Kevin M. Smith

Johan Fredin Haslum, Christos Matsoukas, Karl-Johan Leuchowius et al.

High content imaging assays can capture rich phenotypic response data for large sets of compound treatments, aiding in the characterization and discovery of novel drugs. However, extracting representative features from high content images that can capture subtle nuances in phenotypes remains challenging. The lack of high-quality labels makes it difficult to achieve satisfactory results with supervised deep learning. Self-Supervised learning methods have shown great success on natural images, and offer an attractive alternative also to microscopy images. However, we find that self-supervised learning techniques underperform on high content imaging assays. One challenge is the undesirable domain shifts present in the data known as batch effects, which are caused by biological noise or uncontrolled experimental conditions. To this end, we introduce Cross-Domain Consistency Learning (CDCL), a self-supervised approach that is able to learn in the presence of batch effects. CDCL enforces the learning of biological similarities while disregarding undesirable batch-specific signals, leading to more useful and versatile representations. These features are organised according to their morphological changes and are more useful for downstream tasks -- such as distinguishing treatments and mechanism of action.

Kevin Smith, Hai Lin, Praveen Tiwari et al.

Property Specification Language (PSL) is a form of temporal logic that has been mainly used in discrete domains (e.g. formal hardware verification). In this paper, we show that by merging machine learning techniques with PSL monitors, we can extend PSL to work on continuous domains. We apply this technique in machine learning-based anomaly detection to analyze scenarios of real-time streaming events from continuous variables in order to detect abnormal behaviors of a system. By using machine learning with formal models, we leverage the strengths of both machine learning methods and formal semantics of time. On one hand, machine learning techniques can produce distributions on continuous variables, where abnormalities can be captured as deviations from the distributions. On the other hand, formal methods can characterize discrete temporal behaviors and relations that cannot be easily learned by machine learning techniques. Interestingly, the anomalies detected by machine learning and the underlying time representation used are discrete events. We implemented a temporal monitoring package (TEF) that operates in conjunction with normal data science packages for anomaly detection machine learning systems, and we show that TEF can be used to perform accurate interpretation of temporal correlation between events.

Margaret P. Chapman, Jonathan Lacotte, Aviv Tamar et al.

A classic reachability problem for safety of dynamic systems is to compute the set of initial states from which the state trajectory is guaranteed to stay inside a given constraint set over a given time horizon. In this paper, we leverage existing theory of reachability analysis and risk measures to devise a risk-sensitive reachability approach for safety of stochastic dynamic systems under non-adversarial disturbances over a finite time horizon. Specifically, we first introduce the notion of a risk-sensitive safe set as a set of initial states from which the risk of large constraint violations can be reduced to a required level via a control policy, where risk is quantified using the Conditional Value-at-Risk (CVaR) measure. Second, we show how the computation of a risk-sensitive safe set can be reduced to the solution to a Markov Decision Process (MDP), where cost is assessed according to CVaR. Third, leveraging this reduction, we devise a tractable algorithm to approximate a risk-sensitive safe set, and provide theoretical arguments about its correctness. Finally, we present a realistic example inspired from stormwater catchment design to demonstrate the utility of risk-sensitive reachability analysis. In particular, our approach allows a practitioner to tune the level of risk sensitivity from worst-case (which is typical for Hamilton-Jacobi reachability analysis) to risk-neutral (which is the case for stochastic reachability analysis).