Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space

Proteins are complex molecules responsible for different functions in nature. Enhancing the functionality of proteins and cellular fitness can significantly impact various industries. However, protein optimization using computational methods remains challenging, especially when starting from low-fitness sequences. We propose LatProtRL, an optimization method to efficiently traverse a latent space learned by an encoder-decoder leveraging a large protein language model. To escape local optima, our optimization is modeled as a Markov decision process using reinforcement learning acting directly in latent space. We evaluate our approach on two important fitness optimization tasks, demonstrating its ability to achieve comparable or superior fitness over baseline methods. Our findings and in vitro evaluation show that the generated sequences can reach high-fitness regions, suggesting a substantial potential of LatProtRL in lab-in-the-loop scenarios.

Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2

Protein diffusion models have emerged as a promising approach for protein design. One such pioneering model is Genie, a method that asymmetrically represents protein structures during the forward and backward processes, using simple Gaussian noising for the former and expressive SE(3)-equivariant attention for the latter. In this work we introduce Genie 2, extending Genie to capture a larger and more diverse protein structure space through architectural innovations and massive data augmentation. Genie 2 adds motif scaffolding capabilities via a novel multi-motif framework that designs co-occurring motifs with unspecified inter-motif positions and orientations. This makes possible complex protein designs that engage multiple interaction partners and perform multiple functions. On both unconditional and conditional generation, Genie 2 achieves state-of-the-art performance, outperforming all known methods on key design metrics including designability, diversity, and novelty. Genie 2 also solves more motif scaffolding problems than other methods and does so with more unique and varied solutions. Taken together, these advances set a new standard for structure-based protein design. Genie 2 inference and training code, as well as model weights, are freely available at: https://github.com/aqlaboratory/genie2.

FingerNet: EEG Decoding of A Fine Motor Imagery with Finger-tapping Task Based on A Deep Neural Network

Brain-computer interface (BCI) technology facilitates communication between the human brain and computers, primarily utilizing electroencephalography (EEG) signals to discern human intentions. Although EEG-based BCI systems have been developed for paralysis individuals, ongoing studies explore systems for speech imagery and motor imagery (MI). This study introduces FingerNet, a specialized network for fine MI classification, departing from conventional gross MI studies. The proposed FingerNet could extract spatial and temporal features from EEG signals, improving classification accuracy within the same hand. The experimental results demonstrated that performance showed significantly higher accuracy in classifying five finger-tapping tasks, encompassing thumb, index, middle, ring, and little finger movements. FingerNet demonstrated dominant performance compared to the conventional baseline models, EEGNet and DeepConvNet. The average accuracy for FingerNet was 0.3049, whereas EEGNet and DeepConvNet exhibited lower accuracies of 0.2196 and 0.2533, respectively. Statistical validation also demonstrates the predominance of FingerNet over baseline networks. For biased predictions, particularly for thumb and index classes, we led to the implementation of weighted cross-entropy and also adapted the weighted cross-entropy, a method conventionally employed to mitigate class imbalance. The proposed FingerNet involves optimizing network structure, improving performance, and exploring applications beyond fine MI. Moreover, the weighted Cross Entropy approach employed to address such biased predictions appears to have broader applicability and relevance across various domains involving multi-class classification tasks. We believe that effective execution of motor imagery can be achieved not only for fine MI, but also for local muscle MI

Enhancing Spatiotemporal Traffic Prediction through Urban Human Activity Analysis

Traffic prediction is one of the key elements to ensure the safety and convenience of citizens. Existing traffic prediction models primarily focus on deep learning architectures to capture spatial and temporal correlation. They often overlook the underlying nature of traffic. Specifically, the sensor networks in most traffic datasets do not accurately represent the actual road network exploited by vehicles, failing to provide insights into the traffic patterns in urban activities. To overcome these limitations, we propose an improved traffic prediction method based on graph convolution deep learning algorithms. We leverage human activity frequency data from National Household Travel Survey to enhance the inference capability of a causal relationship between activity and traffic patterns. Despite making minimal modifications to the conventional graph convolutional recurrent networks and graph convolutional transformer architectures, our approach achieves state-of-the-art performance without introducing excessive computational overhead.

Local-Global Temporal Fusion Network with an Attention Mechanism for Multiple and Multiclass Arrhythmia Classification

Clinical decision support systems (CDSSs) have been widely utilized to support the decisions made by cardiologists when detecting and classifying arrhythmia from electrocardiograms (ECGs). However, forming a CDSS for the arrhythmia classification task is challenging due to the varying lengths of arrhythmias. Although the onset time of arrhythmia varies, previously developed methods have not considered such conditions. Thus, we propose a framework that consists of (i) local temporal information extraction, (ii) global pattern extraction, and (iii) local-global information fusion with attention to perform arrhythmia detection and classification with a constrained input length. The 10-class and 4-class performances of our approach were assessed by detecting the onset and offset of arrhythmia as an episode and the duration of arrhythmia based on the MIT-BIH arrhythmia database (MITDB) and MIT-BIH atrial fibrillation database (AFDB), respectively. The results were statistically superior to those achieved by the comparison models. To check the generalization ability of the proposed method, an AFDB-trained model was tested on the MITDB, and superior performance was attained compared with that of a state-of-the-art model. The proposed method can capture local-global information and dynamics without incurring information losses. Therefore, arrhythmias can be recognized more accurately, and their occurrence times can be calculated; thus, the clinical field can create more accurate treatment plans by using the proposed method.

