An Ontology Based Method to Solve Query Identifier Heterogeneity in Post-Genomic Clinical Trials

The increasing amount of information available for biomedical research has led to issues related to knowledge discovery in large collections of data. Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains—e.g. clinical and genetic data. One of the goals, among others, of the ACGT European is to provide seamless and homogeneous access to integrated databases. In this work, we describe an approach to overcome heterogeneities in identifiers inside queries. We present an ontology classifying the most common identifier semantic heterogeneities, and a service that makes use of it to cope with the problem using the described approach. Finally, we illustrate the solution by analysing a set of real queries

Thematic Annotation: extracting concepts out of documents

Contrarily to standard approaches to topic annotation, the technique used in this work does not centrally rely on some sort of -- possibly statistical -- keyword extraction. In fact, the proposed annotation algorithm uses a large scale semantic database -- the EDR Electronic Dictionary -- that provides a concept hierarchy based on hyponym and hypernym relations. This concept hierarchy is used to generate a synthetic representation of the document by aggregating the words present in topically homogeneous document segments into a set of concepts best preserving the document's content. This new extraction technique uses an unexplored approach to topic selection. Instead of using semantic similarity measures based on a semantic resource, the later is processed to extract the part of the conceptual hierarchy relevant to the document content. Then this conceptual hierarchy is searched to extract the most relevant set of concepts to represent the topics discussed in the document. Notice that this algorithm is able to extract generic concepts that are not directly present in the document.Comment: Technical report EPFL/LIA. 81 pages, 16 figure

Improving Generalization in Language Model-Based Text-to-SQL Semantic Parsing: Two Simple Semantic Boundary-Based Techniques

Compositional and domain generalization present significant challenges in semantic parsing, even for state-of-the-art semantic parsers based on pre-trained language models (LMs). In this study, we empirically investigate improving an LM's generalization in semantic parsing with two simple techniques: at the token level, we introduce a token preprocessing method to preserve the semantic boundaries of tokens produced by LM tokenizers; at the sequence level, we propose to use special tokens to mark the boundaries of components aligned between input and output. Our experimental results on two text-to-SQL semantic parsing datasets show that our token preprocessing, although simple, can substantially improve the LM performance on both types of generalization, and our component boundary marking method is particularly helpful for compositional generalization.Comment: 9 pages, to be published in ACL202

Semantic Source Code Models Using Identifier Embeddings

The emergence of online open source repositories in the recent years has led to an explosion in the volume of openly available source code, coupled with metadata that relate to a variety of software development activities. As an effect, in line with recent advances in machine learning research, software maintenance activities are switching from symbolic formal methods to data-driven methods. In this context, the rich semantics hidden in source code identifiers provide opportunities for building semantic representations of code which can assist tasks of code search and reuse. To this end, we deliver in the form of pretrained vector space models, distributed code representations for six popular programming languages, namely, Java, Python, PHP, C, C++, and C#. The models are produced using fastText, a state-of-the-art library for learning word representations. Each model is trained on data from a single programming language; the code mined for producing all models amounts to over 13.000 repositories. We indicate dissimilarities between natural language and source code, as well as variations in coding conventions in between the different programming languages we processed. We describe how these heterogeneities guided the data preprocessing decisions we took and the selection of the training parameters in the released models. Finally, we propose potential applications of the models and discuss limitations of the models.Comment: 16th International Conference on Mining Software Repositories (MSR 2019): Data Showcase Trac

Noise or music? Investigating the usefulness of normalisation for robust sentiment analysis on social media data

In the past decade, sentiment analysis research has thrived, especially on social media. While this data genre is suitable to extract opinions and sentiment, it is known to be noisy. Complex normalisation methods have been developed to transform noisy text into its standard form, but their effect on tasks like sentiment analysis remains underinvestigated. Sentiment analysis approaches mostly include spell checking or rule-based normalisation as preprocess- ing and rarely investigate its impact on the task performance. We present an optimised sentiment classifier and investigate to what extent its performance can be enhanced by integrating SMT-based normalisation as preprocessing. Experiments on a test set comprising a variety of user-generated content genres revealed that normalisation improves sentiment classification performance on tweets and blog posts, showing the model’s ability to generalise to other data genres