AlgoRxplorers | Precision in Mutation -- Enhancing Drug Design with Advanced Protein Stability Prediction Tools

Predicting the impact of single-point amino acid mutations on protein stability is essential for understanding disease mechanisms and advancing drug development. Protein stability, quantified by changes in Gibbs free energy ($\Delta\Delta G$), is influenced by these mutations. However, the scarcity of data and the complexity of model interpretation pose challenges in accurately predicting stability changes. This study proposes the application of deep neural networks, leveraging transfer learning and fusing complementary information from different models, to create a feature-rich representation of the protein stability landscape. We developed four models, with our third model, ThermoMPNN+, demonstrating the best performance in predicting $\Delta\Delta G$ values. This approach, which integrates diverse feature sets and embeddings through latent transfusion techniques, aims to refine $\Delta\Delta G$ predictions and contribute to a deeper understanding of protein dynamics, potentially leading to advancements in disease research and drug discovery.

Leveraging Computation of Expectation Models for Commonsense Affordance Estimation on 3D Scene Graphs

This article studies the commonsense object affordance concept for enabling close-to-human task planning and task optimization of embodied robotic agents in urban environments. The focus of the object affordance is on reasoning how to effectively identify object's inherent utility during the task execution, which in this work is enabled through the analysis of contextual relations of sparse information of 3D scene graphs. The proposed framework develops a Correlation Information (CECI) model to learn probability distributions using a Graph Convolutional Network, allowing to extract the commonsense affordance for individual members of a semantic class. The overall framework was experimentally validated in a real-world indoor environment, showcasing the ability of the method to level with human commonsense. For a video of the article, showcasing the experimental demonstration, please refer to the following link: https://youtu.be/BDCMVx2GiQE

A Tree-based Next-best-trajectory Method for 3D UAV Exploration

This work presents a fully integrated tree-based combined exploration-planning algorithm: Exploration-RRT (ERRT). The algorithm is focused on providing real-time solutions for local exploration in a fully unknown and unstructured environment while directly incorporating exploratory behavior, robot-safe path planning, and robot actuation into the central problem. ERRT provides a complete sampling and tree-based solution for evaluating "where to go next" by considering a trade-off between maximizing information gain, and minimizing the distances travelled and the robot actuation along the path. The complete scheme is evaluated in extensive simulations, comparisons, as well as real-world field experiments in constrained and narrow subterranean and GPS-denied environments. The framework is fully ROS-integrated, straight-forward to use, and we open-source it at https://github.com/LTU-RAI/ExplorationRRT.

Belief Scene Graphs: Expanding Partial Scenes with Objects through Computation of Expectation

In this article, we propose the novel concept of Belief Scene Graphs, which are utility-driven extensions of partial 3D scene graphs, that enable efficient high-level task planning with partial information. We propose a graph-based learning methodology for the computation of belief (also referred to as expectation) on any given 3D scene graph, which is then used to strategically add new nodes (referred to as blind nodes) that are relevant for a robotic mission. We propose the method of Computation of Expectation based on Correlation Information (CECI), to reasonably approximate real Belief/Expectation, by learning histograms from available training data. A novel Graph Convolutional Neural Network (GCN) model is developed, to learn CECI from a repository of 3D scene graphs. As no database of 3D scene graphs exists for the training of the novel CECI model, we present a novel methodology for generating a 3D scene graph dataset based on semantically annotated real-life 3D spaces. The generated dataset is then utilized to train the proposed CECI model and for extensive validation of the proposed method. We establish the novel concept of \textit{Belief Scene Graphs} (BSG), as a core component to integrate expectations into abstract representations. This new concept is an evolution of the classical 3D scene graph concept and aims to enable high-level reasoning for the task planning and optimization of a variety of robotics missions. The efficacy of the overall framework has been evaluated in an object search scenario, and has also been tested on a real-life experiment to emulate human common sense of unseen-objects.

