999 research outputs found
Comparing Attributional and Relational Similarity as a Means to Identify Clinically Relevant Drug-gene Relationships
In emerging domains, such as precision oncology, knowledge extracted from explicit assertions may be insufficient to identify relationships of interest. One solution to this problem involves drawing inference on the basis of similarity. Computational methods have been developed to estimate the semantic similarity and relatedness between terms and relationships that are distributed across corpora of literature such as Medline abstracts and other forms of human readable text. Most research on distributional similarity has focused on the notion of attributional similarity, which estimates the similarity between entities based on the contexts in which they occur across a large corpus. A relatively under-researched area concerns relational similarity, in which the similarity between pairs of entities is estimated from the contexts in which these entity pairs occur together. While it seems intuitive that models capturing the structure of the relationships between entities might mediate the identification of biologically important relationships, there is to date no comparison of the relative utility of attributional and relational models for this purpose. In this research, I compare the performance of a range of relational and attributional similarity methods, on the task of identifying drugs that may be therapeutically useful in the context of particular aberrant genes, as identified by a team of human experts. My hypothesis is that relational similarity will be of greater utility than attributional similarity as a means to identify biological relationships that may provide answers to clinical questions, (such as âwhich drugs INHIBIT gene xâ?) in the context of rapidly evolving domains.
My results show that models based on relational similarity outperformed models based on attributional similarity on this task. As the methods explained in this research can be applied to identify any sort of relationship for which cue pairs exist, my results suggest that relational similarity may be a suitable approach to apply to other biomedical problems. Furthermore, I found models based on neural word embeddings (NWE) to be particularly useful for this task, given their higher performance than Random Indexing-based models, and significantly less computational effort needed to create them. NWE methods (such as those produced by the popular word2vec tool) are a relatively recent development in the domain of distributional semantics, and are considered by many as the state-of-the-art when it comes to semantic language modeling. However, their application in identifying biologically important relationships from Medline in general, and specifically, in the domain of precision oncology has not been well studied.
The results of this research can guide the design and implementation of biomedical question answering and other relationship extraction applications for precision medicine, precision oncology and other similar domains, where there is rapid emergence of novel knowledge. The methods developed and evaluated in this project can help NLP applications provide more accurate results by leveraging corpus based methods that are by design scalable and robust
Dense Text Retrieval based on Pretrained Language Models: A Survey
Text retrieval is a long-standing research topic on information seeking,
where a system is required to return relevant information resources to user's
queries in natural language. From classic retrieval methods to learning-based
ranking functions, the underlying retrieval models have been continually
evolved with the ever-lasting technical innovation. To design effective
retrieval models, a key point lies in how to learn the text representation and
model the relevance matching. The recent success of pretrained language models
(PLMs) sheds light on developing more capable text retrieval approaches by
leveraging the excellent modeling capacity of PLMs. With powerful PLMs, we can
effectively learn the representations of queries and texts in the latent
representation space, and further construct the semantic matching function
between the dense vectors for relevance modeling. Such a retrieval approach is
referred to as dense retrieval, since it employs dense vectors (a.k.a.,
embeddings) to represent the texts. Considering the rapid progress on dense
retrieval, in this survey, we systematically review the recent advances on
PLM-based dense retrieval. Different from previous surveys on dense retrieval,
we take a new perspective to organize the related work by four major aspects,
including architecture, training, indexing and integration, and summarize the
mainstream techniques for each aspect. We thoroughly survey the literature, and
include 300+ related reference papers on dense retrieval. To support our
survey, we create a website for providing useful resources, and release a code
repertory and toolkit for implementing dense retrieval models. This survey aims
to provide a comprehensive, practical reference focused on the major progress
for dense text retrieval
Efficient self-supervised metric information retrieval: A bibliography based method applied to covid literature
The literature on coronaviruses counts more than 300,000 publications. Finding relevant papers concerning arbitrary queries is essential to discovery helpful knowledge. Current best information retrieval (IR) use deep learning approaches and need supervised train sets with labeled data, namely to know a priori the queries and their corresponding relevant papers. Creating such labeled datasets is time-expensive and requires prominent expertsâ efforts, resources insufficiently available under a pandemic time pressure. We present a new self-supervised solution, called SUBLIMER, that does not require labels to learn to search on corpora of scientific papers for most relevant against arbitrary queries. SUBLIMER is a novel efficient IR engine trained on the unsupervised COVID-19 Open Research Dataset (CORD19), using deep metric learning. The core point of our self-supervised approach is that it uses no labels, but exploits the bibliography citations from papers to create a latent space where their spatial proximity is a metric of semantic similarity; for this reason, it can also be applied to other domains of papers corpora. SUBLIMER, despite is self-supervised, outperforms the Precision@5 (P@5) and Bpref of the state-of-the-art competitors on CORD19, which, differently from our approach, require both labeled datasets and a number of trainable parameters that is an order of magnitude higher than our
Construction contract risk identification based on knowledge-augmented language model
Contract review is an essential step in construction projects to prevent
potential losses. However, the current methods for reviewing construction
contracts lack effectiveness and reliability, leading to time-consuming and
error-prone processes. While large language models (LLMs) have shown promise in
revolutionizing natural language processing (NLP) tasks, they struggle with
domain-specific knowledge and addressing specialized issues. This paper
presents a novel approach that leverages LLMs with construction contract
knowledge to emulate the process of contract review by human experts. Our
tuning-free approach incorporates construction contract domain knowledge to
enhance language models for identifying construction contract risks. The use of
a natural language when building the domain knowledge base facilitates
practical implementation. We evaluated our method on real construction
contracts and achieved solid performance. Additionally, we investigated how
large language models employ logical thinking during the task and provide
insights and recommendations for future research
Content Recognition and Context Modeling for Document Analysis and Retrieval
The nature and scope of available documents are changing significantly in many areas of document analysis and retrieval as complex, heterogeneous collections become accessible to virtually everyone via the web. The increasing level of diversity presents a great challenge for document image content categorization, indexing, and retrieval. Meanwhile, the processing of documents with unconstrained layouts and complex formatting often requires effective leveraging of broad contextual knowledge.
