Quantitative remote sensing estimation is critical for environmental monitoring, providing continuous measures of vegetation indices, canopy height, and carbon stock. Traditional radiative-transfer models and empirical regressions require expert knowledge and generalize poorly, while deep learning methods remain task-specific. We propose SatelliteCalculator+, a DINOv3-powered multi-task foundation model for continuous regression of spectral and structural variables. The framework combines prompt-driven cross-attentive adapters with lightweight MLP decoders, enabling efficient dense prediction from frozen features. To overcome limited supervision, we synthesize over one million paired samples from SPOT 6/7 imagery using physically defined formulas. On the Open-Canopy dataset, SatelliteCalculator+ achieves competitive accuracy across eight ecological variables while reducing inference cost, demonstrating the promise of self-supervised transformers and scalable multi-task learning for large-scale Earth observation.

Given the rapid emergence and applications of Multi-Modal Large Language Models (MM-LLMs) across various scientific fields, insights regarding their applicability in agriculture are still only partially explored. This paper conducts an in-depth review of MM-LLMs in agriculture, focusing on understanding how MM-LLMs can be developed and implemented to optimize agricultural processes, increase efficiency, and reduce costs. Recent studies have explored the capabilities of MM-LLMs in agricultural information processing and decision-making. Despite these advancements, significant gaps persist, particularly in addressing domain-specific challenges such as variable data quality and availability, integration with existing agricultural systems, and the creation of robust training datasets that accurately represent complex agricultural environments. Moreover, a comprehensive understanding of the capabilities, challenges, and limitations of MM-LLMs in agricultural information processing and application is still missing. Exploring these areas is crucial to providing the community with a broader perspective and a clearer understanding of MM-LLMs’ applications, establishing a benchmark for the current state and emerging trends in this field. To bridge this gap, this survey reviews the progress of MM-LLMs and their utilization in agriculture, with an additional focus on 11 key research questions (RQs), where 4 RQs are general and 7 RQs are agriculture focused. By addressing these RQs, this review outlines the current opportunities and challenges, limitations, and future roadmap for MM-LLMs in agriculture. The findings indicate that multi-modal MM-LLMs not only simplify complex agricultural challenges but also significantly enhance decision-making and improve the efficiency of agricultural image processing. These advancements position MM-LLMs as an essential tool for the future of farming. For continued research and understanding, an organized and regularly updated list of papers on MM-LLMs is available at https://github.com/JiajiaLi04/Multi-Modal-LLMs-in-Agriculture.

Knee cartilage segmentation for Knee Osteoarthritis (OA) diagnosis is challenging due to domain shifts from varying MRI scanning technologies. Existing cross-modality approaches often use paired order matching or style translation techniques to align features. Still, these methods can sacrifice discrimination in less prominent cartilages and overlook critical higher-order correlations and semantic information. To address this issue, we propose a novel framework called Successive Eigen Noise-assisted Mean Teacher Knowledge Distillation (SEN-MTKD) for adapting 2D knee MRI images across different modalities using partially labeled data. Our approach includes the Eigen Low-rank Subspace (ELRS) module, which employs low-rank approximations to generate meaningful pseudo-labels from domain-invariant feature representations progressively. Complementing this, the Successive Eigen Noise (SEN) module introduces advanced data perturbation to enhance discrimination and diversity in small cartilage classes. Additionally, we propose a subspace-based feature distillation loss mechanism (LRBD) to manage variance and leverage rich intermediate representations within the teacher model, ensuring robust feature representation and labeling. Our framework identifies a mutual cross-domain subspace using higher-order structures and lower energy latent features, providing reliable supervision for the student model. Extensive experiments on public and private datasets demonstrate the effectiveness of our method over state-of-the-art benchmarks. The code is available at github.com/AmmarKhawer/SEN-MTKD.

