Gated Graph Recursive Neural Networks for Molecular Property Prediction

Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule properties, however, because of the heavy computational cost, it is difficult to search a huge number of potential chemical compounds. Machine learning methods for molecular modeling are attractive alternatives, however, the development of expressive, accurate, and scalable graph neural networks for learning molecular representations is still challenging. In this work, we propose a simple and powerful graph neural networks for molecular property prediction. We model a molecular as a directed complete graph in which each atom has a spatial position, and introduce a recursive neural network with simple gating function. We also feed input embeddings for every layers as skip connections to accelerate the training. Experimental results show that our model achieves the state-of-the-art performance on the standard benchmark dataset for molecular property prediction.

Improving Multi-Word Entity Recognition for Biomedical Texts

Biomedical Named Entity Recognition (BioNER) is a crucial step for analyzing Biomedical texts, which aims at extracting biomedical named entities from a given text. Different supervised machine learning algorithms have been applied for BioNER by various researchers. The main requirement of these approaches is an annotated dataset used for learning the parameters of machine learning algorithms. Segment Representation (SR) models comprise of different tag sets used for representing the annotated data, such as IOB2, IOE2 and IOBES. In this paper, we propose an extension of IOBES model to improve the performance of BioNER. The proposed SR model, FROBES, improves the representation of multi-word entities. We used Bidirectional Long Short-Term Memory (BiLSTM) network; an instance of Recurrent Neural Networks (RNN), to design a baseline system for BioNER and evaluated the new SR model on two datasets, i2b2/VA 2010 challenge dataset and JNLPBA 2004 shared task dataset. The proposed SR model outperforms other models for multi-word entities with length greater than two. Further, the outputs of different SR models have been combined using majority voting ensemble method which outperforms the baseline models performance.

Playing by the Book: Towards Agent-based Narrative Understanding through Role-playing and Simulation

Understanding procedural text requires tracking entities, actions and effects as the narrative unfolds (often implicitly). We focus on the challenging real-world problem of structured narrative extraction in the materials science domain, where language is highly specialized and suitable annotated data is not publicly available. We propose an approach, Text2Quest, where procedural text is interpreted as instructions for an interactive game. A reinforcement-learning agent completes the game by understanding and executing the procedure correctly, in a text-based simulated lab environment. The framework is intended to be more broadly applicable to other domain-specific and data-scarce settings. We conclude with a discussion of challenges and interesting potential extensions enabled by the agent-based perspective.

Reduction of Parameter Redundancy in Biaffine Classifiers with Symmetric and Circulant Weight Matrices

Currently, the biaffine classifier has been attracting attention as a method to introduce an attention mechanism into the modeling of binary relations. For instance, in the field of dependency parsing, the Deep Biaffine Parser by Dozat and Manning has achieved state-of-the-art performance as a graph-based dependency parser on the English Penn Treebank and CoNLL 2017 shared task. On the other hand, it is reported that parameter redundancy in the weight matrix in biaffine classifiers, which has O(n^2) parameters, results in overfitting (n is the number of dimensions). In this paper, we attempted to reduce the parameter redundancy by assuming either symmetry or circularity of weight matrices. In our experiments on the CoNLL 2017 shared task dataset, our model achieved better or comparable accuracy on most of the treebanks with more than 16% parameter reduction.

A Fast and Easy Regression Technique for k-NN Classification Without Using Negative Pairs

This paper proposes an inexpensive way to learn an effective dissimilarity function to be used for $k$-nearest neighbor ($k$-NN) classification. Unlike Mahalanobis metric learning methods that map both query (unlabeled) objects and labeled objects to new coordinates by a single transformation, our method learns a transformation of labeled objects to new points in the feature space whereas query objects are kept in their original coordinates. This method has several advantages over existing distance metric learning methods: (i) In experiments with large document and image datasets, it achieves $k$-NN classification accuracy better than or at least comparable to the state-of-the-art metric learning methods. (ii) The transformation can be learned efficiently by solving a standard ridge regression problem. For document and image datasets, training is often more than two orders of magnitude faster than the fastest metric learning methods tested. This speed-up is also due to the fact that the proposed method eliminates the optimization over "negative" object pairs, i.e., objects whose class labels are different. (iii) The formulation has a theoretical justification in terms of reducing hubness in data.

