A Transformer-based Generative Model for De Novo Molecular Design

Deep learning draws a lot of attention as a new way of generating unseen structures for drug discovery. We propose a Transformer-based deep model for de novo target-specific molecular design. The proposed method is capable of generating both drug-like compounds and target-specific compounds. The latter are generated by enforcing different keys and values of the multi-head attention for each target. We allow the generation of SMILES strings to be conditional on the specified target. The sampled compounds largely occupy the real target-specific data's chemical space and also cover a significant fraction of novel compounds.

RFID-Based Indoor Spatial Query Evaluation with Bayesian Filtering Techniques

People spend a significant amount of time in indoor spaces (e.g., office buildings, subway systems, etc.) in their daily lives. Therefore, it is important to develop efficient indoor spatial query algorithms for supporting various location-based applications. However, indoor spaces differ from outdoor spaces because users have to follow the indoor floor plan for their movements. In addition, positioning in indoor environments is mainly based on sensing devices (e.g., RFID readers) rather than GPS devices. Consequently, we cannot apply existing spatial query evaluation techniques devised for outdoor environments for this new challenge. Because Bayesian filtering techniques can be employed to estimate the state of a system that changes over time using a sequence of noisy measurements made on the system, in this research, we propose the Bayesian filtering-based location inference methods as the basis for evaluating indoor spatial queries with noisy RFID raw data. Furthermore, two novel models, indoor walking graph model and anchor point indexing model, are created for tracking object locations in indoor environments. Based on the inference method and tracking models, we develop innovative indoor range and k nearest neighbor (kNN) query algorithms. We validate our solution through use of both synthetic data and real-world data. Our experimental results show that the proposed algorithms can evaluate indoor spatial queries effectively and efficiently. We open-source the code, data, and floor plan at https://github.com/DataScienceLab18/IndoorToolKit.

SpatialNLI: A Spatial Domain Natural Language Interface to Databases Using Spatial Comprehension

A natural language interface (NLI) to databases is an interface that translates a natural language question to a structured query that is executable by database management systems (DBMS). However, an NLI that is trained in the general domain is hard to apply in the spatial domain due to the idiosyncrasy and expressiveness of the spatial questions. Inspired by the machine comprehension model, we propose a spatial comprehension model that is able to recognize the meaning of spatial entities based on the semantics of the context. The spatial semantics learned from the spatial comprehension model is then injected to the natural language question to ease the burden of capturing the spatial-specific semantics. With our spatial comprehension model and information injection, our NLI for the spatial domain, named SpatialNLI, is able to capture the semantic structure of the question and translate it to the corresponding syntax of an executable query accurately. We also experimentally ascertain that SpatialNLI outperforms state-of-the-art methods.

A Transfer-Learnable Natural Language Interface for Databases

Relational database management systems (RDBMSs) are powerful because they are able to optimize and answer queries against any relational database. A natural language interface (NLI) for a database, on the other hand, is tailored to support that specific database. In this work, we introduce a general purpose transfer-learnable NLI with the goal of learning one model that can be used as NLI for any relational database. We adopt the data management principle of separating data and its schema, but with the additional support for the idiosyncrasy and complexity of natural languages. Specifically, we introduce an automatic annotation mechanism that separates the schema and the data, where the schema also covers knowledge about natural language. Furthermore, we propose a customized sequence model that translates annotated natural language queries to SQL statements. We show in experiments that our approach outperforms previous NLI methods on the WikiSQL dataset and the model we learned can be applied to another benchmark dataset OVERNIGHT without retraining.

Adversarial Texts with Gradient Methods

Adversarial samples for images have been extensively studied in the literature. Among many of the attacking methods, gradient-based methods are both effective and easy to compute. In this work, we propose a framework to adapt the gradient attacking methods on images to text domain. The main difficulties for generating adversarial texts with gradient methods are i) the input space is discrete, which makes it difficult to accumulate small noise directly in the inputs, and ii) the measurement of the quality of the adversarial texts is difficult. We tackle the first problem by searching for adversarials in the embedding space and then reconstruct the adversarial texts via nearest neighbor search. For the latter problem, we employ the Word Mover's Distance (WMD) to quantify the quality of adversarial texts. Through extensive experiments on three datasets, IMDB movie reviews, Reuters-2 and Reuters-5 newswires, we show that our framework can leverage gradient attacking methods to generate very high-quality adversarial texts that are only a few words different from the original texts. There are many cases where we can change one word to alter the label of the whole piece of text. We successfully incorporate FGM and DeepFool into our framework. In addition, we empirically show that WMD is closely related to the quality of adversarial texts.