HGNN: Hierarchical graph neural network for predicting the classification of price-limit-hitting stocks

GeNNius: an ultrafast drug-target interaction inference method based on graph neural networks

MOTIVATION

Drug-target interaction (DTI) prediction is a relevant but challenging task in the drug repurposing field. In-silico approaches have drawn particular attention as they can reduce associated costs and time commitment of traditional methodologies. Yet, current state-of-the-art methods present several limitations: existing DTI prediction approaches are computationally expensive, thereby hindering the ability to use large networks and exploit available datasets and, the generalization to unseen datasets of DTI prediction methods remains unexplored, which could potentially improve the development processes of DTI inferring approaches in terms of accuracy and robustness.

RESULTS

In this work, we introduce GeNNius (Graph Embedding Neural Network Interaction Uncovering System), a Graph Neural Network (GNN)-based method that outperforms state-of-the-art models in terms of both accuracy and time efficiency across a variety of datasets. We also demonstrated its prediction power to uncover new interactions by evaluating not previously known DTIs for each dataset. We further assessed the generalization capability of GeNNius by training and testing it on different datasets, showing that this framework can potentially improve the DTI prediction task by training on large datasets and testing on smaller ones. Finally, we investigated qualitatively the embeddings generated by GeNNius, revealing that the GNN encoder maintains biological information after the graph convolutions while diffusing this information through nodes, eventually distinguishing protein families in the node embedding space.

AVAILABILITY AND IMPLEMENTATION

GeNNius code is available at https://github.com/ubioinformat/GeNNius.

Understanding the influence of news on society decision making: application to economic policy uncertainty

The abundance of digital documents offers a valuable chance to gain insights into public opinion, social structure, and dynamics. However, the scale and volume of these digital collections makes manual analysis approaches extremely costly and not scalable. In this paper, we study the potential of using automated methods from natural language processing and machine learning, in particular weak supervision strategies, to understand how news influence decision making in society. Besides proposing a weak supervision solution for the task, which replaces manual labeling to a certain extent, we propose an improvement of a recently published economic index. This index is known as economic policy uncertainty (EPU) index and has been shown to correlate to indicators such as firm investment, employment, and excess market returns. In summary, in this paper, we present an automated data efficient approach based on weak supervision and deep learning (BERT + WS) for identification of news articles about economical uncertainty and adapt the calculation of EPU to the proposed strategy. Experimental results reveal that our approach (BERT + WS) improves over the baseline method centered in keyword search, which is currently used to construct the EPU index. The improvement is over 20 points in precision, reducing the false positive rate typical to the use of keywords.