Knowledge-Rich Self-Supervision for Biomedical Entity Linking

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision ($\tt KRISS$) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces $\tt KRISSBERT$, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy

Knowledge-rich Image Gist Understanding Beyond Literal Meaning

We investigate the problem of understanding the message (gist) conveyed by images and their captions as found, for instance, on websites or news articles. To this end, we propose a methodology to capture the meaning of image-caption pairs on the basis of large amounts of machine-readable knowledge that has previously been shown to be highly effective for text understanding. Our method identifies the connotation of objects beyond their denotation: where most approaches to image understanding focus on the denotation of objects, i.e., their literal meaning, our work addresses the identification of connotations, i.e., iconic meanings of objects, to understand the message of images. We view image understanding as the task of representing an image-caption pair on the basis of a wide-coverage vocabulary of concepts such as the one provided by Wikipedia, and cast gist detection as a concept-ranking problem with image-caption pairs as queries. To enable a thorough investigation of the problem of gist understanding, we produce a gold standard of over 300 image-caption pairs and over 8,000 gist annotations covering a wide variety of topics at different levels of abstraction. We use this dataset to experimentally benchmark the contribution of signals from heterogeneous sources, namely image and text. The best result with a Mean Average Precision (MAP) of 0.69 indicate that by combining both dimensions we are able to better understand the meaning of our image-caption pairs than when using language or vision information alone. We test the robustness of our gist detection approach when receiving automatically generated input, i.e., using automatically generated image tags or generated captions, and prove the feasibility of an end-to-end automated process

TimeMachine: Timeline Generation for Knowledge-Base Entities

We present a method called TIMEMACHINE to generate a timeline of events and relations for entities in a knowledge base. For example for an actor, such a timeline should show the most important professional and personal milestones and relationships such as works, awards, collaborations, and family relationships. We develop three orthogonal timeline quality criteria that an ideal timeline should satisfy: (1) it shows events that are relevant to the entity; (2) it shows events that are temporally diverse, so they distribute along the time axis, avoiding visual crowding and allowing for easy user interaction, such as zooming in and out; and (3) it shows events that are content diverse, so they contain many different types of events (e.g., for an actor, it should show movies and marriages and awards, not just movies). We present an algorithm to generate such timelines for a given time period and screen size, based on submodular optimization and web-co-occurrence statistics with provable performance guarantees. A series of user studies using Mechanical Turk shows that all three quality criteria are crucial to produce quality timelines and that our algorithm significantly outperforms various baseline and state-of-the-art methods.Comment: To appear at ACM SIGKDD KDD'15. 12pp, 7 fig. With appendix. Demo and other info available at http://cs.stanford.edu/~althoff/timemachine

Artificial Intelligence methodologies to early predict student outcome and enrich learning material

L'abstract è presente nell'allegato / the abstract is in the attachmen

LINKING ENTITIES TO A KNOWLEDGE BASE

Ph.DDOCTOR OF PHILOSOPH

A graph-search framework for associating gene identifiers with documents

BACKGROUND: One step in the model organism database curation process is to find, for each article, the identifier of every gene discussed in the article. We consider a relaxation of this problem suitable for semi-automated systems, in which each article is associated with a ranked list of possible gene identifiers, and experimentally compare methods for solving this geneId ranking problem. In addition to baseline approaches based on combining named entity recognition (NER) systems with a "soft dictionary" of gene synonyms, we evaluate a graph-based method which combines the outputs of multiple NER systems, as well as other sources of information, and a learning method for reranking the output of the graph-based method. RESULTS: We show that named entity recognition (NER) systems with similar F-measure performance can have significantly different performance when used with a soft dictionary for geneId-ranking. The graph-based approach can outperform any of its component NER systems, even without learning, and learning can further improve the performance of the graph-based ranking approach. CONCLUSION: The utility of a named entity recognition (NER) system for geneId-finding may not be accurately predicted by its entity-level F1 performance, the most common performance measure. GeneId-ranking systems are best implemented by combining several NER systems. With appropriate combination methods, usefully accurate geneId-ranking systems can be constructed based on easily-available resources, without resorting to problem-specific, engineered components