Domain Representative Keywords Selection: A Probabilistic Approach

We propose a probabilistic approach to select a subset of a \textit{target domain representative keywords} from a candidate set, contrasting with a context domain. Such a task is crucial for many downstream tasks in natural language processing. To contrast the target domain and the context domain, we adapt the \textit{two-component mixture model} concept to generate a distribution of candidate keywords. It provides more importance to the \textit{distinctive} keywords of the target domain than common keywords contrasting with the context domain. To support the \textit{representativeness} of the selected keywords towards the target domain, we introduce an \textit{optimization algorithm} for selecting the subset from the generated candidate distribution. We have shown that the optimization algorithm can be efficiently implemented with a near-optimal approximation guarantee. Finally, extensive experiments on multiple domains demonstrate the superiority of our approach over other baselines for the tasks of keyword summary generation and trending keywords selection.

Improving Candidate Retrieval with Entity Profile Generation for Wikidata Entity Linking

Entity linking (EL) is the task of linking entity mentions in a document to referent entities in a knowledge base (KB). Many previous studies focus on Wikipedia-derived KBs. There is little work on EL over Wikidata, even though it is the most extensive crowdsourced KB. The scale of Wikidata can open up many new real-world applications, but its massive number of entities also makes EL challenging. To effectively narrow down the search space, we propose a novel candidate retrieval paradigm based on entity profiling. Wikidata entities and their textual fields are first indexed into a text search engine (e.g., Elasticsearch). During inference, given a mention and its context, we use a sequence-to-sequence (seq2seq) model to generate the profile of the target entity, which consists of its title and description. We use the profile to query the indexed search engine to retrieve candidate entities. Our approach complements the traditional approach of using a Wikipedia anchor-text dictionary, enabling us to further design a highly effective hybrid method for candidate retrieval. Combined with a simple cross-attention reranker, our complete EL framework achieves state-of-the-art results on three Wikidata-based datasets and strong performance on TACKBP-2010.

BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Residual Convolutional Neural Networks

Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved competitive results on many datasets, they are computationally expensive and contain about 110M parameters. Little is known about the factors contributing to their impressive performance and whether the over-parameterization is needed. In this work, we shed some light on the inner working mechanisms of these large BERT-based models. Through a set of probing experiments, we have found that the entity linking performance only changes slightly when the input word order is shuffled or when the attention scope is limited to a fixed window size. From these observations, we propose an efficient convolutional neural network with residual connections for biomedical entity linking. Because of the sparse connectivity and weight sharing properties, our model has a small number of parameters and is highly efficient. On five public datasets, our model achieves comparable or even better linking accuracy than the state-of-the-art BERT-based models while having about 60 times fewer parameters.

Fine-Grained Chemical Entity Typing with Multimodal Knowledge Representation

Automated knowledge discovery from trending chemical literature is essential for more efficient biomedical research. How to extract detailed knowledge about chemical reactions from the core chemistry literature is a new emerging challenge that has not been well studied. In this paper, we study the new problem of fine-grained chemical entity typing, which poses interesting new challenges especially because of the complex name mentions frequently occurring in chemistry literature and graphic representation of entities. We introduce a new benchmark data set (CHEMET) to facilitate the study of the new task and propose a novel multi-modal representation learning framework to solve the problem of fine-grained chemical entity typing by leveraging external resources with chemical structures and using cross-modal attention to learn effective representation of text in the chemistry domain. Experiment results show that the proposed framework outperforms multiple state-of-the-art methods.

Joint Biomedical Entity and Relation Extraction with Knowledge-Enhanced Collective Inference

Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential growth of biomedical publications, models that do not go beyond their fixed set of parameters will likely fall behind. Inspired by how humans look up relevant information to comprehend a scientific text, we present a novel framework that utilizes external knowledge for joint entity and relation extraction named KECI (Knowledge-Enhanced Collective Inference). Given an input text, KECI first constructs an initial span graph representing its initial understanding of the text. It then uses an entity linker to form a knowledge graph containing relevant background knowledge for the the entity mentions in the text. To make the final predictions, KECI fuses the initial span graph and the knowledge graph into a more refined graph using an attention mechanism. KECI takes a collective approach to link mention spans to entities by integrating global relational information into local representations using graph convolutional networks. Our experimental results show that the framework is highly effective, achieving new state-of-the-art results in two different benchmark datasets: BioRelEx (binding interaction detection) and ADE (adverse drug event extraction). For example, KECI achieves absolute improvements of 4.59% and 4.91% in F1 scores over the state-of-the-art on the BioRelEx entity and relation extraction tasks.

Towards Dark Jargon Interpretation in Underground Forums

Dark jargons are benign-looking words that have hidden, sinister meanings and are used by participants of underground forums for illicit behavior. For example, the dark term "rat" is often used in lieu of "Remote Access Trojan". In this work we present a novel method towards automatically identifying and interpreting dark jargons. We formalize the problem as a mapping from dark words to "clean" words with no hidden meaning. Our method makes use of interpretable representations of dark and clean words in the form of probability distributions over a shared vocabulary. In our experiments we show our method to be effective in terms of dark jargon identification, as it outperforms another related method on simulated data. Using manual evaluation, we show that our method is able to detect dark jargons in a real-world underground forum dataset.

A Level-wise Taxonomic Perspective on Automated Machine Learning to Date and Beyond: Challenges and Opportunities

Automated machine learning (AutoML) is essentially automating the process of applying machine learning to real-world problems. The primary goals of AutoML tools are to provide methods and processes to make Machine Learning available for non-Machine Learning experts (domain experts), to improve efficiency of Machine Learning and to accelerate research on Machine Learning. Although automation and efficiency are some of AutoML's main selling points, the process still requires a surprising level of human involvement. A number of vital steps of the machine learning pipeline, including understanding the attributes of domain-specific data, defining prediction problems, creating a suitable training data set etc. still tend to be done manually by a data scientist on an ad-hoc basis. Often, this process requires a lot of back-and-forth between the data scientist and domain experts, making the whole process more difficult and inefficient. Altogether, AutoML systems are still far from a "real automatic system". In this review article, we present a level-wise taxonomic perspective on AutoML systems to-date and beyond, i.e., we introduce a new classification system with seven levels to distinguish AutoML systems based on their level of autonomy. We first start with a discussion on how an end-to-end Machine learning pipeline actually looks like and which sub-tasks of Machine learning Pipeline has indeed been automated so far. Next, we highlight the sub-tasks which are still done manually by a data-scientist in most cases and how that limits a domain expert's access to Machine learning. Then, we introduce the novel level-based taxonomy of AutoML systems and define each level according to their scope of automation support. Finally, we provide a road-map of future research endeavor in the area of AutoML and discuss some important challenges in achieving this ambitious goal.