The problem of molecular generation has received significant attention recently. Existing methods are typically based on deep neural networks and require training on large datasets with tens of thousands of samples. In practice, however, the size of class-specific chemical datasets is usually limited (e.g., dozens of samples) due to labor-intensive experimentation and data collection. This presents a considerable challenge for the deep learning generative models to comprehensively describe the molecular design space. Another major challenge is to generate only physically synthesizable molecules. This is a non-trivial task for neural network-based generative models since the relevant chemical knowledge can only be extracted and generalized from the limited training data. In this work, we propose a data-efficient generative model that can be learned from datasets with orders of magnitude smaller sizes than common benchmarks. At the heart of this method is a learnable graph grammar that generates molecules from a sequence of production rules. Without any human assistance, these production rules are automatically constructed from training data. Furthermore, additional chemical knowledge can be incorporated in the model by further grammar optimization. Our learned graph grammar yields state-of-the-art results on generating high-quality molecules for three monomer datasets that contain only ${\sim}20$ samples each. Our approach also achieves remarkable performance in a challenging polymer generation task with only $117$ training samples and is competitive against existing methods using $81$k data points. Code is available at https://github.com/gmh14/data_efficient_grammar.
A major challenge in the pharmaceutical industry is to design novel molecules with specific desired properties, especially when the property evaluation is costly. Here, we propose MNCE-RL, a graph convolutional policy network for molecular optimization with molecular neighborhood-controlled embedding grammars through reinforcement learning. We extend the original neighborhood-controlled embedding grammars to make them applicable to molecular graph generation and design an efficient algorithm to infer grammatical production rules from given molecules. The use of grammars guarantees the validity…
Rethinking Repetition Problems of LLMs in Code Generation
Key Laboratory of High Confidence Software Technologies (Peking University), Ministry of Education（高可信软件技术教育部重点实验室（北京大学））；School of Computer Science, Peking University（北京大学计算机学院）
MIT-IBM Watson AI Lab（MIT-IBM沃森人工智能实验室）；IBM Research（IBM研究院）
Molecular optimization aims to discover novel molecules with desirable properties. Two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecule, and therefore, the number of property evaluations is limited. These challenges are to some extent alleviated by a combination of a variational autoencoder (VAE) and Bayesian optimization (BO). VAE converts a molecule into/from its latent continuous vector, and BO optimizes a …
We present an approach to make molecular optimization more efficient. We infer a hypergraph replacement grammar from the ChEMBL database, count the frequencies of particular rules being used to expand particular nonterminals in other rules, and use these as conditional priors for the policy model. Simulating random molecules from the resulting probabilistic grammar, we show that conditional priors result in a molecular distribution closer to the training set than using equal rule probabilities or unconditional priors. We then treat molecular optimization as a reinforcement learning problem, us…
Designers increasingly rely on procedural generation for automatic generation of content in various industries. These techniques require extensive knowledge of the desired content, and about how to actually implement such procedural methods. Algorithms for learning interpretable generative models from example content could alleviate both difficulties. We propose SIGI, a novel method for inferring shapes and inducing a shape grammar from grid-based 3D building examples. This interpretable grammar is well-suited for co-creative design. Applied to Minecraft buildings, we show how the shape gramma…
In this paper, I describe several approaches to automatic or semi-automatic development of symbolic rules for grammar checkers from the information contained in corpora. The rules obtained this way are an important addition to manually-created rules that seem to dominate in rule-based checkers. However, the manual process of creation of rules is costly, time-consuming and error-prone. It seems therefore advisable to use machine-learning algorithms to create the rules automatically or semi-automatically. The results obtained seem to corroborate my initial hypothesis that symbolic machine learni…
Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more tokens than a natural language sentence, and thus it may be inappropriate for RNN to capture such a long sequence. In this paper, we propose a grammar-based structural convolutional neural network (CNN) for code generation. Our model generates a program by predicting the grammar rules of the programming language; we design several CNN modules, including the …
Singapore University of Technology and Design（新加坡科技设计大学）
The massive progress of machine learning has seen its application over a variety of domains in the past decade. But how do we develop a systematic, scalable and modular strategy to validate machine-learning systems? We present, to the best of our knowledge, the first approach, which provides a systematic test framework for machine-learning systems that accepts grammar-based inputs. Our OGMA approach automatically discovers erroneous behaviours in classifiers and leverages these erroneous behaviours to improve the respective models. OGMA leverages inherent robustness properties present in any w…
Massachusetts Institute of Technology（麻省理工学院）；The Chinese University of Hong Kong（香港中文大学）
Polymers are widely-studied materials with diverse properties and applications determined by different molecular structures. It is essential to represent these structures clearly and explore the full space of achievable chemical designs. However, existing approaches are unable to offer comprehensive design models for polymers because of their inherent scale and structural complexity. Here, we present a parametric, context-sensitive grammar designed specifically for the representation and generation of polymers. As a demonstrative example, we implement our grammar for polyurethanes. Using our s…
Faculdade de Ciências da Universidade de Lisboa（里斯本大学理学院）；Carnegie Mellon University（卡内基梅隆大学）；Instituto de Medicina Molecular（分子医学研究所）
Genetic Programming (GP) is an heuristic method that can be applied to many Machine Learning, Optimization and Engineering problems. In particular, it has been widely used in Software Engineering for Test-case generation, Program Synthesis and Improvement of Software (GI). Grammar-Guided Genetic Programming (GGGP) approaches allow the user to refine the domain of valid program solutions. Backus Normal Form is the most popular interface for describing Context-Free Grammars (CFG) for GGGP. BNF and its derivatives have the disadvantage of interleaving the grammar language and the target language …
Gwangju Institute of Science and Technology（光州科学技术院）
The simplified molecular-input line-entry system (SMILES) is the most popular representation of chemical compounds. Therefore, many SMILES-based molecular property prediction models have been developed. In particular, transformer-based models show promising performance because the model utilizes a massive chemical dataset for self-supervised learning. However, there is no transformer-based model to overcome the inherent limitations of SMILES, which result from the generation process of SMILES. In this study, we grammatically parsed SMILES to obtain connectivity between substructures and their …
Domain-general semantic parsing is a long-standing goal in natural language processing, where the semantic parser is capable of robustly parsing sentences from domains outside of which it was trained. Current approaches largely rely on additional supervision from new domains in order to generalize to those domains. We present a generative model of natural language utterances and logical forms and demonstrate its application to semantic parsing. Our approach relies on domain-independent supervision to generalize to new domains. We derive and implement efficient algorithms for training, parsing,…
Seoul National University（首尔大学）；Ewha Womans University（梨花女子大学）
Discovering new materials better suited to specific purposes is an important issue in improving the quality of human life. Here, a neural network that creates molecules that meet some desired conditions based on a deep understanding of chemical language is proposed (Generative Chemical Transformer, GCT). The attention mechanism in GCT allows a deeper understanding of molecular structures beyond the limitations of chemical language itself which cause semantic discontinuity by paying attention to characters sparsely. It is investigated that the significance of language models for inverse molecul…
