Studies of CMS data access patterns with machine learning techniques

This thesis presents a study of the Grid data access patterns in distributed analysis in the CMS experiment at the LHC accelerator. This study ranges from the deep analysis of the historical patterns of access to the most relevant data types in CMS, to the exploitation of a supervised Machine Learning classification system to set-up a machinery able to eventually predict future data access patterns - i.e. the so-called dataset “popularity” of the CMS datasets on the Grid - with focus on specific data types. All the CMS workflows run on the Worldwide LHC Computing Grid (WCG) computing centers (Tiers), and in particular the distributed analysis systems sustains hundreds of users and applications submitted every day. These applications (or “jobs”) access different data types hosted on disk storage systems at a large set of WLCG Tiers. The detailed study of how this data is accessed, in terms of data types, hosting Tiers, and different time periods, allows to gain precious insight on storage occupancy over time and different access patterns, and ultimately to extract suggested actions based on this information (e.g. targetted disk clean-up and/or data replication). In this sense, the application of Machine Learning techniques allows to learn from past data and to gain predictability potential for the future CMS data access patterns. Chapter 1 provides an introduction to High Energy Physics at the LHC. Chapter 2 describes the CMS Computing Model, with special focus on the data management sector, also discussing the concept of dataset popularity. Chapter 3 describes the study of CMS data access patterns with different depth levels. Chapter 4 offers a brief introduction to basic machine learning concepts and gives an introduction to its application in CMS and discuss the results obtained by using this approach in the context of this thesis.

"Going outside": discussing the connection between pedagogical practices with digital tools and outdoor learning in early childhood and primary education

Technology has an important role in children's lives and education. Based on several projects developed with ICT, both in Early Childhood Education (3-6 years old) and Primary Education (6-10 years old), since 1997, the authors argue that research and educational practices need to "go outside", addressing ways to connect technology with outdoor education. The experience with the projects and initiatives developed supported a conceptual framework, developed and discussed with several partners throughout the years and theoretically informed. Three main principles or axis have emerged: strengthening Children's Participation, promoting Critical Citizenship and establishing strong Connections to Pedagogy and Curriculum. In this paper, those axis will be presented and discussed in relation to the challenge posed by Outdoor Education to the way ICT in Early Childhood and Primary Education is understood, promoted and researched. The paper is exploratory, attempting to connect theoretical and conceptual contributions from Early Childhood Pedagogy with contributions from ICT in Education. The research-based knowledge available is still scarce, mostly based on studies developed with other purposes. The paper, therefore, focus the connections and interpellations between concepts established through the theoretical framework and draws on the almost 20 years of experience with large and small scale action-research projects of ICT in schools. The more recent one is already testing the conceptual framework by supporting children in non-formal contexts to explore vineyards and the cycle of wine production with several ICT tools. Approaching Outdoor Education as an arena where pedagogical and cultural dimensions influence decisions and practices, the paper tries to argue that the three axis are relevant in supporting a stronger connection between technology and the outdoor.

Predicting the concentration of residual methanol in industrial formalin using machine learning

In this thesis, a machine learning approach was used to develop a predictive model for residual methanol concentration in industrial formalin produced at the Akzo Nobel factory in Kristinehamn, Sweden. The MATLABTM computational environment supplemented with the Statistics and Machine LearningTM toolbox from the MathWorks were used to test various machine learning algorithms on the formalin production data from Akzo Nobel. As a result, the Gaussian Process Regression algorithm was found to provide the best results and was used to create the predictive model. The model was compiled to a stand-alone application with a graphical user interface using the MATLAB CompilerTM.

An investigation of two real time machine learning techniques that could enhance the adaptability of game AI agents

Developers strive to create innovative Artificial Intelligence (AI) behaviour in their games as a key selling point. Machine Learning is an area of AI that looks at how applications and agents can be programmed to learn their own behaviour without the need to manually design and implement each aspect of it. Machine learning methods have been utilised infrequently within games and are usually trained to learn offline before the game is released to the players. In order to investigate new ways AI could be applied innovatively to games it is wise to explore how machine learning methods could be utilised in real-time as the game is played, so as to allow AI agents to learn directly from the player or their environment. Two machine learning methods were implemented into a simple 2D Fighter test game to allow the agents to fully showcase their learned behaviour as the game is played. The methods chosen were: Q-Learning and an NGram based system. It was found that N-Grams and QLearning could significantly benefit game developers as they facilitate fast, realistic learning at run-time.

