BioBLP: A Modular Framework for Learning on Multimodal Biomedical Knowledge Graphs

Knowledge graphs (KGs) are an important tool for representing complex relationships between entities in the biomedical domain. Several methods have been proposed for learning embeddings that can be used to predict new links in such graphs. Some methods ignore valuable attribute data associated with entities in biomedical KGs, such as protein sequences, or molecular graphs. Other works incorporate such data, but assume that entities can be represented with the same data modality. This is not always the case for biomedical KGs, where entities exhibit heterogeneous modalities that are central to their representation in the subject domain. We propose a modular framework for learning embeddings in KGs with entity attributes, that allows encoding attribute data of different modalities while also supporting entities with missing attributes. We additionally propose an efficient pretraining strategy for reducing the required training runtime. We train models using a biomedical KG containing approximately 2 million triples, and evaluate the performance of the resulting entity embeddings on the tasks of link prediction, and drug-protein interaction prediction, comparing against methods that do not take attribute data into account. In the standard link prediction evaluation, the proposed method results in competitive, yet lower performance than baselines that do not use attribute data. When evaluated in the task of drug-protein interaction prediction, the method compares favorably with the baselines. We find settings involving low degree entities, which make up for a substantial amount of the set of entities in the KG, where our method outperforms the baselines. Our proposed pretraining strategy yields significantly higher performance while reducing the required training runtime. Our implementation is available at https://github.com/elsevier-AI-Lab/BioBLP .

Distributional Reinforcement Learning with Dual Expectile-Quantile Regression

Successful applications of distributional reinforcement learning with quantile regression prompt a natural question: can we use other statistics to represent the distribution of returns? In particular, expectile regression is known to be more efficient than quantile regression for approximating distributions, especially on extreme values, and by providing a straightforward estimator of the mean it is a natural candidate for reinforcement learning. Prior work has answered this question positively in the case of expectiles, with the major caveat that expensive computations must be performed to ensure convergence. In this work, we propose a dual expectile-quantile approach which solves the shortcomings of previous work while leveraging the complementary properties of expectiles and quantiles. Our method outperforms both quantile-based and expectile-based baselines on the MuJoCo continuous control benchmark.

Self-Contained Entity Discovery from Captioned Videos

This paper introduces the task of visual named entity discovery in videos without the need for task-specific supervision or task-specific external knowledge sources. Assigning specific names to entities (e.g. faces, scenes, or objects) in video frames is a long-standing challenge. Commonly, this problem is addressed as a supervised learning objective by manually annotating faces with entity labels. To bypass the annotation burden of this setup, several works have investigated the problem by utilizing external knowledge sources such as movie databases. While effective, such approaches do not work when task-specific knowledge sources are not provided and can only be applied to movies and TV series. In this work, we take the problem a step further and propose to discover entities in videos from videos and corresponding captions or subtitles. We introduce a three-stage method where we (i) create bipartite entity-name graphs from frame-caption pairs, (ii) find visual entity agreements, and (iii) refine the entity assignment through entity-level prototype construction. To tackle this new problem, we outline two new benchmarks SC-Friends and SC-BBT based on the Friends and Big Bang Theory TV series. Experiments on the benchmarks demonstrate the ability of our approach to discover which named entity belongs to which face or scene, with an accuracy close to a supervised oracle, just from the multimodal information present in videos. Additionally, our qualitative examples show the potential challenges of self-contained discovery of any visual entity for future work. The code and the data are available on GitHub.

E2EG: End-to-End Node Classification Using Graph Topology and Text-based Node Attributes

Node classification utilizing text-based node attributes has many real-world applications, ranging from prediction of paper topics in academic citation graphs to classification of user characteristics in social media networks. State-of-the-art node classification frameworks, such as GIANT, use a two-stage pipeline: first embedding the text attributes of graph nodes then feeding the resulting embeddings into a node classification model. In this paper, we eliminate these two stages and instead develop an end-to-end node classification model that builds upon GIANT, called End-to-End-GIANT (E2EG). The tandem utilization of a main and an auxiliary classification objectives in our approach results in a more robust model, thus enabling the BERT backbone to be switched out for a distilled encoder with a 25% - 40% reduction in the number of parameters. Moreover, the end-to-end nature of the model increases ease of use, as it avoids the need of chaining multiple models for node classification. Compared to a GIANT+MLP baseline on the ogbn-arxiv and ogbn-products datasets, our model is able to obtain slightly better accuracy in the transductive setting (+0.5%), while reducing model training time by up to 40%. Our model is also applicable in the inductive setting, outperforming GIANT+MLP by up to +2.23%.

