Molecular property prediction uses molecular structure to infer chemical properties. Chemically interpretable representations that capture meaningful intramolecular interactions enhance the usability and effectiveness of these predictions. However, existing methods often rely on atom-based or rule-based fragment tokenization, which can be chemically suboptimal and lack scalability. We introduce FragmentNet, a graph-to-sequence foundation model with an adaptive, learned tokenizer that decomposes molecular graphs into chemically valid fragments while preserving structural connectivity. FragmentNet integrates VQVAE-GCN for hierarchical fragment embeddings, spatial positional encodings for graph serialization, global molecular descriptors, and a transformer. Pre-trained with Masked Fragment Modeling and fine-tuned on MoleculeNet tasks, FragmentNet outperforms models with similarly scaled architectures and datasets while rivaling larger state-of-the-art models requiring significantly more resources. This novel framework enables adaptive decomposition, serialization, and reconstruction of molecular graphs, facilitating fragment-based editing and visualization of property trends in learned embeddings - a powerful tool for molecular design and optimization.
The SQL-to-text generation task traditionally uses template base, Seq2Seq, tree-to-sequence, and graph-to-sequence models. Recent models take advantage of pre-trained generative language models for this task in the Seq2Seq framework. However, treating SQL as a sequence of inputs to the pre-trained models is not optimal. In this work, we put forward a new SQL intermediate representation called EzSQL to align SQL with the natural language text sequence. EzSQL simplifies the SQL queries and brings them closer to natural language text by modifying operators and keywords, which can usually be described in natural language. EzSQL also removes the need for set operators. Our proposed SQL-to-text generation model uses EzSQL as the input to a pre-trained generative language model for generating the text descriptions. We demonstrate that our model is an effective state-of-the-art method to generate text narrations from SQL queries on the WikiSQL and Spider datasets. We also show that by generating pretraining data using our SQL-to-text generation model, we can enhance the performance of Text-to-SQL parsers.
Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.
The visual question generation (VQG) task aims to generate human-like questions from an image and potentially other side information (e.g. answer type). Previous works on VQG fall in two aspects: i) They suffer from one image to many questions mapping problem, which leads to the failure of generating referential and meaningful questions from an image. ii) They fail to model complex implicit relations among the visual objects in an image and also overlook potential interactions between the side information and image. To address these limitations, we first propose a novel learning paradigm to generate visual questions with answer-awareness and region-reference. Concretely, we aim to ask the right visual questions with Double Hints - textual answers and visual regions of interests, which could effectively mitigate the existing one-to-many mapping issue. Particularly, we develop a simple methodology to self-learn the visual hints without introducing any additional human annotations. Furthermore, to capture these sophisticated relationships, we propose a new double-hints guided Graph-to-Sequence learning framework, which first models them as a dynamic graph and learns the implicit topology end-to-end, and then utilizes a graph-to-sequence model to generate the questions with double hints. Experimental results demonstrate the priority of our proposed method.
Motivation: Retrosynthesis planning poses a formidable challenge in the organic chemical industry. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. Results: This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.
Nowadays, so as to improve services and urban areas livability, multiple smart city initiatives are being carried out throughout the world. SmartSantander is a smart city project in Santander, Spain, which has relied on wireless sensor network technologies to deploy heterogeneous sensors within the city to measure multiple parameters, including outdoor parking information. In this paper, we study the prediction of parking lot availability using historical data from more than 300 outdoor parking sensors with SmartSantander. We design a graph-to-sequence model to capture the periodical fluctuation and geographical proximity of parking lots. For developing and evaluating our model, we use a 3-year dataset of parking lot availability in the city of Santander. Our model achieves a high accuracy compared with existing sequence-to-sequence models, which is accurate enough to provide a parking information service in the city. We apply our model to a smartphone application to be widely used by citizens and tourists.
A critical point of multi-document summarization (MDS) is to learn the relations among various documents. In this paper, we propose a novel abstractive MDS model, in which we represent multiple documents as a heterogeneous graph, taking semantic nodes of different granularities into account, and then apply a graph-to-sequence framework to generate summaries. Moreover, we employ a neural topic model to jointly discover latent topics that can act as cross-document semantic units to bridge different documents and provide global information to guide the summary generation. Since topic extraction can be viewed as a special type of summarization that "summarizes" texts into a more abstract format, i.e., a topic distribution, we adopt a multi-task learning strategy to jointly train the topic and summarization module, allowing the promotion of each other. Experimental results on the Multi-News dataset demonstrate that our model outperforms previous state-of-the-art MDS models on both Rouge metrics and human evaluation, meanwhile learns high-quality topics.