A machine learning approach for recognising woody plants on railway trackbeds

The purpose of this work in progress study was to test the concept of recognising plants using images acquired by image sensors in a controlled noise-free environment. The presence of vegetation on railway trackbeds and embankments presents potential problems. Woody plants (e.g. Scots pine, Norway spruce and birch) often establish themselves on railway trackbeds. This may cause problems because legal herbicides are not effective in controlling them; this is particularly the case for conifers. Thus, if maintenance administrators knew the spatial position of plants along the railway system, it may be feasible to mechanically harvest them. Primary data were collected outdoors comprising around 700 leaves and conifer seedlings from 11 species. These were then photographed in a laboratory environment. In order to classify the species in the acquired image set, a machine learning approach known as Bag-of-Features (BoF) was chosen. Irrespective of the chosen type of feature extraction and classifier, the ability to classify a previously unseen plant correctly was greater than 85%. The maintenance planning of vegetation control could be improved if plants were recognised and localised. It may be feasible to mechanically harvest them (in particular, woody plants). In addition, listed endangered species growing on the trackbeds can be avoided. Both cases are likely to reduce the amount of herbicides, which often is in the interest of public opinion. Bearing in mind that natural objects like plants are often more heterogeneous within their own class rather than outside it, the results do indeed present a stable classification performance, which is a sound prerequisite in order to later take the next step to include a natural background. Where relevant, species can also be listed under the Endangered Species Act.

Machine learning techniques for implicit interaction using mobile sensors

Interactions in mobile devices normally happen in an explicit manner, which means that they are initiated by the users. Yet, users are typically unaware that they also interact implicitly with their devices. For instance, our hand pose changes naturally when we type text messages. Whilst the touchscreen captures finger touches, hand movements during this interaction however are unused. If this implicit hand movement is observed, it can be used as additional information to support or to enhance the users’ text entry experience. This thesis investigates how implicit sensing can be used to improve existing, standard interaction technique qualities. In particular, this thesis looks into enhancing front-of-device interaction through back-of-device and hand movement implicit sensing. We propose the investigation through machine learning techniques. We look into problems on how sensor data via implicit sensing can be used to predict a certain aspect of an interaction. For instance, one of the questions that this thesis attempts to answer is whether hand movement during a touch targeting task correlates with the touch position. This is a complex relationship to understand but can be best explained through machine learning. Using machine learning as a tool, such correlation can be measured, quantified, understood and used to make predictions on future touch position. Furthermore, this thesis also evaluates the predictive power of the sensor data. We show this through a number of studies. In Chapter 5 we show that probabilistic modelling of sensor inputs and recorded touch locations can be used to predict the general area of future touches on touchscreen. In Chapter 7, using SVM classifiers, we show that data from implicit sensing from general mobile interactions is user-specific. This can be used to identify users implicitly. In Chapter 6, we also show that touch interaction errors can be detected from sensor data. In our experiment, we show that there are sufficient distinguishable patterns between normal interaction signals and signals that are strongly correlated with interaction error. In all studies, we show that performance gain can be achieved by combining sensor inputs.

Machine learning per l'idrologia: applicazione del metodo random forests per la previsione degli eventi di piena fluviale con un approccio probabilistico

