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Qiang Lyu

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3 papers

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JBHI Journal 2024 Journal Article

MultiModRLBP: A Deep Learning Approach for Multi-Modal RNA-Small Molecule Ligand Binding Sites Prediction

Junkai Wang
Lijun Quan
Zhi Jin
Hongjie Wu
Xuhao Ma
Xuejiao Wang
Jingxin Xie
Deng Pan

This study aims to tackle the intricate challenge of predicting RNA-small molecule binding sites to explore the potential value in the field of RNA drug targets. To address this challenge, we propose the MultiModRLBP method, which integrates multi-modal features using deep learning algorithms. These features include 3D structural properties at the nucleotide base level of the RNA molecule, relational graphs based on overall RNA structure, and rich RNA semantic information. In our investigation, we gathered 851 interactions between RNA and small molecule ligand from the RNAglib dataset and RLBind training set. Unlike conventional training sets, this collection broadened its scope by including RNA complexes that have the same RNA sequence but change their respective binding sites due to structural differences or the presence of different ligands. This enhancement enables the MultiModRLBP model to more accurately capture subtle changes at the structural level, ultimately improving its ability to discern nuances among similar RNA conformations. Furthermore, we evaluated MultiModRLBP on two classic test sets, Test18 and Test3, highlighting its performance disparities on small molecules based on metal and non-metal ions. Additionally, we conducted a structural sensitivity analysis on specific complex categories, considering RNA instances with varying degrees of structural changes and whether they share the same ligands. The research results indicate that MultiModRLBP outperforms the current state-of-the-art methods on multiple classic test sets, particularly excelling in predicting binding sites for non-metal ions and instances where the binding sites are widely distributed along the sequence. MultiModRLBP also can be used as a potential tool when the RNA structure is perturbed or the RNA experimental tertiary structure is not available. Most importantly, MultiModRLBP exhibits the capability to distinguish binding characteristics of RNA that are structurally diverse yet exhibit sequence similarity. These advancements hold promise in reducing the costs associated with the development of RNA-targeted drugs.

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AAAI Conference 2023 Conference Paper

Compositional Prototypical Networks for Few-Shot Classification

Qiang Lyu
Weiqiang Wang

It is assumed that pre-training provides the feature extractor with strong class transferability and that high novel class generalization can be achieved by simply reusing the transferable feature extractor. In this work, our motivation is to explicitly learn some fine-grained and transferable meta-knowledge so that feature reusability can be further improved. Concretely, inspired by the fact that humans can use learned concepts or components to help them recognize novel classes, we propose Compositional Prototypical Networks (CPN) to learn a transferable prototype for each human-annotated attribute, which we call a component prototype. We empirically demonstrate that the learned component prototypes have good class transferability and can be reused to construct compositional prototypes for novel classes. Then a learnable weight generator is utilized to adaptively fuse the compositional and visual prototypes. Extensive experiments demonstrate that our method can achieve state-of-the-art results on different datasets and settings. The performance gains are especially remarkable in the 5-way 1-shot setting. The code is available at https://github.com/fikry102/CPN.

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JBHI Journal 2021 Journal Article

Quantifying Intensities of Transcription Factor-DNA Binding by Learning From an Ensemble of Protein Binding Microarrays

Lijun Quan
Jie Mei
Ruji He
Xiaoyu Sun
Liangpeng Nie
Kailong Li
Qiang Lyu

The control of the coordinated expression of genes is primarily regulated by the interactions between transcription factors (TFs) and their DNA binding sites, which are an integral part of transcriptional regulatory networks. There are many computational tools focused on determining TF binding or unbinding to a DNA sequence. However, other tools focused on further determining the relative preference of such binding are needed. Here, we propose a regression model with deep learning, called SemanticBI, to predict intensities of TF-DNA binding. SemanticBI is a convolutional neural network (CNN)-recurrent neural network (RNN) architecture model that was trained on an ensemble of protein binding microarray data sets that covered multiple TFs. Using this approach, SemanticBI exhibited superior accuracy in predicting binding intensities compared to other popular methods. Moreover, SemanticBI uncovered vectorized sequence-oriented features using its CNN-RNN architecture, which is an abstract representation of the original DNA sequences. Additionally, the use of SemanticBI raises the question of whether motifs are necessary for computational models of TF binding. The online SemanticBI service can be accessed at http://qianglab.scst.suda.edu.cn/semantic/.

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