Sajib Acharjee Dip

Sajib Acharjee Dip, Kazi Hasan Ibn Arif, Uddip Acharjee Shuvo et al.

In the realm of dermatology, the complexity of diagnosing skin conditions manually necessitates the expertise of dermatologists. Accurate identification of various skin ailments, ranging from cancer to inflammatory diseases, is paramount. However, existing artificial intelligence (AI) models in dermatology face challenges, particularly in accurately diagnosing diseases across diverse skin tones, with a notable performance gap in darker skin. Additionally, the scarcity of publicly available, unbiased datasets hampers the development of inclusive AI diagnostic tools. To tackle the challenges in accurately predicting skin conditions across diverse skin tones, we employ a transfer-learning approach that capitalizes on the rich, transferable knowledge from various image domains. Our method integrates multiple pre-trained models from a wide range of sources, including general and specific medical images, to improve the robustness and inclusiveness of the skin condition predictions. We rigorously evaluated the effectiveness of these models using the Diverse Dermatology Images (DDI) dataset, which uniquely encompasses both underrepresented and common skin tones, making it an ideal benchmark for assessing our approach. Among all methods, Med-ViT emerged as the top performer due to its comprehensive feature representation learned from diverse image sources. To further enhance performance, we conducted domain adaptation using additional skin image datasets such as HAM10000. This adaptation significantly improved model performance across all models.

Kazi Hasan Ibn Arif, Sajib Acharjee Dip, Khizar Hussain et al.

Large Vision Language Models (LVLMs) have demonstrated remarkable capabilities in understanding and describing visual content, achieving state-of-the-art performance across various vision-language tasks. However, these models often generate descriptions containing objects or details that are absent in the input image, a phenomenon commonly known as hallucination. Our work investigates the key reasons behind this issue by analyzing the pattern of self-attention in transformer layers. We find that hallucinations often arise from the progressive weakening of attention weight to visual tokens in the deeper layers of the LLM. Some previous works naively boost the attention of all visual tokens to mitigate this issue, resulting in suboptimal hallucination reduction. To address this, we identify two critical sets of visual tokens that facilitate the transfer of visual information from the vision encoder to the LLM. Local tokens encode grounded information about objects present in an image, while summary tokens capture the overall aggregated representation of the image. Importantly, these two sets of tokens require different levels of weight enhancement. To this end, we propose \textbf{PAINT} (\textbf{P}aying \textbf{A}ttention to \textbf{IN}formed \textbf{T}okens), a plug-and-play framework that intervenes in the self-attention mechanism of the LLM, selectively boosting the attention weights of local and summary tokens with experimentally learned margins. Evaluation on the MSCOCO image captioning dataset demonstrate that our approach reduces hallucination rates by up to 62.3\% compared to baseline models while maintaining accuracy. Code is available at \href{https://github.com/hasanar1f/PAINT}{https://github.com/hasanar1f/PAINT}

Sajib Acharjee Dip, Song Li, Liqing Zhang

Cell-type-specific marker genes are fundamental to plant biology, yet existing resources primarily rely on curated databases or high-throughput studies without explicitly modeling the supporting evidence found in scientific literature. We introduce PlantMarkerBench, a multi-species benchmark for evaluating literature-grounded plant marker evidence interpretation from full-text biological papers. PlantMarkerBench is constructed using a modular curation pipeline integrating large-scale literature retrieval, hybrid search, species-aware biological grounding, structured evidence extraction, and targeted human review. The benchmark spans four plant species -- Arabidopsis, maize, rice, and tomato -- and contains 5,550 sentence-level evidence instances annotated for marker-evidence validity, evidence type, and support strength. We define two benchmark tasks: determining whether a candidate sentence provides valid marker evidence for a gene-cell-type pair, and classifying the evidence into expression, localization, function, indirect, or negative categories. We benchmark diverse open-weight and closed-source language models across species and prompting strategies. Although frontier models achieve relatively strong performance on direct expression evidence, performance drops substantially on functional, indirect, and weak-support evidence, with evidence-type confusion emerging as a dominant failure mode. Open-weight models additionally exhibit elevated false-positive rates under ambiguous biological contexts. PlantMarkerBench provides a challenging and reproducible evaluation framework for literature-grounded biological evidence attribution and supports future research on trustworthy scientific information extraction and AI-assisted plant biology.

