Chemical information extraction is to convert chemical knowledge in text into true chemical database, which is a text processing task heavily relying on chemical compound name identification and standardization. Once a systematic name for a chemical compound is given, it will naturally and much simply convert the name into the eventually required molecular formula. However, for many chemical substances, they have been shown in many other names besides their systematic names which poses a great challenge for this task. In this paper, we propose a framework to do the auto standardization from the non-systematic names to the corresponding systematic names by using the spelling error correction, byte pair encoding tokenization and neural sequence to sequence model. Our framework is trained end to end and is fully data-driven. Our standardization accuracy on the test dataset achieves 54.04% which has a great improvement compared to previous state-of-the-art result. There are more than 100 million named chemical substances in the world. In order to uniquely identify every chemical substance, there are elaborate rules for assigning names to them on the basis of their structures. These names are called systematic names. The rules for these names are defined by International Union of Pure and Applied Chemistry (IUPAC) BID1 .However , besides the systematic name, there can be also many other names for a chemical substance due to many reasons. Firstly , many chemical are so much a part of our life that we know them by their familiar names which we call them common names or trivial names for the sake of simplicity. For example , sucrose is a kind of sugar which we are very familiar with. Its systematic name is much more complicated, which is (2R,3R,4S,5S,6R)-2-[(2S,3S,4S,5R)-3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol.Secondly, in chemistry industry, especially in pharmaceutical industry, many producers always generate new names to a chemical substance in order to distinguish their products from those of their competitors. We call these kind of names proprietary names. The most famous example is Aspirin. Its systematic name is 2-Acetoxybenzoic acid. So due to the history reasons and idiomatic usages, a chemical substance can have many other names.Chemical information extraction is a research that extracts useful chemical knowledge in text and converts it into a database, which strongly relies on the unique standard chemical names. Nowadays, there are many chemical databases such as PubChem and SciFinder, which are designed to store chemical information including chemical names, chemical structures, molecular formulas and other relevant information. For these databases , it is still an ongoing work to extract chemical information from chemical papers to update the databases. If all the chemical substances are expressed by the systematic names, it is easy to generate other information. For example, we can nearly perfectly convert the systematic name to other representations such as Simplified Molecular-Input Line-Entry System (SMILES) BID13 and International Chemical Identifier (InCHI) BID9 and then generate the structural formulas. Some online systems are already well developed for converting automatically systematic names to SMILES string with a very high precision such as Open Parser for Systematic IUPAC Nomenclature (OPSIN) BID7 developed by In the following passage, we consider the differences between non-systematic names and systematic names as "error" 2 . In view of natural language processing, the error types of non-systematic names can be summarized by four types: 1. Spelling error. It means that non-systematic names just have slightly differences from systematic names in spelling; 2. Ordering error. It means that the groups in a non-systematic name are in wrong order; 3. Common name error. As mentioned above, many chemical substances have common names or proprietary names which look totally different from their systematic names; 4. Synonym error. It means that the words in the nonsystematic names are different from those in the systematic names but they share the same root of word. In fact, it is the error type which happens most often. For example, 2-(Acetyloxy)benzoic Acid has synonyms Acetylsalicylic Acid and Acetysal and these three words share the same root of word "Acety". Some examples of different types of errors are shown in TAB0 . What is worth mentioning is that several types of error can appear at the same time in a single non-systematic name, especially for the ordering error and synonym error. The mixed types of error make this task very challenging .Based on these four error types, we propose a framework to convert automatically the non-systematic names to systematic names. Our framework is structured as followed: 1. Spelling error correction. It aims to correct the spelling errors; 2. Byte pair encoding (BPE) tokenization. It aims to split a name into small parts; 3. Sequence to sequence model. It aims to fix all the remaining ordering errors, common name errors and synonym errors.Actually, due to its great challenge, few work has been done on the chemical name standardization. To our best knowledge, BID2 is the only work deserving a citation which developed an online system ChemHits to do the standardization basing on several transformation rules and the queries to online chemical databases. The work of BID2 severely depends on chemical knowledge, limiting its application potential and effectiveness to some extent.Differently, we adopt sequence to sequence model that has been widely used on neural machine translation. The reason why we apply the sequence to sequence model is that our task has some similarities with the machine translation problem. In machine translation, there are source language and target language which correspond to the non-systematic names and the systematic names in our task. Two different languages can be different in: 1. Vocabularies, which corresponds to the common name error and synonym error; 2. Word order, which corresponds to the ordering error. Our framework is trained end-to-end , fully data-driven and without using external chemical knowledge.With this approach, we achieve an accuracy of 54.04% in our test data set.Our work will be done on a corpus containing chemical names extracted from report of Chemical Journals with High Impact factors (CJHIF) 3 . The corpus is collected and checked by paid manual work. It is a parallel corpus which includes non-systematic names and systematic names of chemical substances . In the following passage, we call a non-systematic name and the corresponding systematic name of a chemical substance data pair. In our corpus, there are 384816 data pairs. In FIG1 , we give an overview of the distribution of the Levenshtein distance between the non-systematic names and the systematic names to show how different the non-systematic names and the systematic names are. In the experiment, we use 80%, 19% and 1% data as training set, test set and development set respectively. In this work, we propose a framework to automatically convert non-systematic names to systematic names . Our framework consists of spelling error correction, byte pair encoding tokenization and sequence to sequence model. Our framework achieves an accuracy of 54.04% on our dataset, which is far better than previous rule based system (nine times of accuracy) and thus enables the related chemical information extraction into more practical use stage. The advantage of our framework is that it is trained end to end, fully data-driven and independent of external chemical knowledge. This work starts a brand new research line for the related chemical information extraction as to our best knowledge.
We designed an end-to-end framework using sequence to sequence model to do the  chemical names standardization. Standardizes non systematic names in chemical information extraction by creating a parallel corpus of non-systematic and systematic names and building a seq2seq model. This work presents a method to translate non-systematic names of chemical compounds into their systematic equivalents using a combination of mechanisms