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Science laboratory automation enables accelerated discovery in life sciences and materials. However, it requires interdisciplinary collaboration to address challenges such as robust and flexible autonomy, reproducibility, throughput, standardization, the role of human scientists, and ethics. This article highlights these issues, reflecting perspectives from leading experts in laboratory automation across different disciplines of the natural sciences.

Many therapies are effective in treating multiple diseases. We present an approach that leverages methods developed in natural language processing and real-world data to prioritize potential, new indications for a mechanism of action (MoA). We specifically use representation learning to generate embeddings of indications and prioritize them based on their proximity to the indications with the strongest available evidence for the MoA. We demonstrate the successful deployment of our approach for anti-IL-17A using embeddings generated with SPPMI and present an evaluation framework to determine the quality of indication finding results and the derived embeddings.

Artificial neural networks have been shown to be state-of-the-art machine learning models in a wide variety of applications, including natural language processing and image recognition. However, building a performant neural network is a laborious task and requires substantial computing power. Neural Architecture Search (NAS) addresses this issue by an automatic selection of the optimal network from a set of potential candidates. While many NAS methods still require training of (some) neural networks, zero-cost proxies promise to identify the optimal network without training. In this work, we propose the zero-cost proxy Network Expressivity by Activation Rank (NEAR). It is based on the effective rank of the pre- and post-activation matrix, i.e., the values of a neural network layer before and after applying its activation function. We demonstrate the cutting-edge correlation between this network score and the model accuracy on NAS-Bench-101 and NATS-Bench-SSS/TSS. In addition, we present a simple approach to estimate the optimal layer sizes in multi-layer perceptrons. Furthermore, we show that this score can be utilized to select hyperparameters such as the activation function and the neural network weight initialization scheme., Comment: 12 pages, 4 figures, 10 tables

It is generally accepted that all cyber attacks cannot be prevented, creating a need for the ability to detect and respond to cyber attacks. Both connectionist and symbolic AI are currently being used to support such detection and response. In this paper, we make the case for combining them using neurosymbolic AI. We identify a set of challenges when using AI today and propose a set of neurosymbolic use cases we believe are both interesting research directions for the neurosymbolic AI community and can have an impact on the cyber security field. We demonstrate feasibility through two proof-of-concept experiments., Comment: Accepted to 18th International Conference on Neural-Symbolic Learning and Reasoning

The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations between them e.g., as given by an intrinsic reaction coordinate) have become routine in chemistry, new developments have pushed the frontier in the field to high-throughput calculations. Chemical relations may be created by a search for specific molecular properties in a molecular design attempt or they can be defined by a set of elementary reaction steps that form a chemical reaction network. The software modules of SCINE have been designed to facilitate such studies. The features of the modules are (i) general applicability of the applied methodologies ranging from electronic structure (no restriction to specific elements of the periodic table) to microkinetic modeling (with little restrictions on molecularity), full modularity so that SCINE modules can also be applied as stand-alone programs or be exchanged for external software packages that fulfill a similar purpose (to increase options for computational campaigns and to provide alternatives in case of tasks that are hard or impossible to accomplish with certain programs), (ii) high stability and autonomous operations so that control and steering by an operator is as easy as possible, and (iii) easy embedding into complex heterogeneous environments for molecular structures taken individually or in the context of a reaction network. A graphical user interface unites all modules and ensures interoperability. All components of the software have been made available open source and free of charge., Comment: 27 pages, 10 figures

Understanding and anticipating intraoperative events and actions is critical for intraoperative assistance and decision-making during minimally invasive surgery. Automated prediction of events, actions, and the following consequences is addressed through various computational approaches with the objective of augmenting surgeons' perception and decision-making capabilities. We propose a predictive neural network that is capable of understanding and predicting critical interactive aspects of surgical workflow from intra-abdominal video, while flexibly leveraging surgical knowledge graphs. The approach incorporates a hypergraph-transformer (HGT) structure that encodes expert knowledge into the network design and predicts the hidden embedding of the graph. We verify our approach on established surgical datasets and applications, including the detection and prediction of action triplets, and the achievement of the Critical View of Safety (CVS). Moreover, we address specific, safety-related tasks, such as predicting the clipping of cystic duct or artery without prior achievement of the CVS. Our results demonstrate the superiority of our approach compared to unstructured alternatives.

