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Knowledge graphs are graph-based data models which can represent real-time data that is constantly growing with the addition of new information. The question-answering systems over knowledge graphs (KGQA) retrieve answers to a natural language question from the knowledge graph. Most existing KGQA systems use static knowledge bases for offline training. After deployment, they fail to learn from unseen new entities added to the graph. There is a need for dynamic algorithms which can adapt to the evolving graphs and give interpretable results. In this research work, we propose using new auction algorithms for question answering over knowledge graphs. These algorithms can adapt to changing environments in real-time, making them suitable for offline and online training. An auction algorithm computes paths connecting an origin node to one or more destination nodes in a directed graph and uses node prices to guide the search for the path. The prices are initially assigned arbitrarily and updated dynamically based on defined rules. The algorithm navigates the graph from the high-price to the low-price nodes. When new nodes and edges are dynamically added or removed in an evolving knowledge graph, the algorithm can adapt by reusing the prices of existing nodes and assigning arbitrary prices to the new nodes. For subsequent related searches, the “learned” prices provide the means to “transfer knowledge” and act as a “guide”: to steer it toward the lower-priced nodes. Our approach reduces the search computational effort by 60% in our experiments, thus making the algorithm computationally efficient. The resulting path given by the algorithm can be mapped to the attributes of entities and relations in knowledge graphs to provide an explainable answer to the query. We discuss some applications for which our method can be used. 

Ribonucleic acid (RNA) is a fundamental biological molecule that is essential to all living organisms, performing a versatile array of cellular tasks. The function of many RNA molecules is strongly related to the structure it adopts. As a result, great effort is being dedicated to the design of efficient algorithms that solve the “folding problem”—given a sequence of nucleotides, return a probable list of base pairs, referred to as the secondary structure prediction. Early algorithms largely rely on finding the structure with minimum free energy. However, the predictions rely on effective simplified free energy models that may not correctly identify the correct structure as the one with the lowest free energy. In light of this, new, data-driven approaches that not only consider free energy, but also use machine learning techniques to learn motifs are also investigated and recently been shown to outperform free energy–based algorithms on several experimental data sets. In this work, we introduce the new ExpertRNA algorithm that provides a modular framework that can easily incorporate an arbitrary number of rewards (free energy or nonparametric/data driven) and secondary structure prediction algorithms. We argue that this capability of ExpertRNA has the potential to balance out different strengths and weaknesses of state-of-the-art folding tools. We test ExpertRNA on several RNA sequence-structure data sets, and we compare the performance of ExpertRNA against a state-of-the-art folding algorithm. We find that ExpertRNA produces, on average, more accurate predictions of nonpseudoknotted secondary structures than the structure prediction algorithm used, thus validating the promise of the approach. Summary of Contribution: ExpertRNA is a new algorithm inspired by a biological problem. It is applied to solve the problem of secondary structure prediction for RNA molecules given an input sequence. The computational contribution is given by the design of a multibranch, multiexpert rollout algorithm that enables the use of several state-of-the-art approaches as base heuristics and allowing several experts to evaluate partial candidate solutions generated, thus avoiding assuming the reward being optimized by an RNA molecule when folding. Our implementation allows for the effective use of parallel computational resources as well as to control the size of the rollout tree as the algorithm progresses. The problem of RNA secondary structure prediction is of primary importance within the biology field because the molecule structure is strongly related to its functionality. Whereas the contribution of the paper is in the algorithm, the importance of the application makes ExpertRNA a showcase of the relevance of computationally efficient algorithms in supporting scientific discovery.