Jonathan M. Garibaldi

Qing Xu, Jiaxuan Li, Xiangjian He et al.

The universality of deep neural networks across different modalities and their generalization capabilities to unseen domains play an essential role in medical image segmentation. The recent segment anything model (SAM) has demonstrated strong adaptability across diverse natural scenarios. However, the huge computational costs, demand for manual annotations as prompts and conflict-prone decoding process of SAM degrade its generalization capabilities in medical scenarios. To address these limitations, we propose a modality-decoupled lightweight SAM for domain-generalized medical image segmentation, named De-LightSAM. Specifically, we first devise a lightweight domain-controllable image encoder (DC-Encoder) that produces discriminative visual features for diverse modalities. Further, we introduce the self-patch prompt generator (SP-Generator) to automatically generate high-quality dense prompt embeddings for guiding segmentation decoding. Finally, we design the query-decoupled modality decoder (QM-Decoder) that leverages a one-to-one strategy to provide an independent decoding channel for every modality, preventing mutual knowledge interference of different modalities. Moreover, we design a multi-modal decoupled knowledge distillation (MDKD) strategy to leverage robust common knowledge to complement domain-specific medical feature representations. Extensive experiments indicate that De-LightSAM outperforms state-of-the-arts in diverse medical imaging segmentation tasks, displaying superior modality universality and generalization capabilities. Especially, De-LightSAM uses only 2.0% parameters compared to SAM-H. The source code is available at https://github.com/xq141839/De-LightSAM.

Chao Chen, Christian Wagner, Jonathan M. Garibaldi

Since their introduction, fuzzy sets and systems have become an important area of research known for its versatility in modelling, knowledge representation and reasoning, and increasingly its potential within the context explainable AI. While the applications of fuzzy systems are diverse, there has been comparatively little advancement in their design from a machine learning perspective. In other words, while representations such as neural networks have benefited from a boom in learning capability driven by an increase in computational performance in combination with advances in their training mechanisms and available tool, in particular gradient descent, the impact on fuzzy system design has been limited. In this paper, we discuss gradient-descent-based optimisation of fuzzy systems, focussing in particular on automatic differentiation -- crucial to neural network learning -- with a view to free fuzzy system designers from intricate derivative computations, allowing for more focus on the functional and explainability aspects of their design. As a starting point, we present a use case in FuzzyR which demonstrates how current fuzzy inference system implementations can be adjusted to leverage powerful features of automatic differentiation tools sets, discussing its potential for the future of fuzzy system design.

Zixiao Shen, Xin Chen, Jonathan M. Garibaldi

This paper presents a novel meta learning framework for feature selection (FS) based on fuzzy similarity. The proposed method aims to recommend the best FS method from four candidate FS methods for any given dataset. This is achieved by firstly constructing a large training data repository using data synthesis. Six meta features that represent the characteristics of the training dataset are then extracted. The best FS method for each of the training datasets is used as the meta label. Both the meta features and the corresponding meta labels are subsequently used to train a classification model using a fuzzy similarity measure based framework. Finally the trained model is used to recommend the most suitable FS method for a given unseen dataset. This proposed method was evaluated based on eight public datasets of real-world applications. It successfully recommended the best method for five datasets and the second best method for one dataset, which outperformed any of the four individual FS methods. Besides, the proposed method is computationally efficient for algorithm selection, leading to negligible additional time for the feature selection process. Thus, the paper contributes a novel method for effectively recommending which feature selection method to use for any new given dataset.

Zixiao Shen, Xin Chen, Jonathan M. Garibaldi

In this paper, we propose a novel weighted combination feature selection method using bootstrap and fuzzy sets. The proposed method mainly consists of three processes, including fuzzy sets generation using bootstrap, weighted combination of fuzzy sets and feature ranking based on defuzzification. We implemented the proposed method by combining four state-of-the-art feature selection methods and evaluated the performance based on three publicly available biomedical datasets using five-fold cross validation. Based on the feature selection results, our proposed method produced comparable (if not better) classification accuracies to the best of the individual feature selection methods for all evaluated datasets. More importantly, we also applied standard deviation and Pearson's correlation to measure the stability of the methods. Remarkably, our combination method achieved significantly higher stability than the four individual methods when variations and size reductions were introduced to the datasets.

