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How can we represent hierarchical information present in large type inventories for entity typing? We study the ability of hyperbolic embeddings to capture hierarchical relations between mentions in context and their target types in a shared vector space. We evaluate on two datasets and investigate two different techniques for creating a large hierarchical entity type inventory: from an expert-generated ontology and by automatically mining type co-occurrences. We find that the hyperbolic model yields improvements over its Euclidean counterpart in some, but not all cases. Our analysis suggests that the adequacy of this geometry depends on the granularity of the type inventory and the way hierarchical relations are inferred. 1

BackgroundAn experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols.ResultsIn this paper we present “SMART Protocols ontology”, an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample.ConclusionImproving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/.

Label inventories for fine-grained entity typing have grown in size and complexity. Nonetheless, they exhibit a hierarchical structure. Hyperbolic spaces offer a mathematically appealing approach for learning hierarchical representations of symbolic data. However, it is not clear how to integrate hyperbolic components into downstream tasks. This is the first work that proposes a fully hyperbolic model for multi-class multi-label classification, which performs all operations in hyperbolic space.We evaluate the proposed model on two challenging datasets and compare to different baselines that operate under Euclidean assumptions. Our hyperbolic model infers the latent hierarchy from the class distribution, captures implicit hyponymic relations in the inventory, and shows performance on par with state-ofthe-art methods on fine-grained classification with remarkable reduction of the parameter size. A thorough analysis sheds light on the impact of each component in the final prediction and showcases its ease of integration with Euclidean layers. 1

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