One of the most important aspects of autonomous systems is safety. This includes ensuring safe human-robot and safe robot-environment interaction when autonomously performing complex tasks or in collaborative scenarios. Although several methods have been introduced to tackle this, most are unsuitable for real-time applications and require carefully hand-crafted obstacle descriptions. In this work, we propose a method combining high-frequency and real-time self and environment collision avoidance of a robotic manipulator with low-frequency, multimodal, and high-resolution environmental perceptions accumulated in a digital twin system. Our method is based on geometric primitives, so-called primitive skeletons. These, in turn, are information-compressed and real-time compatible digital representations of the robot's body and environment, automatically generated from ultra-realistic virtual replicas of the real world provided by the digital twin. Our approach is a key enabler for closing the loop between environment perception and robot control by providing the millisecond real-time control stage with a current and accurate world description, empowering it to react to environmental changes. We evaluate our whole-body collision avoidance on a 9-DOFs robot system through five experiments, demonstrating the functionality and efficiency of our framework., Comment: Published at 2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2023)

The optimization algorithm and its hyperparameters can significantly affect the training speed and resulting model accuracy in machine learning applications. The wish list for an ideal optimizer includes fast and smooth convergence to low error, low computational demand, and general applicability. Our recently introduced continual resilient (CoRe) optimizer has shown superior performance compared to other state-of-the-art first-order gradient-based optimizers for training lifelong machine learning potentials. In this work we provide an extensive performance comparison of the CoRe optimizer and nine other optimization algorithms including the Adam optimizer and resilient backpropagation (RPROP) for diverse machine learning tasks. We analyze the influence of different hyperparameters and provide generally applicable values. The CoRe optimizer yields best or competitive performance in every investigated application, while only one hyperparameter needs to be changed depending on mini-batch or batch learning., Comment: 12 pages, 5 figures, 1 table

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model., Comment: 20 pages, 6 figures

In this paper we introduce novel Virtual Reality (VR) and Augmented Reality (AR) treatments to improve the psychological well being of patients in palliative care, based on interviews with a clinical psychologist who has successfully implemented VR assisted interventions on palliative care patients in the Hong Kong hospital system. Our VR and AR assisted interventions are adaptations of traditional palliative care therapies which simultaneously facilitate patients communication with family and friends while isolated in hospital due to physical weakness and COVID-19 related restrictions. The first system we propose is a networked, metaverse platform for palliative care patients to create customized virtual environments with therapists, family and friends which function as immersive and collaborative versions of 'life review' and 'reminiscence therapy'. The second proposed system will investigate the use of Mixed Reality telepresence and haptic touch in an AR environment, which will allow palliative care patients to physically feel friends and family in a virtual space, adding to the sense of presence and immersion in that environment.

We constantly integrate our knowledge and understanding of the world to enhance our interpretation of what we see. This ability is crucial in application domains which entail reasoning about multiple entities and concepts, such as AI-augmented surgery. In this paper, we propose a novel way of integrating conceptual knowledge into temporal analysis tasks via temporal concept graph networks. In the proposed networks, a global knowledge graph is incorporated into the temporal analysis of surgical instances, learning the meaning of concepts and relations as they apply to the data. We demonstrate our results in surgical video data for tasks such as verification of critical view of safety, as well as estimation of Parkland grading scale. The results show that our method improves the recognition and detection of complex benchmarks as well as enables other analytic applications of interest.

Unraveling the atomistic and the electronic structure of solid-liquid interfaces is the key to the design of new materials for many important applications, from heterogeneous catalysis to battery technology. Density functional theory (DFT) calculations can in principle provide a reliable description of such interfaces, but the high computational costs severely restrict the accessible time and length scales. Here, we report machine learning-driven simulations of various interfaces between water and lithium manganese oxide (Li$_x$Mn$_2$O$_4$), an important electrode material in lithium ion batteries and a catalyst for the oxygen evolution reaction. We employ a high-dimensional neural network potential (HDNNP) to compute the energies and forces several orders of magnitude faster than DFT without loss in accuracy. In addition, a high-dimensional neural network for spin prediction (HDNNS) is utilized to analyze the electronic structure of the manganese ions. Combining these methods, a series of interfaces is investigated by large-scale molecular dynamics. The simulations allow us to gain insights into a variety of properties like the dissociation of water molecules, proton transfer processes, and hydrogen bonds, as well as the geometric and electronic structure of the solid surfaces including the manganese oxidation state distribution, Jahn-Teller distortions, and electron hopping., Comment: 21 pages, 13 figures

Comprehension of surgical workflow is the foundation upon which artificial intelligence (AI) and machine learning (ML) holds the potential to assist intraoperative decision-making and risk mitigation. In this work, we move beyond mere identification of past surgical phases, into the prediction of future surgical steps and specification of the transitions between them. We use a novel Generative Adversarial Network (GAN) formulation to sample future surgical phases trajectories conditioned on past video frames from laparoscopic cholecystectomy (LC) videos and compare it to state-of-the-art approaches for surgical video analysis and alternative prediction methods. We demonstrate the GAN formulation's effectiveness through inferring and predicting the progress of LC videos. We quantify the horizon-accuracy trade-off and explored average performance, as well as the performance on the more challenging, and clinically relevant transitions between phases. Furthermore, we conduct a survey, asking 16 surgeons of different specialties and educational levels to qualitatively evaluate predicted surgery phases., Comment: RA-L ICRA 2022