Zhenyu Bi, Sajib Acharjee Dip, Daniel Hajialigol et al.

The capabilities of AI for biomedicine span a wide spectrum, from the atomic level, where it solves partial differential equations for quantum systems, to the molecular level, predicting chemical or protein structures, and further extending to societal predictions like infectious disease outbreaks. Recent advancements in large language models, exemplified by models like ChatGPT, have showcased significant prowess in natural language tasks, such as translating languages, constructing chatbots, and answering questions. When we consider biomedical data, we observe a resemblance to natural language in terms of sequences: biomedical literature and health records presented as text, biological sequences or sequencing data arranged in sequences, or sensor data like brain signals as time series. The question arises: Can we harness the potential of recent large language models to drive biomedical knowledge discoveries? In this survey, we will explore the application of large language models to three crucial categories of biomedical data: 1) textual data, 2) biological sequences, and 3) brain signals. Furthermore, we will delve into large language model challenges in biomedical research, including ensuring trustworthiness, achieving personalization, and adapting to multi-modal data representation

Sajib Acharjee Dip, Uddip Acharjee Shuvo, Dipanwita Mallick et al.

Cancer subtype classification is crucial for personalized treatment and prognostic assessment. However, effectively integrating multi-omic data remains challenging due to the heterogeneous nature of genomic, epigenomic, and transcriptomic features. In this work, we propose Modality-Aware Cross-Attention MoXGATE, a novel deep-learning framework that leverages cross-attention and learnable modality weights to enhance feature fusion across multiple omics sources. Our approach effectively captures inter-modality dependencies, ensuring robust and interpretable integration. Through experiments on Gastrointestinal Adenocarcinoma (GIAC) and Breast Cancer (BRCA) datasets from TCGA, we demonstrate that MoXGATE outperforms existing methods, achieving 95\% classification accuracy. Ablation studies validate the effectiveness of cross-attention over simple concatenation and highlight the importance of different omics modalities. Moreover, our model generalizes well to unseen cancer types e.g., breast cancer, underscoring its adaptability. Key contributions include (1) a cross-attention-based multi-omic integration framework, (2) modality-weighted fusion for enhanced interpretability, (3) application of focal loss to mitigate data imbalance, and (4) validation across multiple cancer subtypes. Our results indicate that MoXGATE is a promising approach for multi-omic cancer subtype classification, offering improved performance and biological generalizability.

Sajib Acharjee Dip, Adrika Zafor, Bikash Kumar Paul et al.

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

Abrar Rahman Abir, Sajib Acharjee Dip, Liqing Zhang

Understanding gene perturbation effects across diverse cellular contexts is a central challenge in functional genomics, with important implications for therapeutic discovery and precision medicine. Single-cell technologies enable high-resolution measurement of transcriptional responses, but collecting such data is costly and time-consuming, especially when repeated for each cell type. Existing computational methods often require separate models per cell type, limiting scalability and generalization. We present CFM-GP, a method for cell type-agnostic gene perturbation prediction. CFM-GP learns a continuous, time-dependent transformation between unperturbed and perturbed gene expression distributions, conditioned on cell type, allowing a single model to predict across all cell types. Unlike prior approaches that use discrete modeling, CFM-GP employs a flow matching objective to capture perturbation dynamics in a scalable manner. We evaluate on five datasets: SARS-CoV-2 infection, IFN-beta stimulated PBMCs, glioblastoma treated with Panobinostat, lupus under IFN-beta stimulation, and Statefate progenitor fate mapping. CFM-GP consistently outperforms state-of-the-art baselines in R-squared and Spearman correlation, and pathway enrichment analysis confirms recovery of key biological pathways. These results demonstrate the robustness and biological fidelity of CFM-GP as a scalable solution for cross-cell type gene perturbation prediction.

Sajib Acharjee Dip, Uddip Acharjee Shuvo, Tran Chau et al.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.