Text-to-SQL is the task of converting a natural language utterance plus the corresponding database schema into a SQL program. The inputs naturally form a heterogeneous graph while the output SQL can be transduced into an abstract syntax tree (AST). Traditional encoder-decoder models ignore higher-order semantics in heterogeneous graph encoding and introduce permutation biases during AST construction, thus incapable of exploiting the refined structure knowledge precisely. In this work, we propose a generic heterogeneous graph to abstract syntax tree (HG2AST) framework to integrate dedicated structure knowledge into statistics-based models. On the encoder side, we leverage a line graph enhanced encoder (LGESQL) to iteratively update both node and edge features through dual graph message passing and aggregation. On the decoder side, a grammar-based decoder first constructs the equivalent SQL AST and then transforms it into the desired SQL via post-processing. To avoid over-fitting permutation biases, we propose a golden tree-oriented learning (GTL) algorithm to adaptively control the expanding order of AST nodes. The graph encoder and tree decoder are combined into a unified framework through two auxiliary modules. Extensive experiments on various text-to-SQL datasets, including single/multi-table, single/cross-domain, and multilingual settings, demonstrate the superiority and broad applicability.
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http://dx.doi.org/10.1109/TPAMI.2023.3298895 | DOI Listing |
J Clin Exp Dent
December 2024
DDS. Titular Professor. Universidad de Antioquia U de A, Medellín, Colombia. Biomedical Stomatology Research Group, Universidad de Antioquia U de A, Medellín, Colombia.
Background: The RTK-VEGF4 receptor family, which includes VEGFR-1, VEGFR-2, and VEGFR-3, plays a crucial role in tissue regeneration by promoting angiogenesis, the formation of new blood vessels, and recruiting stem cells and immune cells. Machine learning, particularly graph neural networks (GNNs), has shown high accuracy in predicting these interactions. This study aims to predict drug-gene interactions of the RTK-VEGF4 receptor family in periodontal regeneration using graph neural networks.
View Article and Find Full Text PDFPLoS Comput Biol
January 2025
School of Mathematics/Harbin Institute of Technology, Harbin, China.
The rapid advance of large-scale atlas-level single cell RNA sequences and single-cell chromatin accessibility data provide extraordinary avenues to broad and deep insight into complex biological mechanism. Leveraging the datasets and transfering labels from scRNA-seq to scATAC-seq will empower the exploration of single-cell omics data. However, the current label transfer methods have limited performance, largely due to the lower capable of preserving fine-grained cell populations and intrinsic or extrinsic heterogeneity between datasets.
View Article and Find Full Text PDFBiomed Opt Express
January 2025
Computer Engineering Department, Taiyuan Institute of Technology, Taiyuan 030008, China.
Gastric cancer is a leading cause of cancer-related deaths globally. As mortality rates continue to rise, predicting cancer survival using multimodal data-including histopathological images, genomic data, and clinical information-has become increasingly crucial. However, extracting effective predictive features from this complex data has posed challenges for survival analysis due to the high dimensionality and heterogeneity of histopathology images and genomic data.
View Article and Find Full Text PDFBMC Bioinformatics
January 2025
Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.
In recent years, combined drug screening has played a very important role in modern drug discovery. Generally, synergistic drug combinations are crucial in treatment for many diseases. However, the toxic side effects of drug combinations are probably increased with the increase of drugs numbers, so the accurate prediction of toxic side effects of drug combinations is equally important.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China.
Alzheimer's Disease (AD) significantly aggravates human dignity and quality of life. While newly approved amyloid immunotherapy has been reported, effective AD drugs remain to be identified. Here, we propose a novel AI-driven drug-repurposing method, DeepDrug, to identify a lead combination of approved drugs to treat AD patients.
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