Browsing by Author "Gahegan M"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites.
    (29/06/2022) Zhang J; Liu B; Wang Z; Lehnert K; Gahegan M
    BACKGROUND: Addressing the laborious nature of traditional biological experiments by using an efficient computational approach to analyze RNA-binding proteins (RBPs) binding sites has always been a challenging task. RBPs play a vital role in post-transcriptional control. Identification of RBPs binding sites is a key step for the anatomy of the essential mechanism of gene regulation by controlling splicing, stability, localization and translation. Traditional methods for detecting RBPs binding sites are time-consuming and computationally-intensive. Recently, the computational method has been incorporated in researches of RBPs. Nevertheless, lots of them not only rely on the sequence data of RNA but also need additional data, for example the secondary structural data of RNA, to improve the performance of prediction, which needs the pre-work to prepare the learnable representation of structural data. RESULTS: To reduce the dependency of those pre-work, in this paper, we introduce DeepPN, a deep parallel neural network that is constructed with a convolutional neural network (CNN) and graph convolutional network (GCN) for detecting RBPs binding sites. It includes a two-layer CNN and GCN in parallel to extract the hidden features, followed by a fully connected layer to make the prediction. DeepPN discriminates the RBP binding sites on learnable representation of RNA sequences, which only uses the sequence data without using other data, for example the secondary or tertiary structure data of RNA. DeepPN is evaluated on 24 datasets of RBPs binding sites with other state-of-the-art methods. The results show that the performance of DeepPN is comparable to the published methods. CONCLUSION: The experimental results show that DeepPN can effectively capture potential hidden features in RBPs and use these features for effective prediction of binding sites.
  • Thumbnail Image
    Item
    Large Multi-Modal Model Cartographic Map Comprehension for Textual Locality Georeferencing
    (Schloss Dagstuhl – Leibniz-Zentrum für Informatik, 2025-08-15) Wijegunarathna K; Stock K; Jones CB; Sila-Nowicka K; Moore A; O’Sullivan D; Adams B; Gahegan M
    Millions of biological sample records collected in the last few centuries archived in natural history collections are un-georeferenced. Georeferencing complex locality descriptions associated with these collection samples is a highly labour-intensive task collection agencies struggle with. None of the existing automated methods exploit maps that are an essential tool for georeferencing complex relations. We present preliminary experiments and results of a novel method that exploits multimodal capabilities of recent Large Multi-Modal Models (LMM). This method enables the model to visually contextualize spatial relations it reads in the locality description. We use a grid-based approach to adapt these auto-regressive models for this task in a zero-shot setting. Our experiments conducted on a small manually annotated dataset show impressive results for our approach (∼1 km Average distance error) compared to uni-modal georeferencing with Large Language Models and existing georeferencing tools. The paper also discusses the findings of the experiments in light of an LMM's ability to comprehend fine-grained maps. Motivated by these results, a practical framework is proposed to integrate this method into a georeferencing workflow.