Le tecniche di Machine Learning sono molto utili in quanto consento di massimizzare l’utilizzo delle informazioni in tempo reale. Il metodo Random Forests può essere annoverato tra le tecniche di Machine Learning più recenti e performanti. Sfruttando le caratteristiche e le potenzialità di questo metodo, la presente tesi di dottorato affronta due casi di studio differenti; grazie ai quali è stato possibile elaborare due differenti modelli previsionali. Il primo caso di studio si è incentrato sui principali fiumi della regione Emilia-Romagna, caratterizzati da tempi di risposta molto brevi. La scelta di questi fiumi non è stata casuale: negli ultimi anni, infatti, in detti bacini si sono verificati diversi eventi di piena, in gran parte di tipo “flash flood”. Il secondo caso di studio riguarda le sezioni principali del fiume Po, dove il tempo di propagazione dell’onda di piena è maggiore rispetto ai corsi d’acqua del primo caso di studio analizzato. Partendo da una grande quantità di dati, il primo passo è stato selezionare e definire i dati in ingresso in funzione degli obiettivi da raggiungere, per entrambi i casi studio. Per l’elaborazione del modello relativo ai fiumi dell’Emilia-Romagna, sono stati presi in considerazione esclusivamente i dati osservati; a differenza del bacino del fiume Po in cui ai dati osservati sono stati affiancati anche i dati di previsione provenienti dalla catena modellistica Mike11 NAM/HD. Sfruttando una delle principali caratteristiche del metodo Random Forests, è stata stimata una probabilità di accadimento: questo aspetto è fondamentale sia nella fase tecnica che in fase decisionale per qualsiasi attività di intervento di protezione civile. L'elaborazione dei dati e i dati sviluppati sono stati effettuati in ambiente R. Al termine della fase di validazione, gli incoraggianti risultati ottenuti hanno permesso di inserire il modello sviluppato nel primo caso studio all’interno dell’architettura operativa di FEWS.

Novel Machine-Learning Based IC Testing Strategy

The final goal of the thesis should be a real-world application in the production test data environment. This includes the pre-processing of the data, building models and visualizing the results. To do this, different machine learning models, outlier prediction oriented, should be investigated using a real dataset. Finally, the different outlier prediction algorithms should be compared, and their performance discussed.

Hybrid Artificial Intelligence to Extract Patterns and Rules from Argumentative and Legal Texts

This Thesis is composed of a collection of works written in the period 2019-2022, whose aim is to find methodologies of Artificial Intelligence (AI) and Machine Learning to detect and classify patterns and rules in argumentative and legal texts. We define our approach “hybrid”, since we aimed at designing hybrid combinations of symbolic and sub-symbolic AI, involving both “top-down” structured knowledge and “bottom-up” data-driven knowledge. A first group of works is dedicated to the classification of argumentative patterns. Following the Waltonian model of argument and the related theory of Argumentation Schemes, these works focused on the detection of argumentative support and opposition, showing that argumentative evidences can be classified at fine-grained levels without resorting to highly engineered features. To show this, our methods involved not only traditional approaches such as TFIDF, but also some novel methods based on Tree Kernel algorithms. After the encouraging results of this first phase, we explored the use of a some emerging methodologies promoted by actors like Google, which have deeply changed NLP since 2018-19 — i.e., Transfer Learning and language models. These new methodologies markedly improved our previous results, providing us with best-performing NLP tools. Using Transfer Learning, we also performed a Sequence Labelling task to recognize the exact span of argumentative components (i.e., claims and premises), thus connecting portions of natural language to portions of arguments (i.e., to the logical-inferential dimension). The last part of our work was finally dedicated to the employment of Transfer Learning methods for the detection of rules and deontic modalities. In this case, we explored a hybrid approach which combines structured knowledge coming from two LegalXML formats (i.e., Akoma Ntoso and LegalRuleML) with sub-symbolic knowledge coming from pre-trained (and then fine-tuned) neural architectures.

Integrating Machine Learning Paradigms for Predictive Maintenance in the Fourth Industrial Revolution era

In the last decade, manufacturing companies have been facing two significant challenges. First, digitalization imposes adopting Industry 4.0 technologies and allows creating smart, connected, self-aware, and self-predictive factories. Second, the attention on sustainability imposes to evaluate and reduce the impact of the implemented solutions from economic and social points of view. In manufacturing companies, the maintenance of physical assets assumes a critical role. Increasing the reliability and the availability of production systems leads to the minimization of systems’ downtimes; In addition, the proper system functioning avoids production wastes and potentially catastrophic accidents. Digitalization and new ICT technologies have assumed a relevant role in maintenance strategies. They allow assessing the health condition of machinery at any point in time. Moreover, they allow predicting the future behavior of machinery so that maintenance interventions can be planned, and the useful life of components can be exploited until the time instant before their fault. This dissertation provides insights on Predictive Maintenance goals and tools in Industry 4.0 and proposes a novel data acquisition, processing, sharing, and storage framework that addresses typical issues machine producers and users encounter. The research elaborates on two research questions that narrow down the potential approaches to data acquisition, processing, and analysis for fault diagnostics in evolving environments. The research activity is developed according to a research framework, where the research questions are addressed by research levers that are explored according to research topics. Each topic requires a specific set of methods and approaches; however, the overarching methodological approach presented in this dissertation includes three fundamental aspects: the maximization of the quality level of input data, the use of Machine Learning methods for data analysis, and the use of case studies deriving from both controlled environments (laboratory) and real-world instances.

