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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., Comment: To be submitted to the Journal of Chemical Information and Modeling

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., Comment: EMNLP 2023

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., Comment: To be published in the Journal of Chemical Information and Modeling

Multi-vector retrieval models improve over single-vector dual encoders on many information retrieval tasks. In this paper, we cast the multi-vector retrieval problem as sparse alignment between query and document tokens. We propose AligneR, a novel multi-vector retrieval model that learns sparsified pairwise alignments between query and document tokens (e.g. `dog' vs. `puppy') and per-token unary saliences reflecting their relative importance for retrieval. We show that controlling the sparsity of pairwise token alignments often brings significant performance gains. While most factoid questions focusing on a specific part of a document require a smaller number of alignments, others requiring a broader understanding of a document favor a larger number of alignments. Unary saliences, on the other hand, decide whether a token ever needs to be aligned with others for retrieval (e.g. `kind' from `kind of currency is used in new zealand}'). With sparsified unary saliences, we are able to prune a large number of query and document token vectors and improve the efficiency of multi-vector retrieval. We learn the sparse unary saliences with entropy-regularized linear programming, which outperforms other methods to achieve sparsity. In a zero-shot setting, AligneR scores 51.1 points nDCG@10, achieving a new retriever-only state-of-the-art on 13 tasks in the BEIR benchmark. In addition, adapting pairwise alignments with a few examples (<= 8) further improves the performance up to 15.7 points nDCG@10 for argument retrieval tasks. The unary saliences of AligneR helps us to keep only 20% of the document token representations with minimal performance loss. We further show that our model often produces interpretable alignments and significantly improves its performance when initialized from larger language models.

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., Comment: To be published in the Journal of Chemical Information and Modeling

The few-shot natural language understanding (NLU) task has attracted much recent attention. However, prior methods have been evaluated under a disparate set of protocols, which hinders fair comparison and measuring progress of the field. To address this issue, we introduce an evaluation framework that improves previous evaluation procedures in three key aspects, i.e., test performance, dev-test correlation, and stability. Under this new evaluation framework, we re-evaluate several state-of-the-art few-shot methods for NLU tasks. Our framework reveals new insights: (1) both the absolute performance and relative gap of the methods were not accurately estimated in prior literature; (2) no single method dominates most tasks with consistent performance; (3) improvements of some methods diminish with a larger pretrained model; and (4) gains from different methods are often complementary and the best combined model performs close to a strong fully-supervised baseline. We open-source our toolkit, FewNLU, that implements our evaluation framework along with a number of state-of-the-art methods.

There have been various types of pretraining architectures including autoencoding models (e.g., BERT), autoregressive models (e.g., GPT), and encoder-decoder models (e.g., T5). However, none of the pretraining frameworks performs the best for all tasks of three main categories including natural language understanding (NLU), unconditional generation, and conditional generation. We propose a General Language Model (GLM) based on autoregressive blank infilling to address this challenge. GLM improves blank filling pretraining by adding 2D positional encodings and allowing an arbitrary order to predict spans, which results in performance gains over BERT and T5 on NLU tasks. Meanwhile, GLM can be pretrained for different types of tasks by varying the number and lengths of blanks. On a wide range of tasks across NLU, conditional and unconditional generation, GLM outperforms BERT, T5, and GPT given the same model sizes and data, and achieves the best performance from a single pretrained model with 1.25x parameters of BERT Large , demonstrating its generalizability to different downstream tasks., Comment: to be published in ACL 2022. 16 pages, 4 figures

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.

Most modern Information Extraction (IE) systems are implemented as sequential taggers and only model local dependencies. Non-local and non-sequential context is, however, a valuable source of information to improve predictions. In this paper, we introduce GraphIE, a framework that operates over a graph representing a broad set of dependencies between textual units (i.e. words or sentences). The algorithm propagates information between connected nodes through graph convolutions, generating a richer representation that can be exploited to improve word-level predictions. Evaluation on three different tasks --- namely textual, social media and visual information extraction --- shows that GraphIE consistently outperforms the state-of-the-art sequence tagging model by a significant margin., Comment: NAACL 2019

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., Comment: IJCAI 2018

Measuring research impact and ranking academic achievement are important and challenging problems. Having an objective picture of research institution is particularly valuable for students, parents and funding agencies, and also attracts attention from government and industry. KDD Cup 2016 proposes the paper acceptance rank prediction task, in which the participants are asked to rank the importance of institutions based on predicting how many of their papers will be accepted at the 8 top conferences in computer science. In our work, we adopt a three-step feature engineering method, including basic features definition, finding similar conferences to enhance the feature set, and dimension reduction using PCA. We propose three ranking models and the ensemble methods for combining such models. Our experiment verifies the effectiveness of our approach. In KDD Cup 2016, we achieved the overall rank of the 2nd place., Comment: 2nd place winner report of KDD Cup 2016. More details can be found at https://kddcup2016.azurewebsites.net