arXiv subjects

Paolo Missier

Publications and source records attributed to Paolo Missier.

At least 19 recordsLinked to original sources

arXiv2024

Probabilistic Modelling of Multiple Long-Term Condition Onset Times

The co-occurrence of multiple long-term conditions (MLTC), or multimorbidity, in an individual can reduce their lifespan and severely impact their quality of life. Exploring the longitudinal patterns, e.g. clusters, of disease accrual can help better understand the genetic and environmental drivers of multimorbidity, and potentially identify individuals who may benefit from early targeted intervention. We introduce $\textit{probabilistic modelling of onset times}$, or $\texttt{ProMOTe}$, for clustering and forecasting MLTC trajectories. $\texttt{ProMOTe}$ seamlessly learns from incomplete and unreliable disease trajectories that is commonplace in Electronic Health Records but often ignored in existing longitudinal clustering methods. We analyse data from 150,000 individuals in the UK Biobank and identify 50 clusters showing patterns of disease accrual that have also been reported by some recent studies. We further discuss the forecasting capabilities of the model given the history of disease accrual.

stat.AP↗

arXiv2024

bursty_dynamics: A Python Package for Exploring the Temporal Properties of Longitudinal Data

Understanding the temporal properties of longitudinal data is critical for identifying trends, predicting future events, and making informed decisions in any field where temporal data is analysed, including health and epidemiology, finance, geosciences, and social sciences. Traditional time-series analysis techniques often fail to capture the complexity of irregular temporal patterns present in such data. To address this gap, we introduce bursty_dynamics, a Python package that enables the quantification of bursty dynamics through the calculation of the Burstiness Parameter (BP) and Memory Coefficient (MC). In temporal data, BP and MC provide insights into the irregularity and temporal dependencies within event sequences, shedding light on complex patterns of disease aetiology, human behaviour, or other information diffusion over time. An event train detection method is also implemented to identify clustered events occurring within a specified time interval, allowing for more focused analysis with reduced noise. With built-in visualisation tools, bursty_dynamics provides an accessible yet powerful platform for researchers to explore and interpret the temporal dynamics of longitudinal data. This paper outlines the core functionalities of the package, demonstrates its applications in diverse research domains, and discusses the advantages of using BP, MC, and event train detection for enhanced temporal data analysis.

q-bio.QM↗

arXiv2023

Handling Overlapping Asymmetric Datasets -- A Twice Penalized P-Spline Approach

Overlapping asymmetric datasets are common in data science and pose questions of how they can be incorporated together into a predictive analysis. In healthcare datasets there is often a small amount of information that is available for a larger number of patients such as an electronic health record, however a small number of patients may have had extensive further testing. Common solutions such as missing imputation can often be unwise if the smaller cohort is significantly different in scale to the larger sample, therefore the aim of this research is to develop a new method which can model the smaller cohort against a particular response, whilst considering the larger cohort also. Motivated by non-parametric models, and specifically flexible smoothing techniques via generalized additive models, we model a twice penalized P-Spline approximation method to firstly prevent over/under-fitting of the smaller cohort and secondly to consider the larger cohort. This second penalty is created through discrepancies in the marginal value of covariates that exist in both the smaller and larger cohorts. Through data simulations, parameter tunings and model adaptations to consider a continuous and binary response, we find our twice penalized approach offers an enhanced fit over a linear B-Spline and once penalized P-Spline approximation. Applying to a real-life dataset relating to a person's risk of developing Non-Alcoholic Steatohepatitis, we see an improved model fit performance of over 65%. Areas for future work within this space include adapting our method to not require dimensionality reduction and also consider parametric modelling methods. However, to our knowledge this is the first work to propose additional marginal penalties in a flexible regression of which we can report a vastly improved model fit that is able to consider asymmetric datasets, without the need for missing data imputation.

stat.ME↗

arXiv2023

Supporting Better Insights of Data Science Pipelines with Fine-grained Provenance