Synthesis planning and reaction outcome prediction are two fundamental problems in computer-aided organic chemistry for which a variety of data-driven approaches have emerged. Natural language approaches that model each problem as a SMILES-to-SMILES translation lead to a simple end-to-end formulation, reduce the need for data preprocessing, and enable the use of well-optimized machine translation model architectures. However, SMILES representations are not an efficient representation for capturing information about molecular structures, as evidenced by the success of SMILES augmentation to boost empirical performance. Here, we describe a novel Graph2SMILES model that combines the power of Transformer models for text generation with the permutation invariance of molecular graph encoders that mitigates the need for input data augmentation. As an end-to-end architecture, Graph2SMILES can be used as a drop-in replacement for the Transformer in any task involving molecule(s)-to-molecule(s) transformations. In our encoder, an attention-augmented directed message passing neural network (D-MPNN) captures local chemical environments, and the global attention encoder allows for long-range and intermolecular interactions, enhanced by graph-aware positional embedding. Graph2SMILES improves the top-1 accuracy of the Transformer baselines by $1.7\%$ and $1.9\%$ for reaction outcome prediction on USPTO_480k and USPTO_STEREO datasets respectively, and by $9.8\%$ for one-step retrosynthesis on the USPTO_50k dataset.
We target the problem of provably computing the equivalence between two complex expression trees. To this end, we formalize the problem of equivalence between two such programs as finding a set of semantics-preserving rewrite rules from one into the other, such that after the rewrite the two programs are structurally identical, and therefore trivially equivalent.We then develop a graph-to-sequence neural network system for program equivalence, trained to produce such rewrite sequences from a carefully crafted automatic example generation algorithm. We extensively evaluate our system on a rich multi-type linear algebra expression language, using arbitrary combinations of 100+ graph-rewriting axioms of equivalence. Our machine learning system guarantees correctness for all true negatives, and ensures 0 false positive by design. It outputs via inference a valid proof of equivalence for 93% of the 10,000 equivalent expression pairs isolated for testing, using up to 50-term expressions. In all cases, the validity of the sequence produced and therefore the provable assertion of program equivalence is always computable, in negligible time.
This paper introduces a graphical representation approach of prosody boundary (GraphPB) in the task of Chinese speech synthesis, intending to parse the semantic and syntactic relationship of input sequences in a graphical domain for improving the prosody performance. The nodes of the graph embedding are formed by prosodic words, and the edges are formed by the other prosodic boundaries, namely prosodic phrase boundary (PPH) and intonation phrase boundary (IPH). Different Graph Neural Networks (GNN) like Gated Graph Neural Network (GGNN) and Graph Long Short-term Memory (G-LSTM) are utilised as graph encoders to exploit the graphical prosody boundary information. Graph-to-sequence model is proposed and formed by a graph encoder and an attentional decoder. Two techniques are proposed to embed sequential information into the graph-to-sequence text-to-speech model. The experimental results show that this proposed approach can encode the phonetic and prosody rhythm of an utterance. The mean opinion score (MOS) of these GNN models shows comparative results with the state-of-the-art sequence-to-sequence models with better performance in the aspect of prosody. This provides an alternative approach for prosody modelling in end-to-end speech synthesis.
Neural machine translation (NMT) usually works in a seq2seq learning way by viewing either source or target sentence as a linear sequence of words, which can be regarded as a special case of graph, taking words in the sequence as nodes and relationships between words as edges. In the light of the current NMT models more or less capture graph information among the sequence in a latent way, we present a graph-to-sequence model facilitating explicit graph information capturing. In detail, we propose a graph-based SAN-based NMT model called Graph-Transformer by capturing information of subgraphs of different orders in every layers. Subgraphs are put into different groups according to their orders, and every group of subgraphs respectively reflect different levels of dependency between words. For fusing subgraph representations, we empirically explore three methods which weight different groups of subgraphs of different orders. Results of experiments on WMT14 English-German and IWSLT14 German-English show that our method can effectively boost the Transformer with an improvement of 1.1 BLEU points on WMT14 English-German dataset and 1.0 BLEU points on IWSLT14 German-English dataset.
Generating longer textual sequences when conditioned on the visual information is an interesting problem to explore. The challenge here proliferate over the standard vision conditioned sentence-level generation (e.g., image or video captioning) as it requires to produce a brief and coherent story describing the visual content. In this paper, we mask this Vision-to-Sequence as Graph-to-Sequence learning problem and approach it with the Transformer architecture. To be specific, we introduce Sparse Graph-to-Sequence Transformer (SGST) for encoding the graph and decoding a sequence. The encoder aims to directly encode graph-level semantics, while the decoder is used to generate longer sequences. Experiments conducted with the benchmark image paragraph dataset show that our proposed achieve 13.3% improvement on the CIDEr evaluation measure when comparing to the previous state-of-the-art approach.
