CERM: Context-aware Literature-based Discovery via Sentiment Analysis

Driven by the abundance of biomedical publications, we introduce a sentiment analysis task to understand food-health relationship. Prior attempts to incorporate health into recipe recommendation and analysis systems have primarily focused on ingredient nutritional components or utilized basic computational models trained on curated labeled data. Enhanced models that capture the inherent relationship between food ingredients and biomedical concepts can be more beneficial for food-related research, given the wealth of information in biomedical texts. Considering the costly data labeling process, these models should effectively utilize both labeled and unlabeled data. This paper introduces Entity Relationship Sentiment Analysis (ERSA), a new task that captures the sentiment of a text based on an entity pair. ERSA extends the widely studied Aspect Based Sentiment Analysis (ABSA) task. Specifically, our study concentrates on the ERSA task applied to biomedical texts, focusing on (entity-entity) pairs of biomedical and food concepts. ERSA poses a significant challenge compared to traditional sentiment analysis tasks, as sentence sentiment may not align with entity relationship sentiment. Additionally, we propose CERM, a semi-supervised architecture that combines different word embeddings to enhance the encoding of the ERSA task. Experimental results showcase the model's efficiency across diverse learning scenarios.

Temporal Positive-unlabeled Learning for Biomedical Hypothesis Generation via Risk Estimation

Understanding the relationships between biomedical terms like viruses, drugs, and symptoms is essential in the fight against diseases. Many attempts have been made to introduce the use of machine learning to the scientific process of hypothesis generation(HG), which refers to the discovery of meaningful implicit connections between biomedical terms. However, most existing methods fail to truly capture the temporal dynamics of scientific term relations and also assume unobserved connections to be irrelevant (i.e., in a positive-negative (PN) learning setting). To break these limits, we formulate this HG problem as future connectivity prediction task on a dynamic attributed graph via positive-unlabeled (PU) learning. Then, the key is to capture the temporal evolution of node pair (term pair) relations from just the positive and unlabeled data. We propose a variational inference model to estimate the positive prior, and incorporate it in the learning of node pair embeddings, which are then used for link prediction. Experiment results on real-world biomedical term relationship datasets and case study analyses on a COVID-19 dataset validate the effectiveness of the proposed model.

Collaborative Graph Walk for Semi-supervised Multi-Label Node Classification

In this work, we study semi-supervised multi-label node classification problem in attributed graphs. Classic solutions to multi-label node classification follow two steps, first learn node embedding and then build a node classifier on the learned embedding. To improve the discriminating power of the node embedding, we propose a novel collaborative graph walk, named Multi-Label-Graph-Walk, to finely tune node representations with the available label assignments in attributed graphs via reinforcement learning. The proposed method formulates the multi-label node classification task as simultaneous graph walks conducted by multiple label-specific agents. Furthermore, policies of the label-wise graph walks are learned in a cooperative way to capture first the predictive relation between node labels and structural attributes of graphs; and second, the correlation among the multiple label-specific classification tasks. A comprehensive experimental study demonstrates that the proposed method can achieve significantly better multi-label classification performance than the state-of-the-art approaches and conduct more efficient graph exploration.

Recurrent Attention Walk for Semi-supervised Classification

In this paper, we study the graph-based semi-supervised learning for classifying nodes in attributed networks, where the nodes and edges possess content information. Recent approaches like graph convolution networks and attention mechanisms have been proposed to ensemble the first-order neighbors and incorporate the relevant neighbors. However, it is costly (especially in memory) to consider all neighbors without a prior differentiation. We propose to explore the neighborhood in a reinforcement learning setting and find a walk path well-tuned for classifying the unlabelled target nodes. We let an agent (of node classification task) walk over the graph and decide where to direct to maximize classification accuracy. We define the graph walk as a partially observable Markov decision process (POMDP). The proposed method is flexible for working in both transductive and inductive setting. Extensive experiments on four datasets demonstrate that our proposed method outperforms several state-of-the-art methods. Several case studies also illustrate the meaningful movement trajectory made by the agent.