Successful data-driven science requires complex data engineering pipelines to clean, transform, and alter data in preparation for machine learning, and robust results can only be achieved when each step in the pipeline can be justified, and its effect on the data explained. In this framework, our aim is to provide data scientists with facilities to gain an in-depth understanding of how each step in the pipeline affects the data, from the raw input to training sets ready to be used for learning. Starting from an extensible set of data preparation operators commonly used within a data science setting, in this work we present a provenance management infrastructure for generating, storing, and querying very granular accounts of data transformations, at the level of individual elements within datasets whenever possible. Then, from the formal definition of a core set of data science preprocessing operators, we derive a provenance semantics embodied by a collection of templates expressed in PROV, a standard model for data provenance. Using those templates as a reference, our provenance generation algorithm generalises to any operator with observable input/output pairs. We provide a prototype implementation of an application-level provenance capture library to produce, in a semi-automatic way, complete provenance documents that account for the entire pipeline. We report on the ability of our implementations to capture provenance in real ML benchmark pipelines and over TCP-DI synthetic data. We finally show how the collected provenance can be used to answer a suite of provenance benchmark queries that underpin some common pipeline inspection questions, as expressed on the Data Science Stack Exchange.

cs.DB↗

arXiv2023

ConvBoost: Boosting ConvNets for Sensor-based Activity Recognition

Human activity recognition (HAR) is one of the core research themes in ubiquitous and wearable computing. With the shift to deep learning (DL) based analysis approaches, it has become possible to extract high-level features and perform classification in an end-to-end manner. Despite their promising overall capabilities, DL-based HAR may suffer from overfitting due to the notoriously small, often inadequate, amounts of labeled sample data that are available for typical HAR applications. In response to such challenges, we propose ConvBoost -- a novel, three-layer, structured model architecture and boosting framework for convolutional network based HAR. Our framework generates additional training data from three different perspectives for improved HAR, aiming to alleviate the shortness of labeled training data in the field. Specifically, with the introduction of three conceptual layers--Sampling Layer, Data Augmentation Layer, and Resilient Layer -- we develop three "boosters" -- R-Frame, Mix-up, and C-Drop -- to enrich the per-epoch training data by dense-sampling, synthesizing, and simulating, respectively. These new conceptual layers and boosters, that are universally applicable for any kind of convolutional network, have been designed based on the characteristics of the sensor data and the concept of frame-wise HAR. In our experimental evaluation on three standard benchmarks (Opportunity, PAMAP2, GOTOV) we demonstrate the effectiveness of our ConvBoost framework for HAR applications based on variants of convolutional networks: vanilla CNN, ConvLSTM, and Attention Models. We achieved substantial performance gains for all of them, which suggests that the proposed approach is generic and can serve as a practical solution for boosting the performance of existing ConvNet-based HAR models. This is an open-source project, and the code can be found at https://github.com/sshao2013/ConvBoost

cs.LG↗

arXiv2022

Simple Yet Surprisingly Effective Training Strategies for LSTMs in Sensor-Based Human Activity Recognition

Human Activity Recognition (HAR) is one of the core research areas in mobile and wearable computing. With the application of deep learning (DL) techniques such as CNN, recognizing periodic or static activities (e.g, walking, lying, cycling, etc.) has become a well studied problem. What remains a major challenge though is the sporadic activity recognition (SAR) problem, where activities of interest tend to be non periodic, and occur less frequently when compared with the often large amount of irrelevant background activities. Recent works suggested that sequential DL models (such as LSTMs) have great potential for modeling nonperiodic behaviours, and in this paper we studied some LSTM training strategies for SAR. Specifically, we proposed two simple yet effective LSTM variants, namely delay model and inverse model, for two SAR scenarios (with and without time critical requirement). For time critical SAR, the delay model can effectively exploit predefined delay intervals (within tolerance) in form of contextual information for improved performance. For regular SAR task, the second proposed, inverse model can learn patterns from the time series in an inverse manner, which can be complementary to the forward model (i.e.,LSTM), and combining both can boost the performance. These two LSTM variants are very practical, and they can be deemed as training strategies without alteration of the LSTM fundamentals. We also studied some additional LSTM training strategies, which can further improve the accuracy. We evaluated our models on two SAR and one non-SAR datasets, and the promising results demonstrated the effectiveness of our approaches in HAR applications.