STAGE: Scalable and Traversability-Aware Graph based Exploration Planner for Dynamically Varying Environments

In this article, we propose a novel navigation framework that leverages a two layered graph representation of the environment for efficient large-scale exploration, while it integrates a novel uncertainty awareness scheme to handle dynamic scene changes in previously explored areas. The framework is structured around a novel goal oriented graph representation, that consists of, i) the local sub-graph and ii) the global graph layer respectively. The local sub-graphs encode local volumetric gain locations as frontiers, based on the direct pointcloud visibility, allowing fast graph building and path planning. Additionally, the global graph is build in an efficient way, using node-edge information exchange only on overlapping regions of sequential sub-graphs. Different from the state-of-the-art graph based exploration methods, the proposed approach efficiently re-uses sub-graphs built in previous iterations to construct the global navigation layer. Another merit of the proposed scheme is the ability to handle scene changes (e.g. blocked pathways), adaptively updating the obstructed part of the global graph from traversable to not-traversable. This operation involved oriented sample space of a path segment in the global graph layer, while removing the respective edges from connected nodes of the global graph in cases of obstructions. As such, the exploration behavior is directing the robot to follow another route in the global re-positioning phase through path-way updates in the global graph. Finally, we showcase the performance of the method both in simulation runs as well as deployed in real-world scene involving a legged robot carrying camera and lidar sensor.

Event Camera and LiDAR based Human Tracking for Adverse Lighting Conditions in Subterranean Environments

In this article, we propose a novel LiDAR and event camera fusion modality for subterranean (SubT) environments for fast and precise object and human detection in a wide variety of adverse lighting conditions, such as low or no light, high-contrast zones and in the presence of blinding light sources. In the proposed approach, information from the event camera and LiDAR are fused to localize a human or an object-of-interest in a robot's local frame. The local detection is then transformed into the inertial frame and used to set references for a Nonlinear Model Predictive Controller (NMPC) for reactive tracking of humans or objects in SubT environments. The proposed novel fusion uses intensity filtering and K-means clustering on the LiDAR point cloud and frequency filtering and connectivity clustering on the events induced in an event camera by the returning LiDAR beams. The centroids of the clusters in the event camera and LiDAR streams are then paired to localize reflective markers present on safety vests and signs in SubT environments. The efficacy of the proposed scheme has been experimentally validated in a real SubT environment (a mine) with a Pioneer 3AT mobile robot. The experimental results show real-time performance for human detection and the NMPC-based controller allows for reactive tracking of a human or object of interest, even in complete darkness.

Towards Energy Efficient Autonomous Exploration of Mars Lava Tube with a Martian Coaxial Quadrotor

Mapping and exploration of a Martian terrain with an aerial vehicle has become an emerging research direction, since the successful flight demonstration of the Mars helicopter Ingenuity. Although the autonomy and navigation capability of the state of the art Mars helicopter has proven to be efficient in an open environment, the next area of interest for exploration on Mars are caves or ancient lava tube like environments, especially towards the never-ending search of life on other planets. This article presents an autonomous exploration mission based on a modified frontier approach along with a risk aware planning and integrated collision avoidance scheme with a special focus on energy aspects of a custom designed Mars Coaxial Quadrotor (MCQ) in a Martian simulated lava tube. One of the biggest novelties of the article stems from addressing the exploration capability, while rapidly exploring in local areas and intelligently global re-positioning of the MCQ when reaching dead ends in order to to efficiently use the battery based consumed energy, while increasing the volume of the exploration. The proposed three layer cost based global re-position point selection assists in rapidly redirecting the MCQ to previously partially seen areas that could lead to more unexplored part of the lava tube. The Martian fully simulated mission presented in this article takes into consideration the fidelity of physics of Mars condition in terms of thin atmosphere, low surface pressure and low gravity of the planet, while proves the efficiency of the proposed scheme in exploring an area that is particularly challenging due to the subterranean-like environment. The proposed exploration-planning framework is also validated in simulation by comparing it against the graph based exploration planner.

