htsint: a Python library for sequencing pipelines that combines data through gene set generation

Background: Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. Results: We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for 'enrichment' or conditional differences using one of a number of commonly available packages. Conclusion: The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint

Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new BioML track at OAEI 2022.Comment: Accepted paper in the 21st International Semantic Web Conference (ISWC-2022); DOI for Bio-ML Dataset: 10.5281/zenodo.651008

On the Evolution of Knowledge Graphs: A Survey and Perspective

Knowledge graphs (KGs) are structured representations of diversified knowledge. They are widely used in various intelligent applications. In this article, we provide a comprehensive survey on the evolution of various types of knowledge graphs (i.e., static KGs, dynamic KGs, temporal KGs, and event KGs) and techniques for knowledge extraction and reasoning. Furthermore, we introduce the practical applications of different types of KGs, including a case study in financial analysis. Finally, we propose our perspective on the future directions of knowledge engineering, including the potential of combining the power of knowledge graphs and large language models (LLMs), and the evolution of knowledge extraction, reasoning, and representation

Aggregated search: a new information retrieval paradigm

International audienceTraditional search engines return ranked lists of search results. It is up to the user to scroll this list, scan within different documents and assemble information that fulfill his/her information need. Aggregated search represents a new class of approaches where the information is not only retrieved but also assembled. This is the current evolution in Web search, where diverse content (images, videos, ...) and relational content (similar entities, features) are included in search results. In this survey, we propose a simple analysis framework for aggregated search and an overview of existing work. We start with related work in related domains such as federated search, natural language generation and question answering. Then we focus on more recent trends namely cross vertical aggregated search and relational aggregated search which are already present in current Web search

Improving Editorial Workflow and Metadata Quality at Springer Nature

Identifying the research topics that best describe the scope of a scientific publication is a crucial task for editors, in particular because the quality of these annotations determine how effectively users are able to discover the right content in online libraries. For this reason, Springer Nature, the world's largest academic book publisher, has traditionally entrusted this task to their most expert editors. These editors manually analyse all new books, possibly including hundreds of chapters, and produce a list of the most relevant topics. Hence, this process has traditionally been very expensive, time-consuming, and confined to a few senior editors. For these reasons, back in 2016 we developed Smart Topic Miner (STM), an ontology-driven application that assists the Springer Nature editorial team in annotating the volumes of all books covering conference proceedings in Computer Science. Since then STM has been regularly used by editors in Germany, China, Brazil, India, and Japan, for a total of about 800 volumes per year. Over the past three years the initial prototype has iteratively evolved in response to feedback from the users and evolving requirements. In this paper we present the most recent version of the tool and describe the evolution of the system over the years, the key lessons learnt, and the impact on the Springer Nature workflow. In particular, our solution has drastically reduced the time needed to annotate proceedings and significantly improved their discoverability, resulting in 9.3 million additional downloads. We also present a user study involving 9 editors, which yielded excellent results in term of usability, and report an evaluation of the new topic classifier used by STM, which outperforms previous versions in recall and F-measure

Concept-Centric Transformers: Enhancing Model Interpretability through Object-Centric Concept Learning within a Shared Global Workspace

To explain "black-box" properties of AI models, many approaches, such as post hoc and intrinsically interpretable models, have been proposed to provide plausible explanations that identify human-understandable features/concepts that a trained model uses to make predictions, and attention mechanisms have been widely used to aid in model interpretability by visualizing that information. However, the problem of configuring an interpretable model that effectively communicates and coordinates among computational modules has received less attention. A recently proposed shared global workspace theory demonstrated that networks of distributed modules can benefit from sharing information with a bandwidth-limited working memory because the communication constraints encourage specialization, compositionality, and synchronization among the modules. Inspired by this, we consider how such shared working memories can be realized to build intrinsically interpretable models with better interpretability and performance. Toward this end, we propose Concept-Centric Transformers, a simple yet effective configuration of the shared global workspace for interpretability consisting of: i) an object-centric-based architecture for extracting semantic concepts from input features, ii) a cross-attention mechanism between the learned concept and input embeddings, and iii) standard classification and additional explanation losses to allow human analysts to directly assess an explanation for the model's classification reasoning. We test our approach against other existing concept-based methods on classification tasks for various datasets, including CIFAR100 (super-classes), CUB-200-2011 (bird species), and ImageNet, and we show that our model achieves better classification accuracy than all selected methods across all problems but also generates more consistent concept-based explanations of classification output.Comment: 21 pages, 9 tables, 13 figure

Measuring Semantic Similarity of Documents by Using Named Entity Recognition Methods

The work presented in this thesis was born from the desire to map documents with similar semantic concepts between them. We decided to address this problem as a named entity recognition task, where we have identified key concepts in the texts we use, and we have categorized them. So, we can apply named entity recognition techniques and automatically recognize these key concepts inside other documents. However, we propose the use of a classification method based on the recognition of named entities or key phrases, where the method can detect similarities between key concepts of the texts to be analyzed, and through the use of Poincaré embeddings, the model can associate the existing relationship between these concepts. Thanks to the Poincaré Embeddings’ ability to capture relationships between words, we were able to implement this feature in our classifier. Consequently for each word in a text we check if there are words close to it that are also close to the words that make up the key phrases that we use as Gold Standard. Therefore when detecting potential close words that make up a named entity, the classifier then applies a series of characteristics to classify it. The methodology used performed better than when we only considered the POS structure of the named entities and their n-grams. However, determining the POS structure and the n-grams were important to improve the recognition of named entities in our research. By improving time to recognize similar key phrases between documents, some common tasks in large companies can have a notorious benefit. An important example is the evaluation of resumes, to determine the best professional for a specific position. This task is characterized by consuming a lot of time to find the best profiles for a position, but our contribution in this research work considerably reduces that time, finding the best profiles for a job. Here the experiments are shown considering job descriptions and real resumes, and the methodology used to determine the representation of each of these documents through their key phrases is explained