Deciding when to stop: efficient experimentation to learn to predict drug-target interactions

The present state and challenges of active learning in drug discovery

Active learning (AL) is an iterative feedback process that efficiently identifies valuable data within vast chemical space, even with limited labeled data. This characteristic renders it a valuable approach to tackle the ongoing challenges faced in drug discovery, such as the ever-expanding explore space and the limitations of labeled data. Consequently, AL is increasingly gaining prominence in the field of drug development. In this paper, we comprehensively review the application of AL at all stages of drug discovery, including compounds-target interaction prediction, virtual screening, molecular generation and optimization, as well as molecular properties prediction. Additionally, we discuss the challenges and prospects associated with the current applications of AL in drug discovery.

MSPEDTI: Prediction of Drug-Target Interactions via Molecular Structure with Protein Evolutionary Information

The key to new drug discovery and development is first and foremost the search for molecular targets of drugs, thus advancing drug discovery and drug repositioning. However, traditional drug-target interactions (DTIs) is a costly, lengthy, high-risk, and low-success-rate system project. Therefore, more and more pharmaceutical companies are trying to use computational technologies to screen existing drug molecules and mine new drugs, leading to accelerating new drug development. In the current study, we designed a deep learning computational model MSPEDTI based on Molecular Structure and Protein Evolutionary to predict the potential DTIs. The model first fuses protein evolutionary information and drug structure information, then a deep learning convolutional neural network (CNN) to mine its hidden features, and finally accurately predicts the associated DTIs by extreme learning machine (ELM). In cross-validation experiments, MSPEDTI achieved 94.19%, 90.95%, 87.95%, and 86.11% prediction accuracy in the gold-standard datasets enzymes, ion channels, G-protein-coupled receptors (GPCRs), and nuclear receptors, respectively. MSPEDTI showed its competitive ability in ablation experiments and comparison with previous excellent methods. Additionally, 7 of 10 potential DTIs predicted by MSPEDTI were substantiated by the classical database. These excellent outcomes demonstrate the ability of MSPEDTI to provide reliable drug candidate targets and strongly facilitate the development of drug repositioning and drug development.

Organizing objects by predicting user preferences through collaborative filtering

As service robots become more and more capable of performing useful tasks for us, there is a growing need to teach robots how we expect them to carry out these tasks. However, different users typically have their own preferences, for example with respect to arranging objects on different shelves. As many of these preferences depend on a variety of factors including personal taste, cultural background, or common sense, it is challenging for an expert to pre-program a robot in order to accommodate all potential users. At the same time, it is impractical for robots to constantly query users about how they should perform individual tasks. In this work, we present an approach to learn patterns in user preferences for the task of tidying up objects in containers, e.g. shelves or boxes. Our method builds upon the paradigm of collaborative filtering for making personalized recommendations and relies on data from different users which we gather using crowdsourcing. To deal with novel objects for which we have no data, we propose a method that compliments standard collaborative filtering by leveraging information mined from the Web. When solving a tidy-up task, we first predict pairwise object preferences of the user. Then, we subdivide the objects in containers by modeling a spectral clustering problem. Our solution is easy to update, does not require complex modeling, and improves with the amount of user data. We evaluate our approach using crowdsourcing data from over 1200 users and demonstrate its effectiveness for two tidy-up scenarios. Additionally, we show that a real robot can reliably predict user preferences using our approach.