REF: A Rapid Exploration Framework for Deploying Autonomous MAVs in Unknown Environments

Exploration and mapping of unknown environments is a fundamental task in applications for autonomous robots. In this article, we present a complete framework for deploying MAVs in autonomous exploration missions in unknown subterranean areas. The main motive of exploration algorithms is to depict the next best frontier for the robot such that new ground can be covered in a fast, safe yet efficient manner. The proposed framework uses a novel frontier selection method that also contributes to the safe navigation of autonomous robots in obstructed areas such as subterranean caves, mines, and urban areas. The framework presented in this work bifurcates the exploration problem in local and global exploration. The proposed exploration framework is also adaptable according to computational resources available onboard the robot which means the trade-off between the speed of exploration and the quality of the map can be made. Such capability allows the proposed framework to be deployed in a subterranean exploration, mapping as well as in fast search and rescue scenarios. The overall system is considered a low-complexity and baseline solution for navigation and object localization in tunnel-like environments. The performance of the proposed framework is evaluated in detailed simulation studies with comparisons made against a high-level exploration-planning framework developed for the DARPA Sub-T challenge as it will be presented in this article.

Design and Model Predictive Control of Mars Coaxial Quadrotor

Mars has been a prime candidate for planetary exploration of the solar system because of the science discoveries that support chances of future habitation on this planet. Martian caves and lava tubes like terrains, which consists of uneven ground, poor visibility and confined space, makes it impossible for wheel based rovers to navigate through these areas. In order to address these limitations and advance the exploration capability in a Martian terrain, this article presents the design and control of a novel coaxial quadrotor Micro Aerial Vehicle (MAV). As it will be presented, the key contributions on the design and control architecture of the proposed Mars coaxial quadrotor, are introducing an alternative and more enhanced, from a control point of view concept, when compared in terms of autonomy to Ingenuity. Based on the presented design, the article will introduce the mathematical modelling and automatic control framework of the vehicle that will consist of a linearised model of a co-axial quadrotor and a corresponding Model Predictive Controller (MPC) for the trajectory tracking. Among the many models, proposed for the aerial flight on Mars, a reliable control architecture lacks in the related state of the art. The MPC based closed loop responses of the proposed MAV will be verified in different conditions during the flight with additional disturbances, induced to replicate a real flight scenario. In order to further validate the proposed control architecture and prove the efficacy of the suggested design, the introduced Mars coaxial quadrotor and the MPC scheme will be compared to a PID-type controller, similar to the Ingenuity helicopter's control architecture for the position and the heading.

Multi-Sparse Gaussian Process: Learning based Semi-Parametric Control

A key challenge with controlling complex dynamical systems is to accurately model them. However, this requirement is very hard to satisfy in practice. Data-driven approaches such as Gaussian processes (GPs) have proved quite effective by employing regression based methods to capture the unmodeled dynamical effects. However, GPs scale cubically with data, and is often a challenge to perform real-time regression. In this paper, we propose a semi-parametric framework exploiting sparsity for learning-based control. We combine the parametric model of the system with multiple sparse GP models to capture any unmodeled dynamics. Multi-Sparse Gaussian Process (MSGP) divides the original dataset into multiple sparse models with unique hyperparameters for each model. Thereby, preserving the richness and uniqueness of each sparse model. For a query point, a weighted sparse posterior prediction is performed based on $N$ neighboring sparse models. Hence, the prediction complexity is significantly reduced from $\mathcal{O}(n^3)$ to $\mathcal{O}(Npu^2)$, where $p$ and $u$ are data points and pseudo-inputs respectively for each sparse model. We validate MSGP's learning performance for a quadrotor using a geometric controller in simulation. Comparison with GP, sparse GP, and local GP shows that MSGP has higher prediction accuracy than sparse and local GP, while significantly lower time complexity than all three. We also validate MSGP on a hardware quadrotor for unmodeled mass, inertia, and disturbances. The experiment video can be seen at: https://youtu.be/zUk1ISux6ao