Antibody-Antigen Interface Characterization with Contextualized Pre-trained Embeddings

Artificial Intelligence (AI) has substantially influenced numerous disciplines in recent years. Biology, chemistry, and bioinformatics are among them, with significant advances in protein structure prediction, paratope prediction, protein-protein interactions (PPIs), and antibody-antigen interactions. Understanding PPIs is critical since they are responsible for practically everything living and have several uses in vaccines, cancer, immunology, and inflammatory illnesses. Machine Learning (ML) offers enormous potential for effectively simulating antibody-antigen interactions and improving in-silico optimization of therapeutic antibodies for desired features, including binding activity, stability, and low immunogenicity. This research looks at the use of AI algorithms to better understand antibody-antigen interactions, and it further expands and explains several difficulties encountered in the field. Furthermore, we contribute by presenting a method that outperforms existing state-of-the-art strategies in paratope prediction from sequence data.

Frame-driven Extraction of Linked Data and Ontologies from Text

Ontology design and population -core aspects of semantic technologies- re- cently have become fields of great interest due to the increasing need of domain-specific knowledge bases that can boost the use of Semantic Web. For building such knowledge resources, the state of the art tools for ontology design require a lot of human work. Producing meaningful schemas and populating them with domain-specific data is in fact a very difficult and time-consuming task. Even more if the task consists in modelling knowledge at a web scale. The primary aim of this work is to investigate a novel and flexible method- ology for automatically learning ontology from textual data, lightening the human workload required for conceptualizing domain-specific knowledge and populating an extracted schema with real data, speeding up the whole ontology production process. Here computational linguistics plays a fundamental role, from automati- cally identifying facts from natural language and extracting frame of relations among recognized entities, to producing linked data with which extending existing knowledge bases or creating new ones. In the state of the art, automatic ontology learning systems are mainly based on plain-pipelined linguistics classifiers performing tasks such as Named Entity recognition, Entity resolution, Taxonomy and Relation extraction [11]. These approaches present some weaknesses, specially in capturing struc- tures through which the meaning of complex concepts is expressed [24]. Humans, in fact, tend to organize knowledge in well-defined patterns, which include participant entities and meaningful relations linking entities with each other. In literature, these structures have been called Semantic Frames by Fill- 6 Introduction more [20], or more recently as Knowledge Patterns [23]. Some NLP studies has recently shown the possibility of performing more accurate deep parsing with the ability of logically understanding the structure of discourse [7]. In this work, some of these technologies have been investigated and em- ployed to produce accurate ontology schemas. The long-term goal is to collect large amounts of semantically structured information from the web of crowds, through an automated process, in order to identify and investigate the cognitive patterns used by human to organize their knowledge.

Vantaggi e limiti dell'integrazione tra sistemi di traduzione assistita e sistemi di traduzione automatica

Computer-assisted translation (or computer-aided translation or CAT) is a form of language translation in which a human translator uses computer software in order to facilitate the translation process. Machine translation (MT) is the automated process by which a computerized system produces a translated text or speech from one natural language to another. Both of them are leading and promising technologies in the translation industry; it therefore seems important that translation students and professional translators become familiar with this relatively new types of technology. Whether used together, not only might these two different types of systems reduce translation time, but also lead to a further improvement in the field of translation technologies. The dissertation consists of four chapters. The first one surveys the chronological development of MT and CAT tools, the emergence of pre-editing, post-editing and controlled language and the very last frontiers in this sector. The second one provide a general overview on the four main CAT tools that are used nowadays and tested hereto. The third chapter is dedicated to the experimentations that have been conducted in order to analyze and evaluate the performance of the four integrated systems that are the core subject of this dissertation. Finally, the fourth chapter deals with the issue of terminological equivalence in interlinguistic translation. The purpose of this dissertation is not to provide an objective and definitive solution to the complex issues that arise at any time in the field of translation technologies, this aim being well away from being achieved, but to supply information about the limits and potentiality that are typical of those instruments which are now essential to any professional translator.

Generare con transformer lineare spiegazioni di concept set medicali costituiti da termini correlati estratti da social post di pazienti

Le malattie rare pongono diversi scogli ai pazienti, ai loro familiari e ai sanitari. Uno fra questi è la mancanza di informazione che deriva dall'assenza di fonti sicure e semplici da consultare su aspetti dell'esperienza del paziente. Il lavoro presentato ha lo scopo di generare da set termini correlati semanticamente, delle frasi che abbiamo la capacità di spiegare il legame fra di essi e aggiungere informazioni utili e veritiere in un linguaggio semplice e comprensibile. Il problema affrontato oggigiorno non è ben documentato in letteratura e rappresenta una sfida interessante si per complessità che per mancanza di dataset per l'addestramento. Questo tipo di task, come altri di NLP, è affrontabile solo con modelli sempre più potenti ma che richiedono risorse sempre più elevate. Per questo motivo, è stato utilizzato il meccanismo di recente pubblicazione del Performer, dimostrando di riuscire a mantenere uno stesso grado di accuratezza e di qualità delle frasi prodotte, con una parallela riduzione delle risorse utilizzate. Ciò apre la strada all'utilizzo delle reti neurali più recenti anche senza avere i centri di calcolo delle multinazionali. Il modello proposto dunque è in grado di generare frasi che illustrano le relazioni semantiche di termini estratti da un mole di documenti testuali, permettendo di generare dei riassunti dell'informazione e della conoscenza estratta da essi e renderla facilmente accessibile e comprensibile al pazienti o a persone non esperte.

Analysis of COVID-related symptoms from a database of Italian tweets

Twitter is a highly popular social media which on one hand allows information transmission in real time and on the other hand represents a source of open access homogeneous text data. We propose an analysis of the most common self-reported COVID symptoms from a dataset of Italian tweets to investigate the evolution of the pandemic in Italy from the end of September 2020 to the end of January 2021. After manually filtering tweets actually describing COVID symptoms from the database - which contains words related to fever, cough and sore throat - we discuss usefulness of such filtering. We then compare our time series with the daily data of new hospitalisations in Italy, with the aim of building a simple linear regression model that accounts for the delay which is observed from the tweets mentioning individual symptoms to new hospitalisations. We discuss both the results and limitations of linear regression given that our data suggests that the relationship between time series of symptoms tweets and of new hospitalisations changes towards the end of the acquisition.