arXiv subjects

Rabeya Tus Sadia

Publications and source records attributed to Rabeya Tus Sadia.

7 recordsLinked to original sources

arXiv2026

OmicSync: Reliability-Aware Spatial Multi-Omics Clustering with Evidence-Constrained LLM Reasoning

Spatial multi-omics technologies jointly profile gene expression, surface proteins, and histology at each tissue spot, yet most spatial domain discovery methods provide only cluster assignments, without indicating assignment reliability, modality contributions, or why a domain decision should be trusted. We present OmicSync, a reliability-aware spatial multi-omics framework that couples unsupervised domain clustering with evidence-constrained LLM reasoning using model-derived per-spot signals, including assignment confidence, epistemic routing uncertainty, and modality-routing weights. These signals are converted into structured evidence dictionaries and used to generate standard, stepwise, counterfactual, contrastive, and uncertainty-focused explanations. OmicSync integrates a KAN-GCN backbone with spatial encoding, cross-modal fusion, uncertainty-aware routing, cell-type supervision, and missing-modality imputation. We further introduce OmicSync-R, which closes the reasoning-clustering loop by using automatically computed reasoning-quality scores as REINFORCE rewards, allowing reasoning coherence to shape the latent structure without backpropagating through the language model. Across four 10x CytAssist FFPE spatial proteomics benchmarks, OmicSync achieves the best average rank on Human Tonsil (1.44), Glioblastoma (1.78), and Tonsil Add-on (1.22), and second-best on Human Breast Cancer (2.33). OmicSync-R further improves ARI on Human Breast Cancer from 45.73 to 46.72 and outperforms existing methods on six of nine clustering metrics. Together, OmicSync and OmicSync-R enable reliability-aware, spot-level auditable spatial domain discovery guided by evidence-constrained reasoning.

cs.CV↗

arXiv2026

CrossLLM-Mamba: Multimodal State Space Fusion of LLMs for RNA Interaction Prediction

Accurate prediction of RNA-associated interactions is essential for understanding cellular regulation and advancing drug discovery. While Biological Large Language Models (BioLLMs) such as ESM-2 and RiNALMo provide powerful sequence representations, existing methods rely on static fusion strategies that fail to capture the dynamic, context-dependent nature of molecular binding. We introduce CrossLLM-Mamba, a novel framework that reformulates interaction prediction as a state-space alignment problem. By leveraging bidirectional Mamba encoders, our approach enables deep ``crosstalk'' between modality-specific embeddings through hidden state propagation, modeling interactions as dynamic sequence transitions rather than static feature overlaps. The framework maintains linear computational complexity, making it scalable to high-dimensional BioLLM embeddings. We further incorporate Gaussian noise injection and Focal Loss to enhance robustness against hard-negative samples. Comprehensive experiments across three interaction categories, RNA-protein, RNA-small molecule, and RNA-RNA demonstrate that CrossLLM-Mamba achieves state-of-the-art performance. On the RPI1460 benchmark, our model attains an MCC of 0.892, surpassing the previous best by 5.2\%. For binding affinity prediction, we achieve Pearson correlations exceeding 0.95 on riboswitch and repeat RNA subtypes. These results establish state-space modeling as a powerful paradigm for multi-modal biological interaction prediction.

q-bio.GN↗

arXiv2025

CrunchLLM: Multitask LLMs for Structured Business Reasoning and Outcome Prediction

Predicting the success of start-up companies, defined as achieving an exit through acquisition or IPO, is a critical problem in entrepreneurship and innovation research. Datasets such as Crunchbase provide both structured information (e.g., funding rounds, industries, investor networks) and unstructured text (e.g., company descriptions), but effectively leveraging this heterogeneous data for prediction remains challenging. Traditional machine learning approaches often rely only on structured features and achieve moderate accuracy, while large language models (LLMs) offer rich reasoning abilities but struggle to adapt directly to domain-specific business data. We present \textbf{CrunchLLM}, a domain-adapted LLM framework for startup success prediction. CrunchLLM integrates structured company attributes with unstructured textual narratives and applies parameter-efficient fine-tuning strategies alongside prompt optimization to specialize foundation models for entrepreneurship data. Our approach achieves accuracy exceeding 80\% on Crunchbase startup success prediction, significantly outperforming traditional classifiers and baseline LLMs. Beyond predictive performance, CrunchLLM provides interpretable reasoning traces that justify its predictions, enhancing transparency and trustworthiness for financial and policy decision makers. This work demonstrates how adapting LLMs with domain-aware fine-tuning and structured--unstructured data fusion can advance predictive modeling of entrepreneurial outcomes. CrunchLLM contributes a methodological framework and a practical tool for data-driven decision making in venture capital and innovation policy.

cs.LG↗

arXiv2025

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.

cs.LG↗

arXiv2025

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.

cs.CV↗

arXiv2024

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.

eess.IV↗

arXiv2022

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.

eess.IV↗