Ahtisham Fazeel Abbasi

Kaito Shiku, Ahtisham Fazeel Abbasi, Ryoma Bise et al.

Histology-based single-cell spatial transcriptomics (ST) estimation aims to predict gene expression for individual cells from histopathological images and cell locations, reducing the need for costly single-cell ST measurements. Unlike existing histology-to-ST methods that mainly predict spot-level profiles for local regions containing multiple cells, this task requires modeling cell-to-cell expression variability, which is strongly structured by cell type. We propose Genomics-Guided Cell-Type-Specific Mixture-of-Experts (GC-MoE), which estimates cell-type probabilities with a routing network and softly combines cell-type-specific experts for gene expression prediction. To further encode cell-type-dependent gene programs, we introduce the Cell-Type-Specific Co-Expression-Aware Predictor (CAP), together with a lightweight Cell-to-Cell Interaction Attention (C2CA) module for neighboring-cell context. Experiments and ablations on public single-cell ST datasets show consistent improvements over existing single-cell and adapted spot-level baselines.

Yuichiro Iwashita, Ahtisham Fazeel Abbasi, Muhammad Nabeel Asim et al.

Single-cell RNA sequencing (scRNA-seq) is inherently affected by sparsity caused by dropout events, in which expressed genes are recorded as zeros due to technical limitations. These artifacts distort gene expression distributions and can compromise downstream analyses. Numerous imputation methods have been proposed to address this, and these methods encompass a wide range of approaches from traditional statistical models to recently developed deep learning (DL)-based methods. However, their comparative performance remains unclear, as existing benchmarking studies typically evaluate only a limited subset of methods, datasets, and downstream analytical tasks. Here, we present a comprehensive benchmark of 15 scRNA-seq imputation methods spanning 7 methodological categories, including traditional and modern DL-based methods. These methods are evaluated across 30 datasets sourced from 10 experimental protocols and assessed in terms of 6 downstream analytical tasks. Our results show that traditional imputation methods, such as model-based, smoothing-based, and low-rank matrix-based methods, generally outperform DL-based methods, such as diffusion-based, GAN-based, GNN-based, and autoencoder-based methods. In addition, strong performance in numerical gene expression recovery does not necessarily translate into improved biological interpretability in downstream analyses. Furthermore, the performance of imputation methods varies substantially across datasets, protocols, and downstream analytical tasks, and no single method consistently outperforms others across all evaluation scenarios. Together, our results provide practical guidance for selecting imputation methods tailored to specific analytical objectives and highlight the importance of task-specific evaluation when assessing imputation performance in scRNA-seq data analysis.