Zixiao Shen, Xin Chen, Jonathan M. Garibaldi

In this paper, based on a fuzzy entropy feature selection framework, different methods have been implemented and compared to improve the key components of the framework. Those methods include the combinations of three ideal vector calculations, three maximal similarity classifiers and three fuzzy entropy functions. Different feature removal orders based on the fuzzy entropy values were also compared. The proposed method was evaluated on three publicly available biomedical datasets. From the experiments, we concluded the optimized combination of the ideal vector, similarity classifier and fuzzy entropy function for feature selection. The optimized framework was also compared with other six classical filter-based feature selection methods. The proposed method was ranked as one of the top performers together with the Correlation and ReliefF methods. More importantly, the proposed method achieved the most stable performance for all three datasets when the features being gradually removed. This indicates a better feature ranking performance than the other compared methods.

Qing Li, Jiasong Zhu, Rui Cao et al.

6DOF camera relocalization is an important component of autonomous driving and navigation. Deep learning has recently emerged as a promising technique to tackle this problem. In this paper, we present a novel relative geometry-aware Siamese neural network to enhance the performance of deep learning-based methods through explicitly exploiting the relative geometry constraints between images. We perform multi-task learning and predict the absolute and relative poses simultaneously. We regularize the shared-weight twin networks in both the pose and feature domains to ensure that the estimated poses are globally as well as locally correct. We employ metric learning and design a novel adaptive metric distance loss to learn a feature that is capable of distinguishing poses of visually similar images from different locations. We evaluate the proposed method on public indoor and outdoor benchmarks and the experimental results demonstrate that our method can significantly improve localization performance. Furthermore, extensive ablation evaluations are conducted to demonstrate the effectiveness of different terms of the loss function.

Simon Miller, Christian Wagner, Uwe Aickelin et al.

An important role carried out by cyber-security experts is the assessment of proposed computer systems, during their design stage. This task is fraught with difficulties and uncertainty, making the knowledge provided by human experts essential for successful assessment. Today, the increasing number of progressively complex systems has led to an urgent need to produce tools that support the expert-led process of system-security assessment. In this research, we use weighted averages (WAs) and ordered weighted averages (OWAs) with evolutionary algorithms (EAs) to create aggregation operators that model parts of the assessment process. We show how individual overall ratings for security components can be produced from ratings of their characteristics, and how these individual overall ratings can be aggregated to produce overall rankings of potential attacks on a system. As well as the identification of salient attacks and weak points in a prospective system, the proposed method also highlights which factors and security components contribute most to a component's difficulty and attack ranking respectively. A real world scenario is used in which experts were asked to rank a set of technical attacks, and to answer a series of questions about the security components that are the subject of the attacks. The work shows how finding good aggregation operators, and identifying important components and factors of a cyber-security problem can be automated. The resulting operators have the potential for use as decision aids for systems designers and cyber-security experts, increasing the amount of assessment that can be achieved with the limited resources available.

Jenna Marie Reps, Jonathan M. Garibaldi, Uwe Aickelin et al.

Big longitudinal observational medical data potentially hold a wealth of information and have been recognised as potential sources for gaining new drug safety knowledge. Unfortunately there are many complexities and underlying issues when analysing longitudinal observational data. Due to these complexities, existing methods for large-scale detection of negative side effects using observational data all tend to have issues distinguishing between association and causality. New methods that can better discriminate causal and non-causal relationships need to be developed to fully utilise the data. In this paper we propose using a set of causality considerations developed by the epidemiologist Bradford Hill as a basis for engineering features that enable the application of supervised learning for the problem of detecting negative side effects. The Bradford Hill considerations look at various perspectives of a drug and outcome relationship to determine whether it shows causal traits. We taught a classifier to find patterns within these perspectives and it learned to discriminate between association and causality. The novelty of this research is the combination of supervised learning and Bradford Hill's causality considerations to automate the Bradford Hill's causality assessment. We evaluated the framework on a drug safety gold standard know as the observational medical outcomes partnership's nonspecified association reference set. The methodology obtained excellent discriminate ability with area under the curves ranging between 0.792-0.940 (existing method optimal: 0.73) and a mean average precision of 0.640 (existing method optimal: 0.141). The proposed features can be calculated efficiently and be readily updated, making the framework suitable for big observational data.