GLDQN: Explicitly Parameterized Quantile Reinforcement Learning for Waste Reduction

We study the problem of restocking a grocery store's inventory with perishable items over time, from a distributional point of view. The objective is to maximize sales while minimizing waste, with uncertainty about the actual consumption by costumers. This problem is of a high relevance today, given the growing demand for food and the impact of food waste on the environment, the economy, and purchasing power. We frame inventory restocking as a new reinforcement learning task that exhibits stochastic behavior conditioned on the agent's actions, making the environment partially observable. We introduce a new reinforcement learning environment based on real grocery store data and expert knowledge. This environment is highly stochastic, and presents a unique challenge for reinforcement learning practitioners. We show that uncertainty about the future behavior of the environment is not handled well by classical supply chain algorithms, and that distributional approaches are a good way to account for the uncertainty. We also present GLDQN, a new distributional reinforcement learning algorithm that learns a generalized lambda distribution over the reward space. We show that GLDQN outperforms other distributional reinforcement learning approaches in our partially observable environments, in both overall reward and generated waste.

Making Table Understanding Work in Practice

Understanding the semantics of tables at scale is crucial for tasks like data integration, preparation, and search. Table understanding methods aim at detecting a table's topic, semantic column types, column relations, or entities. With the rise of deep learning, powerful models have been developed for these tasks with excellent accuracy on benchmarks. However, we observe that there exists a gap between the performance of these models on these benchmarks and their applicability in practice. In this paper, we address the question: what do we need for these models to work in practice? We discuss three challenges of deploying table understanding models and propose a framework to address them. These challenges include 1) difficulty in customizing models to specific domains, 2) lack of training data for typical database tables often found in enterprises, and 3) lack of confidence in the inferences made by models. We present SigmaTyper which implements this framework for the semantic column type detection task. SigmaTyper encapsulates a hybrid model trained on GitTables and integrates a lightweight human-in-the-loop approach to customize the model. Lastly, we highlight avenues for future research that further close the gap towards making table understanding effective in practice.

Relational Graph Convolutional Networks: A Closer Look

In this paper, we describe a reproduction of the Relational Graph Convolutional Network (RGCN). Using our reproduction, we explain the intuition behind the model. Our reproduction results empirically validate the correctness of our implementations using benchmark Knowledge Graph datasets on node classification and link prediction tasks. Our explanation provides a friendly understanding of the different components of the RGCN for both users and researchers extending the RGCN approach. Furthermore, we introduce two new configurations of the RGCN that are more parameter efficient. The code and datasets are available at https://github.com/thiviyanT/torch-rgcn.

GitTables: A Large-Scale Corpus of Relational Tables

The practical success of deep learning has sparked interest in improving relational table tasks, like data search, with models trained on large table corpora. Existing corpora primarily contain tables extracted from HTML pages, limiting the capability to represent offline database tables. To train and evaluate high-capacity models for applications beyond the Web, we need additional resources with tables that resemble relational database tables. Here we introduce GitTables, a corpus of currently 1.7M relational tables extracted from GitHub. Our continuing curation aims at growing the corpus to at least 20M tables. We annotate table columns in GitTables with more than 2K different semantic types from Schema.org and DBpedia. Our column annotations consist of semantic types, hierarchical relations, range types and descriptions. The corpus is available at https://gittables.github.io. Our analysis of GitTables shows that its structure, content, and topical coverage differ significantly from existing table corpora. We evaluate our annotation pipeline on hand-labeled tables from the T2Dv2 benchmark and find that our approach provides results on par with human annotations. We demonstrate a use case of GitTables by training a semantic type detection model on it and obtain high prediction accuracy. We also show that the same model trained on tables from theWeb generalizes poorly.

Reinforcement Learning based Collective Entity Alignment with Adaptive Features

Entity alignment (EA) is the task of identifying the entities that refer to the same real-world object but are located in different knowledge graphs (KGs). For entities to be aligned, existing EA solutions treat them separately and generate alignment results as ranked lists of entities on the other side. Nevertheless, this decision-making paradigm fails to take into account the interdependence among entities. Although some recent efforts mitigate this issue by imposing the 1-to-1 constraint on the alignment process, they still cannot adequately model the underlying interdependence and the results tend to be sub-optimal. To fill in this gap, in this work, we delve into the dynamics of the decision-making process, and offer a reinforcement learning (RL) based model to align entities collectively. Under the RL framework, we devise the coherence and exclusiveness constraints to characterize the interdependence and restrict collective alignment. Additionally, to generate more precise inputs to the RL framework, we employ representative features to capture different aspects of the similarity between entities in heterogeneous KGs, which are integrated by an adaptive feature fusion strategy. Our proposal is evaluated on both cross-lingual and mono-lingual EA benchmarks and compared against state-of-the-art solutions. The empirical results verify its effectiveness and superiority.

Towards Olfactory Information Extraction from Text: A Case Study on Detecting Smell Experiences in Novels

Environmental factors determine the smells we perceive, but societal factors factors shape the importance, sentiment and biases we give to them. Descriptions of smells in text, or as we call them `smell experiences', offer a window into these factors, but they must first be identified. To the best of our knowledge, no tool exists to extract references to smell experiences from text. In this paper, we present two variations on a semi-supervised approach to identify smell experiences in English literature. The combined set of patterns from both implementations offer significantly better performance than a keyword-based baseline.