Imaging spectroscopy integrates traditional computer vision and spectroscopy into a single system and has gained widespread acceptance as a non-destructive scientific instrument for a wide range of applications. The current state of imaging spectroscopy spans diverse applications including but not limited to air-borne and ground-based computer vision systems. This paper presents the current state of research and industrial applications including precision agriculture, material classification, medical science, forensic science, face recognition and document image analysis, environment monitoring, and remote sensing, which can be aided through imaging spectroscopy. In this regard, we further discuss a comprehensive list of applications of imaging spectroscopy, pre-processing techniques, and spectral image acquisition systems. Likewise, publicly available databases and current software tools for spectral data analysis are also documented in this review. This review paper, therefore, could potentially serve as a reference and roadmap for people looking for literature, databases, applications, and tools to undertake additional research in imaging spectroscopy.

Recently attention-based networks have been successful for image restoration tasks. However, existing methods are either computationally expensive or have limited receptive fields, adding constraints to the model. They are also less resilient in spatial and contextual aspects and lack pixel-to-pixel correspondence, which may degrade feature representations. In this paper, we propose a novel and computationally efficient architecture Single Stage Adaptive Multi-Attention Network (SSAMAN) for image restoration tasks, particularly for image denoising and image deblurring. SSAMAN efficiently addresses computational challenges and expands receptive fields, enhancing robustness in spatial and contextual feature representation. Its Adaptive Multi-Attention Module (AMAM), which consists of Adaptive Pixel Attention Branch (APAB) and an Adaptive Channel Attention Branch (ACAB), uniquely integrates channel and pixel-wise dimensions, significantly improving sensitivity to edges, shapes, and textures. We perform extensive experiments and ablation studies to validate the performance of SSAMAN. Our model shows state-of-the-art results on various benchmarks, for example, on image denoising tasks, SSAMAN achieves a notable 40.08 dB PSNR on SIDD dataset, outperforming Restormer by 0.06 dB PSNR, with 41.02% less computational cost, and achieves a 40.05 dB PSNR on the DND dataset. For image deblurring, SSAMAN achieves 33.53 dB PSNR on GoPro dataset. Code and models are available at Github.

BACKGROUND: Subcellular localization of messenger RNA (mRNAs) plays a pivotal role in the regulation of gene expression, cell migration as well as in cellular adaptation. Experiment techniques for pinpointing the subcellular localization of mRNAs are laborious, time-consuming and expensive. Therefore, in silico approaches for this purpose are attaining great attention in the RNA community. METHODS: In this article, we propose MSLP, a machine learning-based method to predict the subcellular localization of mRNA. We propose a novel combination of four types of features representing k-mer, pseudo k-tuple nucleotide composition (PseKNC), physicochemical properties of nucleotides, and 3D representation of sequences based on Z-curve transformation to feed into machine learning algorithm to predict the subcellular localization of mRNAs. RESULTS: Considering the combination of the above-mentioned features, ennsemble-based models achieved state-of-the-art results in mRNA subcellular localization prediction tasks for multiple benchmark datasets. We evaluated the performance of our method in ten subcellular locations, covering cytoplasm, nucleus, endoplasmic reticulum (ER), extracellular region (ExR), mitochondria, cytosol, pseudopodium, posterior, exosome, and the ribosome. Ablation study highlighted k-mer and PseKNC to be more dominant than other features for predicting cytoplasm, nucleus, and ER localizations. On the other hand, physicochemical properties and Z-curve based features contributed the most to ExR and mitochondria detection. SHAP-based analysis revealed the relative importance of features to provide better insights into the proposed approach. AVAILABILITY: We have implemented a Docker container and API for end users to run their sequences on our model. Datasets, the code of API and the Docker are shared for the community in GitHub at: https://github.com/smusleh/MSLP .