eess.SP↗

arXiv2022

Benchmark time series data sets for PyTorch -- the torchtime package

The development of models for Electronic Health Record data is an area of active research featuring a small number of public benchmark data sets. Researchers typically write custom data processing code but this hinders reproducibility and can introduce errors. The Python package torchtime provides reproducible implementations of commonly used PhysioNet and UEA & UCR time series classification repository data sets for PyTorch. Features are provided for working with irregularly sampled and partially observed time series of unequal length. It aims to simplify access to PhysioNet data and enable fair comparisons of models in this exciting area of research.

cs.LG↗

arXiv2022

Technologies for Trustworthy Machine Learning: A Survey in a Socio-Technical Context

Concerns about the societal impact of AI-based services and systems has encouraged governments and other organisations around the world to propose AI policy frameworks to address fairness, accountability, transparency and related topics. To achieve the objectives of these frameworks, the data and software engineers who build machine-learning systems require knowledge about a variety of relevant supporting tools and techniques. In this paper we provide an overview of technologies that support building trustworthy machine learning systems, i.e., systems whose properties justify that people place trust in them. We argue that four categories of system properties are instrumental in achieving the policy objectives, namely fairness, explainability, auditability and safety & security (FEAS). We discuss how these properties need to be considered across all stages of the machine learning life cycle, from data collection through run-time model inference. As a consequence, we survey in this paper the main technologies with respect to all four of the FEAS properties, for data-centric as well as model-centric stages of the machine learning system life cycle. We conclude with an identification of open research problems, with a particular focus on the connection between trustworthy machine learning technologies and their implications for individuals and society.

cs.LG↗

arXiv2021

Knowledge-driven Data Ecosystems Towards Data Transparency

A Data Ecosystem offers a keystone-player or alliance-driven infrastructure that enables the interaction of different stakeholders and the resolution of interoperability issues among shared data. However, despite years of research in data governance and management, trustability is still affected by the absence of transparent and traceable data-driven pipelines. In this work, we focus on requirements and challenges that data ecosystems face when ensuring data transparency. Requirements are derived from the data and organizational management, as well as from broader legal and ethical considerations. We propose a novel knowledge-driven data ecosystem architecture, providing the pillars for satisfying the analyzed requirements. We illustrate the potential of our proposal in a real-world scenario. Lastly, we discuss and rate the potential of the proposed architecture in the fulfillment of these requirements.

cs.DB↗

arXiv2020

Building Rule Hierarchies for Efficient Logical Rule Learning from Knowledge Graphs

Many systems have been developed in recent years to mine logical rules from large-scale Knowledge Graphs (KGs), on the grounds that representing regularities as rules enables both the interpretable inference of new facts, and the explanation of known facts. Among these systems, the walk-based methods that generate the instantiated rules containing constants by abstracting sampled paths in KGs demonstrate strong predictive performance and expressivity. However, due to the large volume of possible rules, these systems do not scale well where computational resources are often wasted on generating and evaluating unpromising rules. In this work, we address such scalability issues by proposing new methods for pruning unpromising rules using rule hierarchies. The approach consists of two phases. Firstly, since rule hierarchies are not readily available in walk-based methods, we have built a Rule Hierarchy Framework (RHF), which leverages a collection of subsumption frameworks to build a proper rule hierarchy from a set of learned rules. And secondly, we adapt RHF to an existing rule learner where we design and implement two methods for Hierarchical Pruning (HPMs), which utilize the generated hierarchies to remove irrelevant and redundant rules. Through experiments over four public benchmark datasets, we show that the application of HPMs is effective in removing unpromising rules, which leads to significant reductions in the runtime as well as in the number of learned rules, without compromising the predictive performance.