Grazziela P. Figueredo, Christian Wagner, Jonathan M. Garibaldi et al.

In this position paper, we present ideas about creating a next generation framework towards an adaptive interface for data communication and visualisation systems. Our objective is to develop a system that accepts large data sets as inputs and provides user-centric, meaningful visual information to assist owners to make sense of their data collection. The proposed framework comprises four stages: (i) the knowledge base compilation, where we search and collect existing state-ofthe-art visualisation techniques per domain and user preferences; (ii) the development of the learning and inference system, where we apply artificial intelligence techniques to learn, predict and recommend new graphic interpretations (iii) results evaluation; and (iv) reinforcement and adaptation, where valid outputs are stored in our knowledge base and the system is iteratively tuned to address new demands. These stages, as well as our overall vision, limitations and possible challenges are introduced in this article. We also discuss further extensions of this framework for other knowledge discovery tasks.

Grazziela P. Figueredo, Peer-Olaf Siebers, Uwe Aickelin et al.

Advances in healthcare and in the quality of life significantly increase human life expectancy. With the ageing of populations, new un-faced challenges are brought to science. The human body is naturally selected to be well-functioning until the age of reproduction to keep the species alive. However, as the lifespan extends, unseen problems due to the body deterioration emerge. There are several age-related diseases with no appropriate treatment; therefore, the complex ageing phenomena needs further understanding. Immunosenescence, the ageing of the immune system, is highly correlated to the negative effects of ageing, such as the increase of auto-inflammatory diseases and decrease in responsiveness to new diseases. Besides clinical and mathematical tools, we believe there is opportunity to further exploit simulation tools to understand immunosenescence. Compared to real-world experimentation, benefits include time and cost effectiveness due to the laborious, resource-intensiveness of the biological environment and the possibility of conducting experiments without ethic restrictions. Contrasted with mathematical models, simulation modelling is more suitable for representing complex systems and emergence. In addition, there is the belief that simulation models are easier to communicate in interdisciplinary contexts. Our work investigates the usefulness of simulations to understand immunosenescence by employing two different simulation methods, agent-based and system dynamics simulation, to a case study of immune cells depletion with age.

Alexandros Ladas, Jonathan M. Garibaldi, Rodrigo Scarpel et al.

Consumer Debt has risen to be an important problem of modern societies, generating a lot of research in order to understand the nature of consumer indebtness, which so far its modelling has been carried out by statistical models. In this work we show that Computational Intelligence can offer a more holistic approach that is more suitable for the complex relationships an indebtness dataset has and Linear Regression cannot uncover. In particular, as our results show, Neural Networks achieve the best performance in modelling consumer indebtness, especially when they manage to incorporate the significant and experimentally verified results of the Data Mining process in the model, exploiting the flexibility Neural Networks offer in designing their topology. This novel method forms an elaborate framework to model Consumer indebtness that can be extended to any other real world application.

Jenna M. Reps, Uwe Aickelin, Jonathan M. Garibaldi

In previous work, a novel supervised framework implementing a binary classifier was presented that obtained excellent results for side effect discovery. Interestingly, unique side effects were identified when different binary classifiers were used within the framework, prompting the investigation of applying a multiple classifier system. In this paper we investigate tuning a side effect multiple classifying system using genetic algorithms. The results of this research show that the novel framework implementing a multiple classifying system trained using genetic algorithms can obtain a higher partial area under the receiver operating characteristic curve than implementing a single classifier. Furthermore, the framework is able to detect side effects efficiently and obtains a low false positive rate.

Jenna Reps, Jonathan M. Garibaldi, Uwe Aickelin et al.

The pharmaceutical industry is plagued by the problem of side effects that can occur anytime a prescribed medication is ingested. There has been a recent interest in using the vast quantities of medical data available in longitudinal observational databases to identify causal relationships between drugs and medical events. Unfortunately the majority of existing post marketing surveillance algorithms measure how dependant or associated an event is on the presence of a drug rather than measuring causality. In this paper we investigate potential attributes that can be used in causal inference to identify side effects based on the Bradford-Hill causality criteria. Potential attributes are developed by considering five of the causality criteria and feature selection is applied to identify the most suitable of these attributes for detecting side effects. We found that attributes based on the specificity criterion may improve side effect signalling algorithms but the experiment and dosage criteria attributes investigated in this paper did not offer sufficient additional information.