In this dissertation, we first present a novel approach for document image content categorization, using a lexicon of shape features. Each lexical word corresponds to a scale and rotation invariant local shape feature that is generic enough to be detected repeatably and is segmentation free. A concise, structurally indexed shape lexicon is learned by clustering and partitioning feature types through graph cuts. Our idea finds successful application in several challenging tasks, including content recognition of diverse web images and language identification on documents composed of mixed machine printed text and handwriting.
Second, we address two fundamental problems in signature-based document image retrieval. Facing continually increasing volumes of documents, detecting and recognizing unique, evidentiary visual entities (\eg, signatures and logos) provides a practical and reliable supplement to the OCR recognition of printed text. We propose a novel multi-scale framework to detect and segment signatures jointly from document images, based on the structural saliency under a signature production model. We formulate the problem of signature retrieval in the unconstrained setting of geometry-invariant deformable shape matching and demonstrate state-of-the-art performance in signature matching and verification.
Third, we present a model-based approach for extracting relevant named entities from unstructured documents. In a wide range of applications that require structured information from diverse, unstructured document images, processing OCR text does not give satisfactory results due to the absence of linguistic context. Our approach enables learning of inference rules collectively based on contextual information from both page layout and text features.
Finally, we demonstrate the importance of mining general web user behavior data for improving document ranking and other web search experience. The context of web user activities reveals their preferences and intents, and we emphasize the analysis of individual user sessions for creating aggregate models. We introduce a novel algorithm for estimating web page and web site importance, and discuss its theoretical foundation based on an intentional surfer model. We demonstrate that our approach significantly improves large-scale document retrieval performance
Information retrieval and text mining technologies for chemistry
Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European
Communityâs Horizon 2020 Program (project reference:
654021 - OpenMinted). M.K. additionally acknowledges the
Encomienda MINETAD-CNIO as part of the Plan for the
Advancement of Language Technology. O.R. and J.O. thank
the Foundation for Applied Medical Research (FIMA),
University of Navarra (Pamplona, Spain). This work was
partially funded by ConselleriÌa
de Cultura, EducacioÌn e OrdenacioÌn Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic
funding of UID/BIO/04469/2013 unit and COMPETE 2020
(POCI-01-0145-FEDER-006684). We thank InÌigo GarciaÌ -Yoldi
for useful feedback and discussions during the preparation of
the manuscript.info:eu-repo/semantics/publishedVersio
Knowledge Graphs Meet Multi-Modal Learning: A Comprehensive Survey
Knowledge Graphs (KGs) play a pivotal role in advancing various AI
applications, with the semantic web community's exploration into multi-modal
dimensions unlocking new avenues for innovation. In this survey, we carefully
review over 300 articles, focusing on KG-aware research in two principal
aspects: KG-driven Multi-Modal (KG4MM) learning, where KGs support multi-modal
tasks, and Multi-Modal Knowledge Graph (MM4KG), which extends KG studies into
the MMKG realm. We begin by defining KGs and MMKGs, then explore their
construction progress. Our review includes two primary task categories:
KG-aware multi-modal learning tasks, such as Image Classification and Visual
Question Answering, and intrinsic MMKG tasks like Multi-modal Knowledge Graph
Completion and Entity Alignment, highlighting specific research trajectories.
For most of these tasks, we provide definitions, evaluation benchmarks, and
additionally outline essential insights for conducting relevant research.
Finally, we discuss current challenges and identify emerging trends, such as
progress in Large Language Modeling and Multi-modal Pre-training strategies.
This survey aims to serve as a comprehensive reference for researchers already
involved in or considering delving into KG and multi-modal learning research,
offering insights into the evolving landscape of MMKG research and supporting
future work.Comment: Ongoing work; 41 pages (Main Text), 55 pages (Total), 11 Tables, 13
Figures, 619 citations; Paper list is available at
https://github.com/zjukg/KG-MM-Surve
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