The accurate diagnosis and molecular profiling of colorectal cancers are critical for planning the best treatment options for patients. Microsatellite instability (MSI) or mismatch repair (MMR) status plays a vital role inappropriate treatment selection, has prognostic implications and is used to investigate the possibility of patients having underlying genetic disorders (Lynch syndrome). NICE recommends that all CRC patients should be offered MMR/microsatellite instability (MSI) testing. Immunohistochemistry is commonly used to assess MMR status with subsequent molecular testing performed as required. This incurs significant extra costs and requires additional resources. The introduction of automated methods that can predict MSI or MMR status from a target image could substantially reduce the cost associated with MMR testing. Unlike previous studies on MSI prediction involving training a CNN using coarse labels (Microsatellite Instable vs Microsatellite Stable), we have utilised fine-grain MMR labels for training purposes. In this paper, we present our work on predicting MSI status in a two-stage process using a single target slide either stained with CK8/18 or H\&E. First, we trained a multi-headed convolutional neural network model where each head was responsible for predicting one of the MMR protein expressions. To this end, we performed the registration of MMR stained slides to the target slide as a pre-processing step. In the second stage, statistical features computed from the MMR prediction maps were used for the final MSI prediction. Our results demonstrated that MSI classification can be improved by incorporating fine-grained MMR labels in comparison to the previous approaches in which only coarse labels were utilised.
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A recent cohort study revealed a positive correlate between major structural birth defects in infants and a certain medication taken by pregnant women. To draw valid causal inference, an outstanding problem to overcome was the missing birth defect outcomes among pregnancy losses resulting from spontaneous abortion. This led to missing not at random since, according to the theory of "terathanasia", a defected fetus is more likely to be spontaneously aborted. Other complications in the data included left truncation, right censoring, observational nature, and rare events. In addition, the previous analysis stratified on live birth against spontaneous abortion, which was itself a post-exposure variable and hence did not lead to a causal interpretation of the stratified results. In this paper we aim to estimate and provide inference for the causal parameters of scientific interest, including the principal effects, making use of the missing data mechanism informed by "terathanasia". The rare events with missing outcomes led to multiple sensitivity analyses where the causal parameters can be estimated with better confidence in each setting. Our findings should shed light on how studies on causal effects of medication or other exposures during pregnancy may be analyzed using state-of-the-art methodologies.
Landscape-aware algorithm selection approaches have so far mostly been relying on landscape feature extraction as a preprocessing step, independent of the execution of optimization algorithms in the portfolio. This introduces a significant overhead in computational cost for many practical applications, as features are extracted and computed via sampling and evaluating the problem instance at hand, similarly to what the optimization algorithm would perform anyway within its search trajectory. As suggested in Jankovic et al. (EvoAPPs 2021), trajectory-based algorithm selection circumvents the problem of costly feature extraction by computing landscape features from points that a solver sampled and evaluated during the optimization process. Features computed in this manner are used to train algorithm performance regression models, upon which a per-run algorithm selector is then built. In this work, we apply the trajectory-based approach onto a portfolio of five algorithms. We study the quality and accuracy of performance regression and algorithm selection models in the scenario of predicting different algorithm performances after a fixed budget of function evaluations. We rely on landscape features of the problem instance computed using one portion of the aforementioned budget of the same function evaluations. Moreover, we consider the possibility of switching between the solvers once, which requires them to be warm-started, i.e. when we switch, the second solver continues the optimization process already being initialized appropriately by making use of the information collected by the first solver. In this new context, we show promising performance of the trajectory-based per-run algorithm selection with warm-starting.
Modern vehicles rely on a fleet of electronic control units (ECUs) connected through controller area network (CAN) buses for critical vehicular control. However, with the expansion of advanced connectivity features in automobiles and the elevated risks of internal system exposure, the CAN bus is increasingly prone to intrusions and injection attacks. The ordinary injection attacks disrupt the typical timing properties of the CAN data stream, and the rule-based intrusion detection systems (IDS) can easily detect them. However, advanced attackers can inject false data to the time series sensory data (signal), while looking innocuous by the pattern/frequency of the CAN messages. Such attacks can bypass the rule-based IDS or any anomaly-based IDS built on binary payload data. To make the vehicles robust against such intelligent attacks, we propose CANShield, a signal-based intrusion detection framework for the CAN bus. CANShield consists of three modules: a data preprocessing module that handles the high-dimensional CAN data stream at the signal level and makes them suitable for a deep learning model; a data analyzer module consisting of multiple deep autoencoder (AE) networks, each analyzing the time-series data from a different temporal perspective; and finally an attack detection module that uses an ensemble method to make the final decision. Evaluation results on two high-fidelity signal-based CAN attack datasets show the high accuracy and responsiveness of CANShield in detecting wide-range of advanced intrusion attacks.