Jenna M. Reps, Jonathan M. Garibaldi, Uwe Aickelin et al.

Background: Children are frequently prescribed medication off-label, meaning there has not been sufficient testing of the medication to determine its safety or effectiveness. The main reason this safety knowledge is lacking is due to ethical restrictions that prevent children from being included in the majority of clinical trials. Objective: The objective of this paper is to investigate whether an ensemble of simple study designs can be implemented to signal acutely occurring side effects effectively within the paediatric population by using historical longitudinal data. The majority of pharmacovigilance techniques are unsupervised, but this research presents a supervised framework. Methods: Multiple measures of association are calculated for each drug and medical event pair and these are used as features that are fed into a classiffier to determine the likelihood of the drug and medical event pair corresponding to an adverse drug reaction. The classiffier is trained using known adverse drug reactions or known non-adverse drug reaction relationships. Results: The novel ensemble framework obtained a false positive rate of 0:149, a sensitivity of 0:547 and a specificity of 0:851 when implemented on a reference set of drug and medical event pairs. The novel framework consistently outperformed each individual simple study design. Conclusion: This research shows that it is possible to exploit the mechanism of causality and presents a framework for signalling adverse drug reactions effectively.

Jenna Reps, Jonathan M. Garibaldi, Uwe Aickelin et al.

Drugs are frequently prescribed to patients with the aim of improving each patient's medical state, but an unfortunate consequence of most prescription drugs is the occurrence of undesirable side effects. Side effects that occur in more than one in a thousand patients are likely to be signalled efficiently by current drug surveillance methods, however, these same methods may take decades before generating signals for rarer side effects, risking medical morbidity or mortality in patients prescribed the drug while the rare side effect is undiscovered. In this paper we propose a novel computational meta-analysis framework for signalling rare side effects that integrates existing methods, knowledge from the web, metric learning and semi-supervised clustering. The novel framework was able to signal many known rare and serious side effects for the selection of drugs investigated, such as tendon rupture when prescribed Ciprofloxacin or Levofloxacin, renal failure with Naproxen and depression associated with Rimonabant. Furthermore, for the majority of the drug investigated it generated signals for rare side effects at a more stringent signalling threshold than existing methods and shows the potential to become a fundamental part of post marketing surveillance to detect rare side effects.

Jenna Reps, Jonathan M. Garibaldi, Uwe Aickelin et al.

The electronic healthcare databases are starting to become more readily available and are thought to have excellent potential for generating adverse drug reaction signals. The Health Improvement Network (THIN) database is an electronic healthcare database containing medical information on over 11 million patients that has excellent potential for detecting ADRs. In this paper we apply four existing electronic healthcare database signal detecting algorithms (MUTARA, HUNT, Temporal Pattern Discovery and modified ROR) on the THIN database for a selection of drugs from six chosen drug families. This is the first comparison of ADR signalling algorithms that includes MUTARA and HUNT and enabled us to set a benchmark for the adverse drug reaction signalling ability of the THIN database. The drugs were selectively chosen to enable a comparison with previous work and for variety. It was found that no algorithm was generally superior and the algorithms' natural thresholds act at variable stringencies. Furthermore, none of the algorithms perform well at detecting rare ADRs.

Jenna Reps, Jonathan M. Garibaldi, Uwe Aickelin et al.

Longitudinal observational databases have become a recent interest in the post marketing drug surveillance community due to their ability of presenting a new perspective for detecting negative side effects. Algorithms mining longitudinal observation databases are not restricted by many of the limitations associated with the more conventional methods that have been developed for spontaneous reporting system databases. In this paper we investigate the robustness of four recently developed algorithms that mine longitudinal observational databases by applying them to The Health Improvement Network (THIN) for six drugs with well document known negative side effects. Our results show that none of the existing algorithms was able to consistently identify known adverse drug reactions above events related to the cause of the drug and no algorithm was superior.

Jenna Reps, Jonathan M. Garibaldi, Uwe Aickelin et al.

