New Constructions for Competitive and Minimal-Adaptive Group Testing

Group testing (GT) was originally proposed during the World War II in an attempt to minimize the \emph{cost} and \emph{waiting time} in performing identical blood tests of the soldiers for a low-prevalence disease. Formally, the GT problem asks to find $d\ll n$ \emph{defective} elements out of $n$ elements by querying subsets (pools) for the presence of defectives. By the information-theoretic lower bound, essentially $d\log_2 n$ queries are needed in the worst-case. An \emph{adaptive} strategy proceeds sequentially by performing one query at a time, and it can achieve the lower bound. In various applications, nothing is known about $d$ beforehand and a strategy for this scenario is called \emph{competitive}. Such strategies are usually adaptive and achieve query optimality within a constant factor called the \emph{competitive ratio}. In many applications, queries are time-consuming. Therefore, \emph{minimal-adaptive} strategies which run in a small number $s$ of stages of parallel queries are favorable. This work is mainly devoted to the design of minimal-adaptive strategies combined with other demands of both theoretical and practical interest. First we target unknown $d$ and show that actually competitive GT is possible in as few as $2$ stages only. The main ingredient is our randomized estimate of a previously unknown $d$ using nonadaptive queries. In addition, we have developed a systematic approach to obtain optimal competitive ratios for our strategies. When $d$ is a known upper bound, we propose randomized GT strategies which asymptotically achieve query optimality in just $2$, $3$ or $4$ stages depending upon the growth of $d$ versus $n$. Inspired by application settings, such as at American Red Cross, where in most cases GT is applied to small instances, \textit{e.g.}, $n=16$. We extended our study of query-optimal GT strategies to solve a given problem instance with fixed values $n$, $d$ and $s$. We also considered the situation when elements to test cannot be divided physically (electronic devices), thus the pools must be disjoint. For GT with \emph{disjoint} simultaneous pools, we show that $\Theta (sd(n/d)^{1/s})$ tests are sufficient, and also necessary for certain ranges of the parameters

Engineering Competitive and Query-Optimal Minimal-Adaptive Randomized Group Testing Strategies

Suppose that given is a collection of $n$ elements where $d$ of them are \emph{defective}. We can query an arbitrarily chosen subset of elements which returns Yes if the subset contains at least one defective and No if the subset is free of defectives. The problem of group testing is to identify the defectives with a minimum number of such queries. By the information-theoretic lower bound at least $\log_2 \binom {n}{d} \approx d\log_2 (\frac{n}{d}) \approx d\log_2 n$ queries are needed. Using adaptive group testing, i.e., asking one query at a time, the lower bound can be easily achieved. However, strategies are preferred that work in a fixed small number of stages, where queries in a stage are asked in parallel. A group testing strategy is called \emph{competitive} if it works for completely unknown $d$ and requires only $O(d\log_2 n)$ queries. Usually competitive group testing is based on sequential queries. We have shown that actually competitive group testing with expected $O(d\log_2 n)$ queries is possible in only $2$ or $3$ stages. Then we have focused on minimizing the hidden constant factor in the query number and proposed a systematic approach for this purpose. Another main result is related to the design of query-optimal and minimal-adaptive strategies. We have shown that a $2$-stage randomized strategy with prescribed success probability can asymptotically achieve the information-theoretic lower bound for $d \ll n$ and growing much slower than $n$. Similarly, we can approach the entropy lower bound in $4$ stages when $d=o(n)$

A prognostic algorithm to prescribe improvement measures on throughput bottlenecks

Throughput bottleneck analysis is important in prioritising production and maintenance measures in a production system. Due to system dynamics, bottlenecks shift between different production resources and across production runs. Therefore, it is important to predict where the bottlenecks will shift to and understand the root causes of predicted bottlenecks. Previous research efforts on bottlenecks are limited to only predicting the shifting location of throughput bottlenecks; they do not give any insights into root causes. Therefore, the aim of this paper is to propose a data-driven prognostic algorithm (using the active-period bottleneck analysis theory) to forecast the durations of individual active states of bottleneck machines from machine event-log data from the manufacturing execution system (MES). Forecasting the duration of active states helps explain the root causes of bottlenecks and enables the prescription of specific measures for them. It thus forms a machine-states-based prescriptive approach to bottleneck management. Data from real-world production systems is used to demonstrate the effectiveness of the proposed algorithm. The practical implications of these results are that shop-floor production and maintenance teams can be forewarned, before a production run, about bottleneck locations, root causes (in terms of machine states) and any prescribed measures, thus forming a prescriptive approach. This approach will enhance the understanding of bottleneck behaviour in production systems and allow data-driven decision making to manage bottlenecks proactively