Ensemble forecasting is, so far, the most successful approach to produce relevant forecasts with an estimation of their uncertainty. The main limitations of ensemble forecasting are the high computational cost and the difficulty to capture and quantify different sources of uncertainty, particularly those associated with model errors. In this work we perform toy-model and state-of-the-art model experiments to analyze to what extent artificial neural networks (ANNs) are able to model the different sources of uncertainty present in a forecast. In particular those associated with the accuracy of the initial conditions and those introduced by the model error. We also compare different training strategies: one based on a direct training using the mean and spread of an ensemble forecast as target, the other ones rely on an indirect training strategy using an analyzed state as target in which the uncertainty is implicitly learned from the data. Experiments using the Lorenz'96 model show that the ANNs are able to emulate some of the properties of ensemble forecasts like the filtering of the most unpredictable modes and a state-dependent quantification of the forecast uncertainty. Moreover, ANNs provide a reliable estimation of the forecast uncertainty in the presence of model error. Preliminary experiments conducted with a state-of-the-art forecasting system also confirm the ability of ANNs to produce a reliable quantification of the forecast uncertainty.
Cancer is a fatal disease caused by a combination of genetic diseases and a variety of biochemical abnormalities. Lung and colon cancer have emerged as two of the leading causes of death and disability in humans. The histopathological detection of such malignancies is usually the most important component in determining the best course of action. Early detection of the ailment on either front considerably decreases the likelihood of mortality. Machine learning and deep learning techniques can be utilized to speed up such cancer detection, allowing researchers to study a large number of patients in a much shorter amount of time and at a lower cost. In this research work, we introduced a hybrid ensemble feature extraction model to efficiently identify lung and colon cancer. It integrates deep feature extraction and ensemble learning with high-performance filtering for cancer image datasets. The model is evaluated on histopathological (LC25000) lung and colon datasets. According to the study findings, our hybrid model can detect lung, colon, and (lung and colon) cancer with accuracy rates of 99.05%, 100%, and 99.30%, respectively. The study's findings show that our proposed strategy outperforms existing models significantly. Thus, these models could be applicable in clinics to support the doctor in the diagnosis of cancers.
The remarkable success of deep learning has prompted interest in its application to medical diagnosis. Even tough state-of-the-art deep learning models have achieved human-level accuracy on the classification of different types of medical data, these models are hardly adopted in clinical workflows, mainly due to their lack of interpretability. The black-box-ness of deep learning models has raised the need for devising strategies to explain the decision process of these models, leading to the creation of the topic of eXplainable Artificial Intelligence (XAI). In this context, we provide a thorough survey of XAI applied to medical diagnosis, including visual, textual, and example-based explanation methods. Moreover, this work reviews the existing medical imaging datasets and the existing metrics for evaluating the quality of the explanations . Complementary to most existing surveys, we include a performance comparison among a set of report generation-based methods. Finally, the major challenges in applying XAI to medical imaging are also discussed.
Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.
With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
Recent years have witnessed significant advances in technologies and services in modern network applications, including smart grid management, wireless communication, cybersecurity as well as multi-agent autonomous systems. Considering the heterogeneous nature of networked entities, emerging network applications call for game-theoretic models and learning-based approaches in order to create distributed network intelligence that responds to uncertainties and disruptions in a dynamic or an adversarial environment. This paper articulates the confluence of networks, games and learning, which establishes a theoretical underpinning for understanding multi-agent decision-making over networks. We provide an selective overview of game-theoretic learning algorithms within the framework of stochastic approximation theory, and associated applications in some representative contexts of modern network systems, such as the next generation wireless communication networks, the smart grid and distributed machine learning. In addition to existing research works on game-theoretic learning over networks, we highlight several new angles and research endeavors on learning in games that are related to recent developments in artificial intelligence. Some of the new angles extrapolate from our own research interests. The overall objective of the paper is to provide the reader a clear picture of the strengths and challenges of adopting game-theoretic learning methods within the context of network systems, and further to identify fruitful future research directions on both theoretical and applied studies.
It has been a long time that computer architecture and systems are optimized to enable efficient execution of machine learning (ML) algorithms or models. Now, it is time to reconsider the relationship between ML and systems, and let ML transform the way that computer architecture and systems are designed. This embraces a twofold meaning: the improvement of designers' productivity, and the completion of the virtuous cycle. In this paper, we present a comprehensive review of work that applies ML for system design, which can be grouped into two major categories, ML-based modelling that involves predictions of performance metrics or some other criteria of interest, and ML-based design methodology that directly leverages ML as the design tool. For ML-based modelling, we discuss existing studies based on their target level of system, ranging from the circuit level to the architecture/system level. For ML-based design methodology, we follow a bottom-up path to review current work, with a scope of (micro-)architecture design (memory, branch prediction, NoC), coordination between architecture/system and workload (resource allocation and management, data center management, and security), compiler, and design automation. We further provide a future vision of opportunities and potential directions, and envision that applying ML for computer architecture and systems would thrive in the community.
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