Since December 2019, COVID-19 has posed the most serious threat to living beings. With the advancement of vaccination programs around the globe, the need to quickly diagnose COVID-19 in general with little logistics is fore important. As a consequence, the fastest diagnostic option to stop COVID-19 from spreading, especially among senior patients, should be the development of an automated detection system. This study aims to provide a lightweight deep learning method that incorporates a convolutional neural network (CNN), discrete wavelet transform (DWT), and a long short-term memory (LSTM), called CORONA-NET for diagnosing COVID-19 from chest X-ray images. In this system, deep feature extraction is performed by CNN, the feature vector is reduced yet strengthened by DWT, and the extracted feature is detected by LSTM for prediction. The dataset included 3000 X-rays, 1000 of which were COVID-19 obtained locally. Within minutes of the test, the proposed test platform's prototype can accurately detect COVID-19 patients. The proposed method achieves state-of-the-art performance in comparison with the existing deep learning methods. We hope that the suggested method will hasten clinical diagnosis and may be used for patients in remote areas where clinical labs are not easily accessible due to a lack of resources, location, or other factors.

Lung cancer is a major cause of cancer deaths worldwide, and has a very low survival rate. Non-small cell lung cancer (NSCLC) is the largest subset of lung cancers, which accounts for about 85% of all cases. It has been well established that a mutation in the epidermal growth factor receptor (EGFR) can lead to lung cancer. EGFR Tyrosine Kinase Inhibitors (TKIs) are developed to target the kinase domain of EGFR. These TKIs produce promising results at the initial stage of therapy, but the efficacy becomes limited due to the development of drug resistance. In this paper, we provide a comprehensive overview of computational methods, for understanding drug resistance mechanisms. The important EGFR mutants and the different generations of EGFR-TKIs, with the survival and response rates are discussed. Next, we evaluate the role of important EGFR parameters in drug resistance mechanism, including structural dynamics, hydrogen bonds, stability, dimerization, binding free energies, and signaling pathways. Personalized drug resistance prediction models, drug response curve, drug synergy, and other data-driven methods are also discussed. Recent advancements in deep learning; such as AlphaFold2, deep generative models, big data analytics, and the applications of statistics and permutation are also highlighted. We explore limitations in the current methodologies, and discuss strategies to overcome them. We believe this review will serve as a reference for researchers; to apply computational techniques for precision medicine, analyzing structures of protein-drug complexes, drug discovery, and understanding the drug response and resistance mechanisms in lung cancer patients.

Lung cancer is one of the most prevalent contributors to cancer deaths worldwide. The over-expression of Epidermal growth factor receptor (EGFR) is found in about 60% of non-small cell lung cancer (NSCLC) patients. Food and Drug Administration (FDA) has approved small molecule inhibitors, targeting the kinase domain of EGFR and to stop the abnormal growth of the cancer cells. These inhibitors produce encouraging results, but the long term efficacy remains limited due to secondary point mutations. In this work, we have developed a framework, using molecular dynamics (MD) simulation and machine learning to predict the drug response in lung cancer patients and to understand the mechanism of drug resistance. The experiments on an independent cohort of 61 patients shows the effectiveness of the proposed approach.

Non-small cell lung cancer with an activating epidermal growth factor receptor (EGFR) mutation responds well to targeted drugs. In most cases, drug resistance appears after about a year. Several studies have been conducted on the kinase domain of EGFR to understand the drug resistance mechanism. Since EGFR is a multi-domain protein, mutation in the kinase domain may affect the other domains as well. In this study, we examine the complete structure of the multi-domain EGFR protein and its mutants. We performed molecular dynamics simulations for wildtype EGFR, EGFR with L858R mutation, and EGFR with L858R and T790M mutations. We applied normal mode analysis and complex network analysis to extract the correlated motions in the domains of EGFR. The normal modes are used to construct the dynamic cross-correlation map (DCCM). Simulation results show different patterns of correlated motions in each domain of EGFR mutants compared to the wildtype. In Domains 1 and 3 of the extracellular region, a small number of weak positively correlated motions are extracted. Domains 2 and 4 show large numbers of both positive and negative motions. However, the negatively correlated motions are stronger in mutant structures compared to the wildtype. In Domain 7, some residues showed a positive correlation around the main diagonal. We also identified different communities, nodes and crucial residues in the domains of the structures, which can be important for the function of EGFR. Moreover, hydrogen bond analysis is performed for the stability analysis. The mutant structures have fewer hydrogen bonds compared to the wildtype. Overall, these findings are useful for understanding the dynamics and communications in EGFR domains.

