Information extraction from chemistry literature is vital for constructing up-to-date reaction databases for data-driven chemistry. Complete extraction requires combining information across text, tables, and figures, whereas prior work has mainly investigated extracting reactions from single modalities. In this paper, we present OpenChemIE to address this complex challenge and enable the extraction of reaction data at the document level. OpenChemIE approaches the problem in two steps: extracting relevant information from individual modalities and then integrating the results to obtain a final list of reactions. For the first step, we employ specialized neural models that each address a specific task for chemistry information extraction, such as parsing molecules or reactions from text or figures. We then integrate the information from these modules using chemistry-informed algorithms, allowing for the extraction of fine-grained reaction data from reaction condition and substrate scope investigations. Our machine learning models attain state-of-the-art performance when evaluated individually, and we meticulously annotate a challenging dataset of reaction schemes with R-groups to evaluate our pipeline as a whole, achieving an F1 score of 69.5%. Additionally, the reaction extraction results of \ours attain an accuracy score of 64.3% when directly compared against the Reaxys chemical database. We provide OpenChemIE freely to the public as an open-source package, as well as through a web interface.

This paper focuses on using natural language descriptions to enhance predictive models in the chemistry field. Conventionally, chemoinformatics models are trained with extensive structured data manually extracted from the literature. In this paper, we introduce TextReact, a novel method that directly augments predictive chemistry with texts retrieved from the literature. TextReact retrieves text descriptions relevant for a given chemical reaction, and then aligns them with the molecular representation of the reaction. This alignment is enhanced via an auxiliary masked LM objective incorporated in the predictor training. We empirically validate the framework on two chemistry tasks: reaction condition recommendation and one-step retrosynthesis. By leveraging text retrieval, TextReact significantly outperforms state-of-the-art chemoinformatics models trained solely on molecular data.

Prompting a pretrained language model with natural language patterns has been proved effective for natural language understanding (NLU). However, our preliminary study reveals that manual discrete prompts often lead to unstable performance -- e.g., changing a single word in the prompt might result in substantial performance drop. We propose a novel method P-Tuning that employs trainable continuous prompt embeddings in concatenation with discrete prompts. Empirically, P-Tuning not only stabilizes training by minimizing the gap between various discrete prompts, but also improves performance by a sizeable margin on a wide range of NLU tasks including LAMA and SuperGLUE. P-Tuning is generally effective for both frozen and tuned language models, under both the fully-supervised and few-shot settings.

Reaction diagram parsing is the task of extracting reaction schemes from a diagram in the chemistry literature. The reaction diagrams can be arbitrarily complex, thus robustly parsing them into structured data is an open challenge. In this paper, we present RxnScribe, a machine learning model for parsing reaction diagrams of varying styles. We formulate this structured prediction task with a sequence generation approach, which condenses the traditional pipeline into an end-to-end model. We train RxnScribe on a dataset of 1,378 diagrams and evaluate it with cross validation, achieving an 80.0% soft match F1 score, with significant improvements over previous models. Our code and data are publicly available at https://github.com/thomas0809/RxnScribe.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

There have been various types of pretraining architectures including autoregressive models (e.g., GPT), autoencoding models (e.g., BERT), and encoder-decoder models (e.g., T5). On the other hand, NLP tasks are different in nature, with three main categories being classification, unconditional generation, and conditional generation. However, none of the pretraining frameworks performs the best for all tasks, which introduces inconvenience for model development and selection. We propose a novel pretraining framework GLM (General Language Model) to address this challenge. Compared to previous work, our architecture has three major benefits: (1) it performs well on classification, unconditional generation, and conditional generation tasks with one single pretrained model; (2) it outperforms BERT-like models on classification due to improved pretrain-finetune consistency; (3) it naturally handles variable-length blank filling which is crucial for many downstream tasks. Empirically, GLM substantially outperforms BERT on the SuperGLUE natural language understanding benchmark with the same amount of pre-training data. Moreover, GLM with 1.25x parameters of BERT-Large achieves the best performance in NLU, conditional and unconditional generation at the same time, which demonstrates its generalizability to different downstream tasks.

We study the extent to which we can infer users' geographical locations from social media. Location inference from social media can benefit many applications, such as disaster management, targeted advertising, and news content tailoring. The challenges, however, lie in the limited amount of labeled data and the large scale of social networks. In this paper, we formalize the problem of inferring location from social media into a semi-supervised factor graph model (SSFGM). The model provides a probabilistic framework in which various sources of information (e.g., content and social network) can be combined together. We design a two-layer neural network to learn feature representations, and incorporate the learned latent features into SSFGM. To deal with the large-scale problem, we propose a Two-Chain Sampling (TCS) algorithm to learn SSFGM. The algorithm achieves a good trade-off between accuracy and efficiency. Experiments on Twitter and Weibo show that the proposed TCS algorithm for SSFGM can substantially improve the inference accuracy over several state-of-the-art methods. More importantly, TCS achieves over 100x speedup comparing with traditional propagation-based methods (e.g., loopy belief propagation).

In online question-and-answer (QA) websites like Quora, one central issue is to find (invite) users who are able to provide answers to a given question and at the same time would be unlikely to say "no" to the invitation. The challenge is how to trade off the matching degree between users' expertise and the question topic, and the likelihood of positive response from the invited users. In this paper, we formally formulate the problem and develop a weakly supervised factor graph (WeakFG) model to address the problem. The model explicitly captures expertise matching degree between questions and users. To model the likelihood that an invited user is willing to answer a specific question, we incorporate a set of correlations based on social identity theory into the WeakFG model. We use two different genres of datasets: QA-Expert and Paper-Reviewer, to validate the proposed model. Our experimental results show that the proposed model can significantly outperform (+1.5-10.7% by MAP) the state-of-the-art algorithms for matching users (experts) with community questions. We have also developed an online system to further demonstrate the advantages of the proposed method.