Biology subjects

Maleki, F.

Publications and source records attributed to Maleki, F..

3 recordsLinked to original sources

bioRxiv2025

A Multi-Agent Approach to Generating Context-Rich Gene Sets

Gene sets are collections of genes that share a common biological function, process, or component that can be used to get insight into the biological relevance of genomic data. Databases containing these gene sets aids in a wide array of analytical methods. The results of these methods, such as gene set analysis or phenotype-based gene prioritization, depend on the quality of the gene sets. Despite the extensive literature and genetic data available for constructing these databases, they often lack sufficient biological context. Current curation methods rely on labour-intensive expert manual curation from literature and datasets, as well as automated methods that are not context-aware. Therefore, there is a significant opportunity to utilize publicly available literature to bridge this gap and create more precise gene sets. With the advancement of natural language processing technologies, particularly large language models, this task can be performed more efficiently. In this work, we present a multi-agent system that utilizes the Llama 3, DeepSeek, and Qwen open-source large language models to analyze PubMed abstracts, allowing us to reconstruct gene sets in existing databases that better reflect specific biological contexts. Our approach consists of two pipelines. One verifies the inclusion of genes in a gene set by proof of evidence in the abstracts showing the association between the gene and the gene set. The second pipeline parses through the abstracts to identify genes not already included in the gene set for potential inclusion. To evaluate the proposed approach, we reconstructed a random selection of gene sets within the Human Ontology Phenotype (HPO). Our analysis shows that 149 of these gene sets have a similarity of 65.18% when compared to the original HPO gene sets, aligning well with the current HPO database. Additionally, we found an average of 3.15 new genes not included in the HPO gene sets, each supported by verified literature linking them to their respective gene sets. This highlights that our updated gene set database better reflects the current state of biological findings.

bioinformatics↗

bioRxiv2022

Semi-Self-Supervised Learning for Semantic Segmentation in Images with Dense Patterns

Deep learning has shown potential in domains where large-scale annotated datasets are available. However, manual annotation is expensive, time-consuming, and tedious. Pixel-level annotations are particularly costly for semantic segmentation in images with dense irregular patterns of object instances, such as in plant images. In this work, we propose a method for developing high-performing deep learning models for semantic segmentation of wheat heads utilizing little manual annotation. We simulate a computationally-annotated dataset using a few annotated images, a short unannotated video clip of a wheat field, and several video clips from fields with no wheat. This dataset is then used to train a customized U-Net model for wheat head segmentation. Considering the distribution shift between the simulated and real data, we apply three domain adaptation steps to gradually bridge the domain gap. Only using two annotated images, we achieved a Dice score of 0.89 on the internal test set, i.e., images extracted from the wheat field video. The model trained using only two annotated images was evaluated on a diverse external dataset collected from 18 different domains across five countries and achieved a Dice score of 0.73. To further expose the model to images from different growth stages and environmental conditions, we incorporated two annotated images from each of the 18 domains and further fine-tuned the model. This resulted in improving the Dice score to 0.91. These promising results highlight the utility of the proposed approach in the absence of large-annotated datasets. Although the utility of the proposed method is shown on a wheat head dataset, it can be extended to other segmentation tasks with similar characteristics of irregularly repeating patterns of object instances.

plant biology↗

bioRxiv2018

The Effect of Gene Set Overlap on Specificity of Over-representation Analysis

Gene set analysis methods are widely used to analyze data from high-throughput "omics" technologies. One drawback of these methods is their low specificity or high false positive rate. Over-representation analysis is one of the most commonly used gene set analysis methods. In this paper, we propose a systematic approach to investigate the hypothesis that gene set overlap is an underlying cause of low specificity in over-representation analysis. We quantify gene set overlap and show that it is a ubiquitous phenomenon across gene set databases. Statistical analysis indicates a strong negative correlation between gene set overlap and the specificity of over-representation analysis. We conclude that gene set overlap is an underlying cause of the low specificity. This result highlights the importance of considering gene set overlap in gene set analysis and explains the lack of specificity of methods that ignore gene set overlap. This research also establishes the direction for developing new gene set analysis methods.

bioinformatics↗