Machine learning-based investigation of the cancer protein secretory pathway

Deregulation of the protein secretory pathway (PSP) is linked to many hallmarks of cancer, such as promoting tissue invasion and modulating cell-cell signaling. The collection of secreted proteins processed by the PSP, known as the secretome, is often studied due to its potential as a reservoir of tumor biomarkers. However, there has been less focus on the protein components of the secretory machinery itself. We therefore investigated the expression changes in secretory pathway components across many different cancer types. Specifically, we implemented a dual approach involving differential expression analysis and machine learning to identify PSP genes whose expression was associated with key tumor characteristics: mutation of p53, cancer status, and tumor stage. Eight different machine learning algorithms were included in the analysis to enable comparison between methods and to focus on signals that were robust to algorithm type. The machine learning approach was validated by identifying PSP genes known to be regulated by p53, and even outperformed the differential expression analysis approach. Among the different analysis methods and cancer types, the kinesin family members KIF20A and KIF23 were consistently among the top genes associated with malignant transformation or tumor stage. However, unlike most cancer types which exhibited elevated KIF20A expression that remained relatively constant across tumor stages, renal carcinomas displayed a more gradual increase that continued with increasing disease severity. Collectively, our study demonstrates the complementary nature of a combined differential expression and machine learning approach for analyzing gene expression data, and highlights key PSP components relevant to features of tumor pathophysiology that may constitute potential therapeutic targets

A data-driven approach to diagnosing throughput bottlenecks from a maintenance perspective

Prioritising maintenance activities in throughput bottlenecks increases the throughput from the production system. To facilitate the planning and execution of maintenance activities, throughput bottlenecks in the production system must be identified and diagnosed. Various research efforts have developed data-driven approaches using real-time machine data to identify throughput bottlenecks in the system. However, these efforts have mainly focused on identifying bottlenecks and only offer limited maintenance-related diagnostics for them. Moreover, these research efforts have been proposed from an academic perspective using rigorous scientific methods. A number of challenges must be addressed, if existing data-driven approaches are to be adapted to real-world practice. These include identifying relevant data types, data pre-processing and data modelling. Such challenges can be better addressed by including maintenance-practitioner input when developing data-driven approaches. The aim of this paper is therefore to demonstrate a data-driven approach to diagnosing throughput bottlenecks, using the combined knowledge of the maintenance and data-science domains. Diagnostic insights into throughput bottlenecks are obtained using unsupervised machine-learning techniques. The demonstration uses real-world machine datasets extracted from the production line. The novelty of the research presented in this paper is that it shows how inputs from maintenance practitioners can be used to develop data-driven approaches for diagnosing throughput bottlenecks having more practical relevance. By gaining these diagnostic insights, maintenance practitioners can better understand shop-floor throughput bottleneck behaviours from a maintenance perspective and thus prioritise various maintenance actions

Artificial intelligence for throughput bottleneck analysis – State-of-the-art and future directions

Identifying, and eventually eliminating throughput bottlenecks, is a key means to increase throughput and productivity in production systems. In the real world, however, eliminating throughput bottlenecks is a challenge. This is due to the landscape of complex factory dynamics, with several hundred machines operating at any given time. Academic researchers have tried to develop tools to help identify and eliminate throughput bottlenecks. Historically, research efforts have focused on developing analytical and discrete event simulation modelling approaches to identify throughput bottlenecks in production systems. However, with the rise of industrial digitalisation and artificial intelligence (AI), academic researchers explored different ways in which AI might be used to eliminate throughput bottlenecks, based on the vast amounts of digital shop floor data. By conducting a systematic literature review, this paper aims to present state-of-the-art research efforts into the use of AI for throughput bottleneck analysis. To make the work of the academic AI solutions more accessible to practitioners, the research efforts are classified into four categories: (1) identify, (2) diagnose, (3) predict and (4) prescribe. This was inspired by real-world throughput bottleneck management practice. The categories, identify and diagnose focus on analysing historical throughput bottlenecks, whereas predict and prescribe focus on analysing future throughput bottlenecks. This paper also provides future research topics and practical recommendations which may help to further push the boundaries of the theoretical and practical use of AI in throughput bottleneck analysis