Interpretable Adversarial Perturbation in Input Embedding Space for Text

Following great success in the image processing field, the idea of adversarial training has been applied to tasks in the natural language processing (NLP) field. One promising approach directly applies adversarial training developed in the image processing field to the input word embedding space instead of the discrete input space of texts. However, this approach abandons such interpretability as generating adversarial texts to significantly improve the performance of NLP tasks. This paper restores interpretability to such methods by restricting the directions of perturbations toward the existing words in the input embedding space. As a result, we can straightforwardly reconstruct each input with perturbations to an actual text by considering the perturbations to be the replacement of words in the sentence while maintaining or even improving the task performance.

Knowledge Transfer for Out-of-Knowledge-Base Entities: A Graph Neural Network Approach

Knowledge base completion (KBC) aims to predict missing information in a knowledge base.In this paper, we address the out-of-knowledge-base (OOKB) entity problem in KBC:how to answer queries concerning test entities not observed at training time. Existing embedding-based KBC models assume that all test entities are available at training time, making it unclear how to obtain embeddings for new entities without costly retraining. To solve the OOKB entity problem without retraining, we use graph neural networks (Graph-NNs) to compute the embeddings of OOKB entities, exploiting the limited auxiliary knowledge provided at test time.The experimental results show the effectiveness of our proposed model in the OOKB setting.Additionally, in the standard KBC setting in which OOKB entities are not involved, our model achieves state-of-the-art performance on the WordNet dataset. The code and dataset are available at https://github.com/takuo-h/GNN-for-OOKB

A* CCG Parsing with a Supertag and Dependency Factored Model

We propose a new A* CCG parsing model in which the probability of a tree is decomposed into factors of CCG categories and its syntactic dependencies both defined on bi-directional LSTMs. Our factored model allows the precomputation of all probabilities and runs very efficiently, while modeling sentence structures explicitly via dependencies. Our model achieves the state-of-the-art results on English and Japanese CCG parsing.

An Algebraic Formalization of Forward and Forward-backward Algorithms

In this paper, we propose an algebraic formalization of the two important classes of dynamic programming algorithms called forward and forward-backward algorithms. They are generalized extensively in this study so that a wide range of other existing algorithms is subsumed. Forward algorithms generalized in this study subsume the ordinary forward algorithm on trellises for sequence labeling, the inside algorithm on derivation forests for CYK parsing, a unidirectional message passing on acyclic factor graphs, the forward mode of automatic differentiation on computation graphs with addition and multiplication, and so on. In addition, we reveal algebraic structures underlying complicated computation with forward algorithms. By the aid of the revealed algebraic structures, we also propose a systematic framework to design complicated variants of forward algorithms. Forward-backward algorithms generalized in this study subsume the ordinary forward-backward algorithm on trellises for sequence labeling, the inside-outside algorithm on derivation forests for CYK parsing, the sum-product algorithm on acyclic factor graphs, the reverse mode of automatic differentiation (a.k.a. back propagation) on computation graphs with addition and multiplication, and so on. We also propose an algebraic characterization of what can be computed by forward-backward algorithms and elucidate the relationship between forward and forward-backward algorithms.

Dependency Parsing with LSTMs: An Empirical Evaluation

We propose a transition-based dependency parser using Recurrent Neural Networks with Long Short-Term Memory (LSTM) units. This extends the feedforward neural network parser of Chen and Manning (2014) and enables modelling of entire sequences of shift/reduce transition decisions. On the Google Web Treebank, our LSTM parser is competitive with the best feedforward parser on overall accuracy and notably achieves more than 3% improvement for long-range dependencies, which has proved difficult for previous transition-based parsers due to error propagation and limited context information. Our findings additionally suggest that dropout regularisation on the embedding layer is crucial to improve the LSTM's generalisation.