DepMicroDiff: Diffusion-Based Dependency-Aware Multimodal Imputation for Microbiome Data

Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation methods, including recent diffusion-based models, often fail to capture the complex interdependencies between microbial taxa and overlook contextual metadata that can inform imputation. We introduce DepMicroDiff, a novel framework that combines diffusion-based generative modeling with a Dependency-Aware Transformer (DAT) to explicitly capture both mutual pairwise dependencies and autoregressive relationships. DepMicroDiff is further enhanced by VAE-based pretraining across diverse cancer datasets and conditioning on patient metadata encoded via a large language model (LLM). Experiments on TCGA microbiome datasets show that DepMicroDiff substantially outperforms state-of-the-art baselines, achieving higher Pearson correlation (up to 0.712), cosine similarity (up to 0.812), and lower RMSE and MAE across multiple cancer types, demonstrating its robustness and generalizability for microbiome imputation.

CausalGeD: Blending Causality and Diffusion for Spatial Gene Expression Generation

The integration of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data is crucial for understanding gene expression in spatial context. Existing methods for such integration have limited performance, with structural similarity often below 60\%, We attribute this limitation to the failure to consider causal relationships between genes. We present CausalGeD, which combines diffusion and autoregressive processes to leverage these relationships. By generalizing the Causal Attention Transformer from image generation to gene expression data, our model captures regulatory mechanisms without predefined relationships. Across 10 tissue datasets, CausalGeD outperformed state-of-the-art baselines by 5- 32\% in key metrics, including Pearson's correlation and structural similarity, advancing both technical and biological insights.

Multiscale Latent Diffusion Model for Enhanced Feature Extraction from Medical Images

Various imaging modalities are used in patient diagnosis, each offering unique advantages and valuable insights into anatomy and pathology. Computed Tomography (CT) is crucial in diagnostics, providing high-resolution images for precise internal organ visualization. CT's ability to detect subtle tissue variations is vital for diagnosing diseases like lung cancer, enabling early detection and accurate tumor assessment. However, variations in CT scanner models and acquisition protocols introduce significant variability in the extracted radiomic features, even when imaging the same patient. This variability poses considerable challenges for downstream research and clinical analysis, which depend on consistent and reliable feature extraction. Current methods for medical image feature extraction, often based on supervised learning approaches, including GAN-based models, face limitations in generalizing across different imaging environments. In response to these challenges, we propose LTDiff++, a multiscale latent diffusion model designed to enhance feature extraction in medical imaging. The model addresses variability by standardizing non-uniform distributions in the latent space, improving feature consistency. LTDiff++ utilizes a UNet++ encoder-decoder architecture coupled with a conditional Denoising Diffusion Probabilistic Model (DDPM) at the latent bottleneck to achieve robust feature extraction and standardization. Extensive empirical evaluations on both patient and phantom CT datasets demonstrate significant improvements in image standardization, with higher Concordance Correlation Coefficients (CCC) across multiple radiomic feature categories. Through these advancements, LTDiff++ represents a promising solution for overcoming the inherent variability in medical imaging data, offering improved reliability and accuracy in feature extraction processes.

Examining the behaviour of state-of-the-art convolutional neural networks for brain tumor detection with and without transfer learning

Distinguishing normal from malignant and determining the tumor type are critical components of brain tumor diagnosis. Two different kinds of dataset are investigated using state-of-the-art CNN models in this research work. One dataset(binary) has images of normal and tumor types, while another(multi-class) provides all images of tumors classified as glioma, meningioma, or pituitary. The experiments were conducted in these dataset with transfer learning from pre-trained weights from ImageNet as well as initializing the weights randomly. The experimental environment is equivalent for all models in this study in order to make a fair comparison. For both of the dataset, the validation set are same for all the models where train data is 60% while the rest is 40% for validation. With the proposed techniques in this research, the EfficientNet-B5 architecture outperforms all the state-of-the-art models in the binary-classification dataset with the accuracy of 99.75% and 98.61% accuracy for the multi-class dataset. This research also demonstrates the behaviour of convergence of validation loss in different weight initialization techniques.