Meaning Representations (AMRs) are broad-coverage sentence-level semantic graphs. Existing approaches to generating text from AMR have focused on training sequence-to-sequence or graph-to-sequence models on AMR annotated data only. In this paper, we propose an alternative approach that combines a strong pre-trained language model with cycle consistency-based re-scoring. Despite the simplicity of the approach, our experimental results show these models outperform all previous techniques on the English LDC2017T10dataset, including the recent use of transformer architectures. In addition to the standard evaluation metrics, we provide human evaluation experiments that further substantiate the strength of our approach.
Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.
Static knowledge graph has been incorporated extensively into sequence-to-sequence framework for text generation. While effectively representing structured context, static knowledge graph failed to represent knowledge evolution, which is required in modeling dynamic events. In this paper, an automatic commenting task is proposed for long novels, which involves understanding context of more than tens of thousands of words. To model the dynamic storyline, especially the transitions of the characters and their relations, Evolutionary Knowledge Graph(EKG) is proposed and learned within a multi-task framework. Given a specific passage to comment, sequential modeling is used to incorporate historical and future embedding for context representation. Further, a graph-to-sequence model is designed to utilize the EKG for comment generation. Extensive experimental results show that our EKG-based method is superior to several strong baselines on both automatic and human evaluations.
This paper leverages the graph-to-sequence method in neural text-to-speech (GraphTTS), which maps the graph embedding of the input sequence to spectrograms. The graphical inputs consist of node and edge representations constructed from input texts. The encoding of these graphical inputs incorporates syntax information by a GNN encoder module. Besides, applying the encoder of GraphTTS as a graph auxiliary encoder (GAE) can analyse prosody information from the semantic structure of texts. This can remove the manual selection of reference audios process and makes prosody modelling an end-to-end procedure. Experimental analysis shows that GraphTTS outperforms the state-of-the-art sequence-to-sequence models by 0.24 in Mean Opinion Score (MOS). GAE can adjust the pause, ventilation and tones of synthesised audios automatically. This experimental conclusion may give some inspiration to researchers working on improving speech synthesis prosody.
In this work we target the problem of provably computing the equivalence between two programs represented as dataflow graphs. To this end, we formalize the problem of equivalence between two programs as finding a set of semantics-preserving rewrite rules from one into the other, such that after the rewrite the two programs are structurally identical, and therefore trivially equivalent. We then develop the first graph-to-sequence neural network system for program equivalence, trained to produce such rewrite sequences from a carefully crafted automatic example generation algorithm. We extensively evaluate our system on a rich multi-type linear algebra expression language, using arbitrary combinations of 100+ graph-rewriting axioms of equivalence. Our system outputs via inference a correct rewrite sequence for 96% of the 10,000 program pairs isolated for testing, using 30-term programs. And in all cases, the validity of the sequence produced and therefore the provable assertion of program equivalence is computable, in negligible time.
Recent graph-to-text models generate text from graph-based data using either global or local aggregation to learn node representations. Global node encoding allows explicit communication between two distant nodes, thereby neglecting graph topology as all nodes are directly connected. In contrast, local node encoding considers the relations between neighbor nodes capturing the graph structure, but it can fail to capture long-range relations. In this work, we gather both encoding strategies, proposing novel neural models which encode an input graph combining both global and local node contexts, in order to learn better contextualized node embeddings. In our experiments, we demonstrate that our approaches lead to significant improvements on two graph-to-text datasets achieving BLEU scores of 18.01 on AGENDA dataset, and 63.69 on the WebNLG dataset for seen categories, outperforming state-of-the-art models by 3.7 and 3.1 points, respectively.
The dominant graph-to-sequence transduction models employ graph neural networks for graph representation learning, where the structural information is reflected by the receptive field of neurons. Unlike graph neural networks that restrict the information exchange between immediate neighborhood, we propose a new model, known as Graph Transformer, that uses explicit relation encoding and allows direct communication between two distant nodes. It provides a more efficient way for global graph structure modeling. Experiments on the applications of text generation from Abstract Meaning Representation (AMR) and syntax-based neural machine translation show the superiority of our proposed model. Specifically, our model achieves 27.4 BLEU on LDC2015E86 and 29.7 BLEU on LDC2017T10 for AMR-to-text generation, outperforming the state-of-the-art results by up to 2.2 points. On the syntax-based translation tasks, our model establishes new single-model state-of-the-art BLEU scores, 21.3 for English-to-German and 14.1 for English-to-Czech, improving over the existing best results, including ensembles, by over 1 BLEU.
Natural question generation (QG) aims to generate questions from a passage and an answer. In this paper, we propose a novel reinforcement learning (RL) based graph-to-sequence (Graph2Seq) model for QG. Our model consists of a Graph2Seq generator where a novel Bidirectional Gated Graph Neural Network is proposed to embed the passage, and a hybrid evaluator with a mixed objective combining both cross-entropy and RL losses to ensure the generation of syntactically and semantically valid text. The proposed model outperforms previous state-of-the-art methods by a large margin on the SQuAD dataset.