cs.AI↗

arXiv2020

Towards Learning Instantiated Logical Rules from Knowledge Graphs

Efficiently inducing high-level interpretable regularities from knowledge graphs (KGs) is an essential yet challenging task that benefits many downstream applications. In this work, we present GPFL, a probabilistic rule learner optimized to mine instantiated first-order logic rules from KGs. Instantiated rules contain constants extracted from KGs. Compared to abstract rules that contain no constants, instantiated rules are capable of explaining and expressing concepts in more details. GPFL utilizes a novel two-stage rule generation mechanism that first generalizes extracted paths into templates that are acyclic abstract rules until a certain degree of template saturation is achieved, then specializes the generated templates into instantiated rules. Unlike existing works that ground every mined instantiated rule for evaluation, GPFL shares groundings between structurally similar rules for collective evaluation. Moreover, we reveal the presence of overfitting rules, their impact on the predictive performance, and the effectiveness of a simple validation method filtering out overfitting rules. Through extensive experiments on public benchmark datasets, we show that GPFL 1.) significantly reduces the runtime on evaluating instantiated rules; 2.) discovers much more quality instantiated rules than existing works; 3.) improves the predictive performance of learned rules by removing overfitting rules via validation; 4.) is competitive on knowledge graph completion task compared to state-of-the-art baselines.

cs.AI↗

arXiv2019

A customisable pipeline for continuously harvesting socially-minded Twitter users

On social media platforms and Twitter in particular, specific classes of users such as influencers have been given satisfactory operational definitions in terms of network and content metrics. Others, for instance online activists, are not less important but their characterisation still requires experimenting. We make the hypothesis that such interesting users can be found within temporally and spatially localised contexts, i.e., small but topical fragments of the network containing interactions about social events or campaigns with a significant footprint on Twitter. To explore this hypothesis, we have designed a continuous user profile discovery pipeline that produces an ever-growing dataset of user profiles by harvesting and analysing contexts from the Twitter stream. The profiles dataset includes key network and content-based users metrics, enabling experimentation with user-defined score functions that characterise specific classes of online users. The paper describes the design and implementation of the pipeline and its empirical evaluation on a case study consisting of healthcare-related campaigns in the UK, showing how it supports the operational definitions of online activism, by comparing three experimental ranking functions. The code is publicly available.

cs.IR↗

arXiv2018

Mind My Value: a decentralized infrastructure for fair and trusted IoT data trading

Internet of Things (IoT) data are increasingly viewed as a new form of massively distributed and large scale digital assets, which are continuously generated by millions of connected devices. The real value of such assets can only be realized by allowing IoT data trading to occur on a marketplace that rewards every single producer and consumer, at a very granular level. Crucially, we believe that such a marketplace should not be owned by anybody, and should instead fairly and transparently self-enforce a well defined set of governance rules. In this paper we address some of the technical challenges involved in realizing such a marketplace. We leverage emerging blockchain technologies to build a decentralized, trusted, transparent and open architecture for IoT traffic metering and contract compliance, on top of the largely adopted IoT brokered data infrastructure. We discuss an Ethereum-based prototype implementation and experimentally evaluate the overhead cost associated with Smart Contract transactions, concluding that a viable business model can indeed be associated with our technical approach.

cs.DC↗

arXiv2018

Design and evaluation of a genomics variant analysis pipeline using GATK Spark tools

Scalable and efficient processing of genome sequence data, i.e. for variant discovery, is key to the mainstream adoption of High Throughput technology for disease prevention and for clinical use. Achieving scalability, however, requires a significant effort to enable the parallel execution of the analysis tools that make up the pipelines. This is facilitated by the new Spark versions of the well-known GATK toolkit, which offer a black-box approach by transparently exploiting the underlying Map Reduce architecture. In this paper we report on our experience implementing a standard variant discovery pipeline using GATK 4.0 with Docker-based deployment over a cluster. We provide a preliminary performance analysis, comparing the processing times and cost to those of the new Microsoft Genomics Services.

