Incremental execution of temporal graph queries over runtime models with history and its applications

Modern software systems are intricate and operate in highly dynamic environments for which few assumptions can be made at design-time. This setting has sparked an interest in solutions that use a runtime model which reflects the system state and operational context to monitor and adapt the system in reaction to changes during its runtime. Few solutions focus on the evolution of the model over time, i.e., its history, although history is required for monitoring temporal behaviors and may enable more informed decision-making. One reason is that handling the history of a runtime model poses an important technical challenge, as it requires tracing a part of the model over multiple model snapshots in a timely manner. Additionally, the runtime setting calls for memory-efficient measures to store and check these snapshots. Following the common practice of representing a runtime model as a typed attributed graph, we introduce a language which supports the formulation of temporal graph queries, i.e., queries on the ordering and timing in which structural changes in the history of a runtime model occurred. We present a querying scheme for the execution of temporal graph queries over history-aware runtime models. Features such as temporal logic operators in queries, the incremental execution, the option to discard history that is no longer relevant to queries, and the in-memory storage of the model, distinguish our scheme from relevant solutions. By incorporating temporal operators, temporal graph queries can be used for runtime monitoring of temporal logic formulas. Building on this capability, we present an implementation of the scheme that is evaluated for runtime querying, monitoring, and adaptation scenarios from two application domains.

Ligand-Based Virtual Screening Based on the Graph Edit Distance

Chemical compounds can be represented as attributed graphs. An attributed graph is a mathematical model of an object composed of two types of representations: nodes and edges. Nodes are individual components, and edges are relations between these components. In this case, pharmacophore-type node descriptions are represented by nodes and chemical bounds by edges. If we want to obtain the bioactivity dissimilarity between two chemical compounds, a distance between attributed graphs can be used. The Graph Edit Distance allows computing this distance, and it is defined as the cost of transforming one graph into another. Nevertheless, to define this dissimilarity, the transformation cost must be properly tuned. The aim of this paper is to analyse the structural-based screening methods to verify the quality of the Harper transformation costs proposal and to present an algorithm to learn these transformation costs such that the bioactivity dissimilarity is properly defined in a ligand-based virtual screening application. The goodness of the dissimilarity is represented by the classification accuracy. Six publicly available datasets—CAPST, DUD-E, GLL&GDD, NRLiSt-BDB, MUV and ULS-UDS—have been used to validate our methodology and show that with our learned costs, we obtain the highest ratios in identifying the bioactivity similarity in a structurally diverse group of molecules.

On the Use of Real-World Datasets for Reaction Yield Prediction

The lack of publicly available, large, and unbiased datasets is a key bottleneck for the application of machine learning (ML) methods in synthetic chemistry. Data from electronic laboratory notebooks (ELNs) could provide less biased, large datasets, but no such datasets have been made publicly available. The first real-world dataset from the ELNs of a large pharmaceutical company is disclosed and its relationship to high-throughput experimentation (HTE) datasets is described. For chemical yield predictions, a key task in chemical synthesis, an attributed graph neural network (AGNN) performs as good or better than the best previous models on two HTE datasets for the Suzuki and Buchwald-Hartwig reactions. However, training of the AGNN on the ELN dataset does not lead to a predictive model. The implications of using ELN data for training ML-based models are discussed in the context of yield predictions.