) reduces radiation exposure but introduces protocol-dependent noise and artifacts that vary across institutions. While federated learning enables collaborative training without centralizing patient data, existing methods personalize in image space, making it difficult to separate scanner noise from patient anatomy. We propose ProFed (Projection Guided Personalized Federated Learning), a framework that complements the image space approach by performing dual-level personalization in the projection space, where noise originates during CT measurements before reconstruction combines protocol and anatomy effects. ProFed introduces: (i) anatomy-aware and protocol-aware networks that personalize CT reconstruction to patient and scanner-specific features, (ii) multi-constraint projection losses that enforce consistency with CT measurements, and (iii) uncertainty-guided selective aggregation that weights clients by prediction confidence. Extensive experiments on the Mayo Clinic 2016 dataset demonstrate that ProFed achieves 42.56 dB PSNR with CNN backbones and 44.83 dB with Transformers, outperforming 11 federated learning baselines, including the physics-informed SCAN-PhysFed by +1.42 dB.

Hikmat Khan, Syed Farhan Alam Zaidi, Pir Masoom Shah et al.

Domain generalization in computational histopathology is hindered by heterogeneity in whole slide images (WSIs), caused by variations in tissue preparation, staining, and imaging conditions across institutions. Unlike machine learning systems, pathologists rely on domain-invariant morphological cues such as nuclear atypia (enlargement, irregular contours, hyperchromasia, chromatin texture, spatial disorganization), structural atypia (abnormal architecture and gland formation), and overall morphological atypia that remain diagnostic across diverse settings. Motivated by this, we hypothesize that explicitly modeling biologically robust nuclear morphology and spatial organization will enable the learning of cancer representations that are resilient to domain shifts. We propose MorphGen (Morphology-Guided Generalization), a method that integrates histopathology images, augmentations, and nuclear segmentation masks within a supervised contrastive learning framework. By aligning latent representations of images and nuclear masks, MorphGen prioritizes diagnostic features such as nuclear and morphological atypia and spatial organization over staining artifacts and domain-specific features. To further enhance out-of-distribution robustness, we incorporate stochastic weight averaging (SWA), steering optimization toward flatter minima. Attention map analyses revealed that MorphGen primarily relies on nuclear morphology, cellular composition, and spatial cell organization within tumors or normal regions for final classification. Finally, we demonstrate resilience of the learned representations to image corruptions (such as staining artifacts) and adversarial attacks, showcasing not only OOD generalization but also addressing critical vulnerabilities in current deep learning systems for digital pathology. Code, datasets, and trained models are available at: https://github.com/hikmatkhan/MorphGen

Sadaqat ur Rehman, Zhongliang Yang, Muhammad Shahid et al.

Water supplies are crucial for the development of living beings. However, change in the hydrological process i.e. climate and land usage are the key issues. Sustaining water level and accurate estimating for dynamic conditions is a critical job for hydrologists, but predicting hydrological extremes is an open issue. In this paper, we proposed two deep learning techniques and three machine learning algorithms to predict stream flow, given the present climate conditions. The results showed that the Recurrent Neural Network (RNN) or Long Short-term Memory (LSTM), an artificial neural network based method, outperform other conventional and machine-learning algorithms for predicting stream flow. Furthermore, we analyzed that stream flow is directly affected by precipitation, land usage, and temperature. These indexes are critical, which can be used by hydrologists to identify the potential for stream flow. We make the dataset publicly available (https://github.com/sadaqat007/Dataset) so that others should be able to replicate and build upon the results published.

Muhammad Ahmad, Muhammad Waqas, Ameer Hamza et al.

Hope is a positive emotional state involving the expectation of favorable future outcomes, while hope speech refers to communication that promotes optimism, resilience, and support, particularly in adverse contexts. Although hope speech detection has gained attention in Natural Language Processing (NLP), existing research mainly focuses on high-resource languages and standardized scripts, often overlooking informal and underrepresented forms such as Roman Urdu. To the best of our knowledge, this is the first study to address hope speech detection in code-mixed Roman Urdu by introducing a carefully annotated dataset, thereby filling a critical gap in inclusive NLP research for low-resource, informal language varieties. This study makes four key contributions: (1) it introduces the first multi-class annotated dataset for Roman Urdu hope speech, comprising Generalized Hope, Realistic Hope, Unrealistic Hope, and Not Hope categories; (2) it explores the psychological foundations of hope and analyzes its linguistic patterns in code-mixed Roman Urdu to inform dataset development; (3) it proposes a custom attention-based transformer model optimized for the syntactic and semantic variability of Roman Urdu, evaluated using 5-fold cross-validation; and (4) it verifies the statistical significance of performance gains using a t-test. The proposed model, XLM-R, achieves the best performance with a cross-validation score of 0.78, outperforming the baseline SVM (0.75) and BiLSTM (0.76), with gains of 4% and 2.63% respectively.

Muhammad Waqas, Rukhmini Bandyopadhyay, Eman Showkatian et al.

Foundation models have recently emerged as powerful feature extractors in computational pathology, yet they typically omit mechanisms for leveraging the global spatial structure of tissues and the local contextual relationships among diagnostically relevant regions - key elements for understanding the tumor microenvironment. Multiple instance learning (MIL) remains an essential next step following foundation model, designing a framework to aggregate patch-level features into slide-level predictions. We present EAGLE-Net, a structure-preserving, attention-guided MIL architecture designed to augment prediction and interpretability. EAGLE-Net integrates multi-scale absolute spatial encoding to capture global tissue architecture, a top-K neighborhood-aware loss to focus attention on local microenvironments, and background suppression loss to minimize false positives. We benchmarked EAGLE-Net on large pan-cancer datasets, including three cancer types for classification (10,260 slides) and seven cancer types for survival prediction (4,172 slides), using three distinct histology foundation backbones (REMEDIES, Uni-V1, Uni2-h). Across tasks, EAGLE-Net achieved up to 3% higher classification accuracy and the top concordance indices in 6 of 7 cancer types, producing smooth, biologically coherent attention maps that aligned with expert annotations and highlighted invasive fronts, necrosis, and immune infiltration. These results position EAGLE-Net as a generalizable, interpretable framework that complements foundation models, enabling improved biomarker discovery, prognostic modeling, and clinical decision support

Sadaqat ur Rehman, Muhammad Waqas, Shanshan Tu et al.

With the advancement in technology and the expansion of broadcasting, cross-media retrieval has gained much attention. It plays a significant role in big data applications and consists in searching and finding data from different types of media. In this paper, we provide a novel taxonomy according to the challenges faced by multi-modal deep learning approaches in solving cross-media retrieval, namely: representation, alignment, and translation. These challenges are evaluated on deep learning (DL) based methods, which are categorized into four main groups: 1) unsupervised methods, 2) supervised methods, 3) pairwise based methods, and 4) rank based methods. Then, we present some well-known cross-media datasets used for retrieval, considering the importance of these datasets in the context in of deep learning based cross-media retrieval approaches. Moreover, we also present an extensive review of the state-of-the-art problems and its corresponding solutions for encouraging deep learning in cross-media retrieval. The fundamental objective of this work is to exploit Deep Neural Networks (DNNs) for bridging the "media gap", and provide researchers and developers with a better understanding of the underlying problems and the potential solutions of deep learning assisted cross-media retrieval. To the best of our knowledge, this is the first comprehensive survey to address cross-media retrieval under deep learning methods.