A generic hierarchical clustering approach for detecting bottlenecks in manufacturing

The advancements in machine learning (ML) techniques open new opportunities for analysing production system dynamics and augmenting the domain expert\u27s decision-making. A common problem for domain experts on the shop floor is detecting throughput bottlenecks, as they constrain the system throughput. Detecting throughput bottlenecks is necessary to prioritise maintenance and improvement actions and obtain greater system throughput. The existing literature provides many ways to detect bottlenecks from machine data, using statistical-based approaches. These statistical-based approaches can be best applied in environments where the statistical descriptors of machine data (such as distribution of machine data, correlations and stationarity) are known beforehand. Computing statistical descriptors involves statistical assumptions. When the machine data doesn\u27t comply with these assumptions, there is a risk of the results being disconnected from actual production system dynamics. An alternative approach to detecting throughput bottlenecks is to use ML- based techniques. These techniques, particularly unsupervised ML techniques, require no prior statistical information on machine data. This paper proposes a generic, unsupervised ML-based hierarchical clustering approach to detect throughput bottlenecks. The proposed approach is the outcome of systematic and careful selection of ML techniques. It begins by generating a time series of the chosen bottleneck detection metric and then clustering the time series using a dynamic time-wrapping measure and a complete-linkage agglomerative hierarchical clustering technique. The results are clusters of machines with similar production dynamic profiles, revealed from the historical data and enabling the detection of bottlenecks. The proposed approach is demonstrated in two real-world production systems. The approach integrates the concept of humans in-loop by using the domain expert\u27s knowledge

How Does Interleukin-22 Mediate Liver Regeneration and Prevent Injury and Fibrosis?

Interleukin-22 (IL-22) is a pluripotent T cell-derived cytokine which is a member of IL-10 cytokine family. It is the only interleukin produced by immune cells but does not target immune system components. IL-22 is mainly produced by dendritic cells (DCs) and TH17, TH22, NK, and NKT cells and targets a number of body tissues including liver, pancreas, and other epithelial tissues. It provokes a series of downstream signaling pathways upon binding with IL-22R complex which protects liver damage through STAT3 activation. IL-22BP is an inhibitor of IL-22 which has 20-1000x more affinity to bind with IL-22 compared to IL-22R1 that inhibits IL-22 activity. Its level was found to be positively correlated with the severity of liver damage and fibrosis. So, the present review is an effort to reveal the exact mechanism lying in the hepatoprotective activity of IL-22 and some of its future therapeutic implications

Data-driven algorithm for throughput bottleneck analysis of production systems

The digital transformation of manufacturing industries is expected to yield increased productivity. Companies collect large volumes of real-time machine data and are seeking new ways to use it in furthering data-driven decision making. A\ua0challenge for these companies is identifying throughput bottlenecks using the real-time machine data they collect. This paper proposes a data-driven algorithm to better identify bottleneck groups and provide diagnostic insights. The algorithm is based on the active period theory of throughput bottleneck analysis. It integrates available manufacturing execution systems (MES) data from the machines and tests the statistical significance of any bottlenecks detected. The algorithm can be automated to allow data-driven decision making on the shop floor, thus improving throughput. Real-world MES datasets were used to develop and test the algorithm, producing research outcomes useful to\ua0manufacturing industries. This research pushes standards in throughput bottleneck analysis, using an interdisciplinary approach based on production and data sciences

Bayesian optimization in ab initio nuclear physics

Theoretical models of the strong nuclear interaction contain unknown coupling constants (parameters) that must be determined using a pool of calibration data. In cases where the models are complex, leading to time consuming calculations, it is particularly challenging to systematically search the corresponding parameter domain for the best fit to the data. In this paper, we explore the prospect of applying Bayesian optimization to constrain the coupling constants in chiral effective field theory descriptions of the nuclear interaction. We find that Bayesian optimization performs rather well with low-dimensional parameter domains and foresee that it can be particularly useful for optimization of a smaller set of coupling constants. A specific example could be the determination of leading three-nucleon forces using data from finite nuclei or three-nucleon scattering experiments