A machine learning based method to detect genomic imbalances exploiting X chromosome exome reads

Whole Exome Sequencing (WES) is rapidly becoming the first-tier test in clinics, both thanks to its declining costs and the development of new platforms that help clinicians in the analysis and interpretation of SNV and InDels. However, we still know very little on how CNV detection could increase WES diagnostic yield. A plethora of exome CNV callers have been published over the years, all showing good performances towards specific CNV classes and sizes, suggesting that the combination of multiple tools is needed to obtain an overall good detection performance. Here we present TrainX, a ML-based method for calling heterozygous CNVs in WES data using EXCAVATOR2 Normalized Read Counts. We select males and females’ non pseudo-autosomal chromosome X alignments to construct our dataset and train our model, make predictions on autosomes target regions and use HMM to call CNVs. We compared TrainX against a set of CNV tools differing for the detection method (GATK4 gCNV, ExomeDepth, DECoN, CNVkit and EXCAVATOR2) and found that our algorithm outperformed them in terms of stability, as we identified both deletions and duplications with good scores (0.87 and 0.82 F1-scores respectively) and for sizes reaching the minimum resolution of 2 target regions. We also evaluated the method robustness using a set of WES and SNP array data (n=251), part of the Italian cohort of Epi25 collaborative, and were able to retrieve all clinical CNVs previously identified by the SNP array. TrainX showed good accuracy in detecting heterozygous CNVs of different sizes, making it a promising tool to use in a diagnostic setting.

Machine learning as a service for high energy physics (MLaaS4HEP): a service for ML-based data analyses

With the CERN LHC program underway, there has been an acceleration of data growth in the High Energy Physics (HEP) field and the usage of Machine Learning (ML) in HEP will be critical during the HL-LHC program when the data that will be produced will reach the exascale. ML techniques have been successfully used in many areas of HEP nevertheless, the development of a ML project and its implementation for production use is a highly time-consuming task and requires specific skills. Complicating this scenario is the fact that HEP data is stored in ROOT data format, which is mostly unknown outside of the HEP community. The work presented in this thesis is focused on the development of a ML as a Service (MLaaS) solution for HEP, aiming to provide a cloud service that allows HEP users to run ML pipelines via HTTP calls. These pipelines are executed by using the MLaaS4HEP framework, which allows reading data, processing data, and training ML models directly using ROOT files of arbitrary size from local or distributed data sources. Such a solution provides HEP users non-expert in ML with a tool that allows them to apply ML techniques in their analyses in a streamlined manner. Over the years the MLaaS4HEP framework has been developed, validated, and tested and new features have been added. A first MLaaS solution has been developed by automatizing the deployment of a platform equipped with the MLaaS4HEP framework. Then, a service with APIs has been developed, so that a user after being authenticated and authorized can submit MLaaS4HEP workflows producing trained ML models ready for the inference phase. A working prototype of this service is currently running on a virtual machine of INFN-Cloud and is compliant to be added to the INFN Cloud portfolio of services.