cs.DC↗

arXiv2017

Loom: Query-aware Partitioning of Online Graphs

As with general graph processing systems, partitioning data over a cluster of machines improves the scalability of graph database management systems. However, these systems will incur additional network cost during the execution of a query workload, due to inter-partition traversals. Workload-agnostic partitioning algorithms typically minimise the likelihood of any edge crossing partition boundaries. However, these partitioners are sub-optimal with respect to many workloads, especially queries, which may require more frequent traversal of specific subsets of inter-partition edges. Furthermore, they largely unsuited to operating incrementally on dynamic, growing graphs. We present a new graph partitioning algorithm, Loom, that operates on a stream of graph updates and continuously allocates the new vertices and edges to partitions, taking into account a query workload of graph pattern expressions along with their relative frequencies. First we capture the most common patterns of edge traversals which occur when executing queries. We then compare sub-graphs, which present themselves incrementally in the graph update stream, against these common patterns. Finally we attempt to allocate each match to single partitions, reducing the number of inter-partition edges within frequently traversed sub-graphs and improving average query performance. Loom is extensively evaluated over several large test graphs with realistic query workloads and various orderings of the graph updates. We demonstrate that, given a workload, our prototype produces partitionings of significantly better quality than existing streaming graph partitioning algorithms Fennel and LDG.

cs.DB↗

arXiv2017

Recruiting from the network: discovering Twitter users who can help combat Zika epidemics

Tropical diseases like \textit{Chikungunya} and \textit{Zika} have come to prominence in recent years as the cause of serious, long-lasting, population-wide health problems. In large countries like Brasil, traditional disease prevention programs led by health authorities have not been particularly effective. We explore the hypothesis that monitoring and analysis of social media content streams may effectively complement such efforts. Specifically, we aim to identify selected members of the public who are likely to be sensitive to virus combat initiatives that are organised in local communities. Focusing on Twitter and on the topic of Zika, our approach involves (i) training a classifier to select topic-relevant tweets from the Twitter feed, and (ii) discovering the top users who are actively posting relevant content about the topic. We may then recommend these users as the prime candidates for direct engagement within their community. In this short paper we describe our analytical approach and prototype architecture, discuss the challenges of dealing with noisy and sparse signal, and present encouraging preliminary results.

cs.LG↗

arXiv2016

Preserving the value of large scale data analytics over time through selective re-computation

A pervasive problem in Data Science is that the knowledge generated by possibly expensive analytics processes is subject to decay over time, as the data used to compute it drifts, the algorithms used in the processes are improved, and the external knowledge embodied by reference datasets used in the computation evolves. Deciding when such knowledge outcomes should be refreshed, following a sequence of data change events, requires problem-specific functions to quantify their value and its decay over time, as well as models for estimating the cost of their re-computation. What makes this problem challenging is the ambition to develop a decision support system for informing data analytics re-computation decisions over time, that is both generic and customisable. With the help of a case study from genomics, in this vision paper we offer an initial formalisation of this problem, highlight research challenges, and outline a possible approach based on the collection and analysis of metadata from a history of past computations.

cs.DB↗

arXiv2016

TAPER: query-aware, partition-enhancement for large, heterogenous, graphs

Graph partitioning has long been seen as a viable approach to address Graph DBMS scalability. A partitioning, however, may introduce extra query processing latency unless it is sensitive to a specific query workload, and optimised to minimise inter-partition traversals for that workload. Additionally, it should also be possible to incrementally adjust the partitioning in reaction to changes in the graph topology, the query workload, or both. Because of their complexity, current partitioning algorithms fall short of one or both of these requirements, as they are designed for offline use and as one-off operations. The TAPER system aims to address both requirements, whilst leveraging existing partitioning algorithms. TAPER takes any given initial partitioning as a starting point, and iteratively adjusts it by swapping chosen vertices across partitions, heuristically reducing the probability of inter-partition traversals for a given pattern matching queries workload. Iterations are inexpensive thanks to time and space optimisations in the underlying support data structures. We evaluate TAPER on two different large test graphs and over realistic query workloads. Our results indicate that, given a hash-based partitioning, TAPER reduces the number of inter-partition traversals by around 80%; given an unweighted METIS partitioning, by around 30%. These reductions are achieved within 8 iterations and with the additional advantage of being workload-aware and usable online.

cs.DB↗