The wealth of computerised medical information becoming readily available presents the opportunity to examine patterns of illnesses, therapies and responses. These patterns may be able to predict illnesses that a patient is likely to develop, allowing the implementation of preventative actions. In this paper sequential rule mining is applied to a General Practice database to find rules involving a patients age, gender and medical history. By incorporating these rules into current health-care a patient can be highlighted as susceptible to a future illness based on past or current illnesses, gender and year of birth. This knowledge has the ability to greatly improve health-care and reduce health-care costs.

Naisan Benatar, Uwe Aickelin, Jonathan M. Garibaldi

It has been suggested that, when faced with large amounts of uncertainty in situations of automated control, type-2 fuzzy logic based controllers will out-perform the simpler type-1 varieties due to the latter lacking the flexibility to adapt accordingly. This paper aims to investigate this problem in detail in order to analyse when a type-2 controller will improve upon type-1 performance. A robotic sailing boat is subjected to several experiments in which the uncertainty and difficulty of the sailing problem is increased in order to observe the effects on measured performance. Improved performance is observed but not in every case. The size of the FOU is shown to be have a large effect on performance with potentially severe performance penalties for incorrectly sized footprints.

Jenna Reps, Jan Feyereisl, Jonathan M. Garibaldi et al.

Data-mining techniques have frequently been developed for Spontaneous reporting databases. These techniques aim to find adverse drug events accurately and efficiently. Spontaneous reporting databases are prone to missing information, under reporting and incorrect entries. This often results in a detection lag or prevents the detection of some adverse drug events. These limitations do not occur in electronic health-care databases. In this paper, existing methods developed for spontaneous reporting databases are implemented on both a spontaneous reporting database and a general practice electronic health-care database and compared. The results suggests that the application of existing methods to the general practice database may help find signals that have gone undetected when using the spontaneous reporting system database. In addition the general practice database provides far more supplementary information, that if incorporated in analysis could provide a wealth of information for identifying adverse events more accurately.

Naisan Benatar, Uwe Aickelin, Jonathan M. Garibaldi

Type-1 fuzzy logic has frequently been used in control systems. However this method is sometimes shown to be too restrictive and unable to adapt in the presence of uncertainty. In this paper we compare type-1 fuzzy control with several other fuzzy approaches under a range of uncertain conditions. Interval type-2 and non-stationary fuzzy controllers are compared, along with 'dual surface' type-2 control, named due to utilising both the lower and upper values produced from standard interval type-2 systems. We tune a type-1 controller, then derive the membership functions and footprints of uncertainty from the type-1 system and evaluate them using a simulated autonomous sailing problem with varying amounts of environmental uncertainty. We show that while these more sophisticated controllers can produce better performance than the type-1 controller, this is not guaranteed and that selection of Footprint of Uncertainty (FOU) size has a large effect on this relative performance.

Simon Miller, Susan Appleby, Jonathan M. Garibaldi et al.

The task of designing secure software systems is fraught with uncertainty, as data on uncommon attacks is limited, costs are difficult to estimate, and technology and tools are continually changing. Consequently, experts may interpret the security risks posed to a system in different ways, leading to variation in assessment. This paper presents research into measuring the variability in decision making between security professionals, with the ultimate goal of improving the quality of security advice given to software system designers. A set of thirty nine cyber-security experts took part in an exercise in which they independently assessed a realistic system scenario. This study quantifies agreement in the opinions of experts, examines methods of aggregating opinions, and produces an assessment of attacks from ratings of their components. We show that when aggregated, a coherent consensus view of security emerges which can be used to inform decisions made during systems design.

Amanda Whitbrook, Uwe Aickelin, Jonathan M. Garibaldi

In mobile robotics, a solid test for adaptation is the ability of a control system to function not only in a diverse number of physical environments, but also on a number of different robotic platforms. This paper demonstrates that a set of behaviours evolved in simulation on a miniature robot (epuck) can be transferred to a much larger-scale platform (Pioneer), both in simulation and in the real world. The chosen architecture uses artificial evolution of epuck behaviours to obtain a genetic sequence, which is then employed to seed an idiotypic, artificial immune system (AIS) on the Pioneers. Despite numerous hardware and software differences between the platforms, navigation and target-finding experiments show that the evolved behaviours transfer very well to the larger robot when the idiotypic AIS technique is used. In contrast, transferability is poor when reinforcement learning alone is used, which validates the adaptability of the chosen architecture.