Applying machine learning: a multi-role perspective

Machine (and deep) learning technologies are more and more present in several fields. It is undeniable that many aspects of our society are empowered by such technologies: web searches, content filtering on social networks, recommendations on e-commerce websites, mobile applications, etc., in addition to academic research. Moreover, mobile devices and internet sites, e.g., social networks, support the collection and sharing of information in real time. The pervasive deployment of the aforementioned technological instruments, both hardware and software, has led to the production of huge amounts of data. Such data has become more and more unmanageable, posing challenges to conventional computing platforms, and paving the way to the development and widespread use of the machine and deep learning. Nevertheless, machine learning is not only a technology. Given a task, machine learning is a way of proceeding (a way of thinking), and as such can be approached from different perspectives (points of view). This, in particular, will be the focus of this research. The entire work concentrates on machine learning, starting from different sources of data, e.g., signals and images, applied to different domains, e.g., Sport Science and Social History, and analyzed from different perspectives: from a non-data scientist point of view through tools and platforms; setting a problem stage from scratch; implementing an effective application for classification tasks; improving user interface experience through Data Visualization and eXtended Reality. In essence, not only in a quantitative task, not only in a scientific environment, and not only from a data-scientist perspective, machine (and deep) learning can do the difference.

Developing a radiomic based machine learning model to identify patients with resected non-small-cell lung cancer at high risk of relapse

Background There is a wide variation of recurrence risk of Non-small-cell lung cancer (NSCLC) within the same Tumor Node Metastasis (TNM) stage, suggesting that other parameters are involved in determining this probability. Radiomics allows extraction of quantitative information from images that can be used for clinical purposes. The primary objective of this study is to develop a radiomic prognostic model that predicts a 3 year disease free-survival (DFS) of resected Early Stage (ES) NSCLC patients. Material and Methods 56 pre-surgery non contrast Computed Tomography (CT) scans were retrieved from the PACS of our institution and anonymized. Then they were automatically segmented with an open access deep learning pipeline and reviewed by an experienced radiologist to obtain 3D masks of the NSCLC. Images and masks underwent to resampling normalization and discretization. From the masks hundreds Radiomic Features (RF) were extracted using Py-Radiomics. Hence, RF were reduced to select the most representative features. The remaining RF were used in combination with Clinical parameters to build a DFS prediction model using Leave-one-out cross-validation (LOOCV) with Random Forest. Results and Conclusion A poor agreement between the radiologist and the automatic segmentation algorithm (DICE score of 0.37) was found. Therefore, another experienced radiologist manually segmented the lesions and only stable and reproducible RF were kept. 50 RF demonstrated a high correlation with the DFS but only one was confirmed when clinicopathological covariates were added: Busyness a Neighbouring Gray Tone Difference Matrix (HR 9.610). 16 clinical variables (which comprised TNM) were used to build the LOOCV model demonstrating a higher Area Under the Curve (AUC) when RF were included in the analysis (0.67 vs 0.60) but the difference was not statistically significant (p=0,5147).

Machine learning "as a service" for high energy physics (MLaaS4HEP): evolution of a framework for ML-based physics analyses

The scientific success of the LHC experiments at CERN highly depends on the availability of computing resources which efficiently store, process, and analyse the amount of data collected every year. This is ensured by the Worldwide LHC Computing Grid infrastructure that connect computing centres distributed all over the world with high performance network. LHC has an ambitious experimental program for the coming years, which includes large investments and improvements both for the hardware of the detectors and for the software and computing systems, in order to deal with the huge increase in the event rate expected from the High Luminosity LHC (HL-LHC) phase and consequently with the huge amount of data that will be produced. Since few years the role of Artificial Intelligence has become relevant in the High Energy Physics (HEP) world. Machine Learning (ML) and Deep Learning algorithms have been successfully used in many areas of HEP, like online and offline reconstruction programs, detector simulation, object reconstruction, identification, Monte Carlo generation, and surely they will be crucial in the HL-LHC phase. This thesis aims at contributing to a CMS R&D project, regarding a ML "as a Service" solution for HEP needs (MLaaS4HEP). It consists in a data-service able to perform an entire ML pipeline (in terms of reading data, processing data, training ML models, serving predictions) in a completely model-agnostic fashion, directly using ROOT files of arbitrary size from local or distributed data sources. This framework has been updated adding new features in the data preprocessing phase, allowing more flexibility to the user. Since the MLaaS4HEP framework is experiment agnostic, the ATLAS Higgs Boson ML challenge has been chosen as physics use case, with the aim to test MLaaS4HEP and the contribution done with this work.