Non-small cell lung cancer (NSCLC) caused by mutation of the epidermal growth factor receptor (EGFR) is a major cause of death worldwide. Tyrosine kinase inhibitors (TKIs) of EGFR have been developed and show promising results at the initial stage of therapy. However, in most cases, their efficacy becomes limited due to the emergence of secondary mutations causing drug resistance after about a year. In this work, we investigated the mechanism of drug resistance due to these mutations. We performed molecular dynamics (MD) simulations of EGFR-drug interactions to obtain Euclidean distance and binding free energy values to analyse drug resistance and visualize drug-protein interactions. A PCA-based method is proposed to find normal, rigid, flexible, and critical residues. We have established a systematic method for the visualization of protein-drug interactions, which provides an effective framework for the analysis of drug resistance in lung cancer at the atomic level.

With the increasing computing power of processors, more complex web and mobile applications are being developed by the developers. To meet the consistent high standard software deliverables, software developers need to follow the software design life cycle as a standard practice. The conventional way suffers certain drawbacks in project management that need to be addressed. The newer approach called agile methodology is much efficient and improves the quality of the product if followed by the team members as per the agile values. Agile is one of the software development methodologies that have a lot of features and flexibility which play a vital role to bring improvement in educational as well as industrial sectors. As the traditional methodologies are not flexible with changes, whereas Agile methodologies main advantages are interacting with the customer, respond to changes and strong communication and collaboration. In this research, we have conducted a critical survey based on three fundamental modules including design and learning strategies, team building, and profiling. The consequences showed that the conducted survey brought up the current situation of organization and opening new research direction to bring Agility in existing systems.

Non-small cell lung cancer (NSCLC) with activating epidermal growth factor receptor (EGFR) is a major cause of death worldwide. Tyrosine kinase inhibitors (TKIs) have been developed to target the EGFR, stop the downstream signaling and the tumor growth. Despite of initial good results, drug resistance is developed after one year due to a secondary mutation. The L858R, T790M mutation and their combination change the conformational redistribution of EGFR. To combat drug resistance caused by the T790M mutation, AZD9291 third generation drug was approved by the food and drug administration agency, FDA, USA. However, resistance to AZD9291 is developed due to C797S mutation. In this paper, we investigate the drug resistance due to these genomic variations. We perform molecular dynamics (MD) simulation for EGFR, EGFR with L858R single point mutation, EGFR with L858R and T790M double point mutation and EGFR with L858R, T790M and C797S triple point mutation. We apply principal component analysis PCA and clustering to the atomic trajectories of EGFR and its mutants and extract the dominant motions. The first PC captures 29.04%, 51.17% 53.79% and 51.67% variance in WT, L858R, T790M and C797S mutants, respectively. First 20 PCs are used to explain the dynamics of the system, that captures about 90% of the variance in the system. This shows that the mutation increases the variance which leads to structural and dynamical changes and can be one of the reasons for the drug resistance. Our results provide new insights to the conformational dynamics and structural changes in EGFR and its mutants, that can be helpful for understanding the drug resistance mechanism and designing future therapies for NSCLC patients.

Extraction of salient object from blurred and similar background color image is very difficult task. Many image segmentation methods have been proposed to overcome this problem but their performance is unsatisfactory when the target object and background has similar color appearance. In this paper, we have proposed a technique to overcome this problem with fast fuzzy-c-mean membership maps. These maps are blended by using Porter-Duff compositing method. The composite process is accomplished under different blending modes where foreground element of one map blend on the dropback element of the second map. These blended maps contain some outliers, which are removed by applying morphological technique. Finally an image mask, which is the composite form of frequency prior, color prior and location prior of an image is used to extract the final salient map from the given blended maps. Experiments on four well-known datasets (MSRA, MSRA-1000, THUR15000 and SED) are conducted; The results indicate the efficiency of proposed method. Our approach produces more accurate image segmentation, where the background and foreground maps have similarity in color appearance.