Evaluation of Output Embeddings for Fine-Grained Image Classification

Image classification has advanced significantly in recent years with the availability of large-scale image sets. However, fine-grained classification remains a major challenge due to the annotation cost of large numbers of fine-grained categories. This project shows that compelling classification performance can be achieved on such categories even without labeled training data. Given image and class embeddings, we learn a compatibility function such that matching embeddings are assigned a higher score than mismatching ones; zero-shot classification of an image proceeds by finding the label yielding the highest joint compatibility score. We use state-of-the-art image features and focus on different supervised attributes and unsupervised output embeddings either derived from hierarchies or learned from unlabeled text corpora. We establish a substantially improved state-of-the-art on the Animals with Attributes and Caltech-UCSD Birds datasets. Most encouragingly, we demonstrate that purely unsupervised output embeddings (learned from Wikipedia and improved with fine-grained text) achieve compelling results, even outperforming the previous supervised state-of-the-art. By combining different output embeddings, we further improve results.Comment: @inproceedings {ARWLS15, title = {Evaluation of Output Embeddings for Fine-Grained Image Classification}, booktitle = {IEEE Computer Vision and Pattern Recognition}, year = {2015}, author = {Zeynep Akata and Scott Reed and Daniel Walter and Honglak Lee and Bernt Schiele}

Ontology-driven and weakly supervised rare disease identification from clinical notes

BACKGROUND: Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. METHODS: We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. RESULTS: The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). CONCLUSION: The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies

A Factoid Question Answering System for Vietnamese

In this paper, we describe the development of an end-to-end factoid question answering system for the Vietnamese language. This system combines both statistical models and ontology-based methods in a chain of processing modules to provide high-quality mappings from natural language text to entities. We present the challenges in the development of such an intelligent user interface for an isolating language like Vietnamese and show that techniques developed for inflectional languages cannot be applied "as is". Our question answering system can answer a wide range of general knowledge questions with promising accuracy on a test set.Comment: In the proceedings of the HQA'18 workshop, The Web Conference Companion, Lyon, Franc

Learning to detect chest radiographs containing lung nodules using visual attention networks

Machine learning approaches hold great potential for the automated detection of lung nodules in chest radiographs, but training the algorithms requires vary large amounts of manually annotated images, which are difficult to obtain. Weak labels indicating whether a radiograph is likely to contain pulmonary nodules are typically easier to obtain at scale by parsing historical free-text radiological reports associated to the radiographs. Using a repositotory of over 700,000 chest radiographs, in this study we demonstrate that promising nodule detection performance can be achieved using weak labels through convolutional neural networks for radiograph classification. We propose two network architectures for the classification of images likely to contain pulmonary nodules using both weak labels and manually-delineated bounding boxes, when these are available. Annotated nodules are used at training time to deliver a visual attention mechanism informing the model about its localisation performance. The first architecture extracts saliency maps from high-level convolutional layers and compares the estimated position of a nodule against the ground truth, when this is available. A corresponding localisation error is then back-propagated along with the softmax classification error. The second approach consists of a recurrent attention model that learns to observe a short sequence of smaller image portions through reinforcement learning. When a nodule annotation is available at training time, the reward function is modified accordingly so that exploring portions of the radiographs away from a nodule incurs a larger penalty. Our empirical results demonstrate the potential advantages of these architectures in comparison to competing methodologies

Analysing the problem and main approaches for ontology population

Knowledge systems are a suitable computational approach to solve complex problems and to provide decision support. Ontologies are an approach for knowledge representation and Ontology Population looks for instantiating the constituent elements of an ontology, like properties and non-taxonomic relationships. Manual population by domain experts and knowledge engineers is an expensive and time consuming task. Thus, automatic or semi-automatic approaches are needed. This paper discusses the problem of Automatic Ontology Population and proposes a generic process specifying its phases and what kind of techniques can be used to perform the activities of each phase. Some techniques representing the state of the art of this field are also described along with the solutions they adopt for each phase of the AOP process with their advantages and limitations. This work is part of HERMES, a Brazil/Portugal research cooperation project looking for techniques and tools for automating the process of ontology learning and population.This work is supported by CNPq, CAPES and FAPEMA, research funding agencies of the Brazilian government