Uncertain Pose Estimation during Contact Tasks using Differentiable Contact Features

For many robotic manipulation and contact tasks, it is crucial to accurately estimate uncertain object poses, for which certain geometry and sensor information are fused in some optimal fashion. Previous results for this problem primarily adopt sampling-based or end-to-end learning methods, which yet often suffer from the issues of efficiency and generalizability. In this paper, we propose a novel differentiable framework for this uncertain pose estimation during contact, so that it can be solved in an efficient and accurate manner with gradient-based solver. To achieve this, we introduce a new geometric definition that is highly adaptable and capable of providing differentiable contact features. Then we approach the problem from a bi-level perspective and utilize the gradient of these contact features along with differentiable optimization to efficiently solve for the uncertain pose. Several scenarios are implemented to demonstrate how the proposed framework can improve existing methods.

Modular and Parallelizable Multibody Physics Simulation via Subsystem-Based ADMM

In this paper, we present a new multibody physics simulation framework that utilizes the subsystem-based structure and the Alternating Direction Method of Multiplier (ADMM). The major challenge in simulating complex high degree of freedom systems is a large number of coupled constraints and large-sized matrices. To address this challenge, we first split the multibody into several subsystems and reformulate the dynamics equation into a subsystem perspective based on the structure of their interconnection. Then we utilize ADMM with our novel subsystem-based variable splitting scheme to solve the equation, which allows parallelizable and modular architecture. The resulting algorithm is fast, scalable, versatile, and converges well while maintaining solution consistency. Several illustrative examples are implemented with performance evaluation results showing advantages over other state-of-the-art algorithms.

Multi-image Super-resolution via Quality Map Associated Temporal Attention Network

With the rising interest in deep learning-based methods in remote sensing, neural networks have made remarkable advancements in multi-image fusion and super-resolution. To fully exploit the advantages of multi-image super-resolution, temporal attention is crucial as it allows a model to focus on reliable features rather than noises. Despite the presence of quality maps (QMs) that indicate noises in images, most of the methods tested in the PROBA-V dataset have not been used QMs for temporal attention. We present a quality map associated temporal attention network (QA-Net), a novel method that incorporates QMs into both feature representation and fusion processes for the first time. Low-resolution features are temporally attended by QM features in repeated multi-head attention modules. The proposed method achieved state-of-the-art results in the PROBA-V dataset.

Fast and Accurate Data-Driven Simulation Framework for Contact-Intensive Tight-Tolerance Robotic Assembly Tasks

We propose a novel fast and accurate simulation framework for contact-intensive tight-tolerance robotic assembly tasks. The key components of our framework are as follows: 1) data-driven contact point clustering with a certain variable-input network, which is explicitly trained for simulation accuracy (with real experimental data) and able to accommodate complex/non-convex object shapes; 2) contact force solving, which precisely/robustly enforces physics of contact (i.e., no penetration, Coulomb friction, maximum energy dissipation) with contact mechanics of contact nodes augmented with that of their object; 3) contact detection with a neural network, which is parallelized for each contact point, thus, can be computed very quickly even for complex shape objects with no exhaust pair-wise test; and 4) time integration with PMI (passive mid-point integration), whose discrete-time passivity improves overall simulation accuracy, stability, and speed. We then implement our proposed framework for two widely-encountered/benchmarked contact-intensive tight-tolerance tasks, namely, peg-in-hole assembly and bolt-nut assembly, and validate its speed and accuracy against real experimental data. It is worthwhile to mention that our proposed simulation framework is applicable to other general contact-intensive tight-tolerance robotic assembly tasks as well. We also compare its performance with other physics engines and manifest its robustness via haptic rendering of virtual bolting task.

Large-Dimensional Multibody Dynamics Simulation Using Contact Nodalization and Diagonalization

We propose a novel multibody dynamics simulation framework that can efficiently deal with large-dimensionality and complementarity multi-contact conditions. Typical contact simulation approaches perform contact impulse-level fixed-point iteration (IL-FPI), which has high time-complexity from large-size matrix inversion and multiplication, as well as susceptibility to ill-conditioned contact situations. To circumvent this, we propose a novel framework based on velocity-level fixed-point iteration (VL-FPI), which, by utilizing a certain surrogate dynamics and contact nodalization (with virtual nodes), can achieve not only inter-contact decoupling but also their inter-axes decoupling (i.e., contact diagonalization). This then enables us to one-shot/parallel-solve the contact problem during each VL-FPI iteration-loop, while the surrogate dynamics structure allows us to circumvent large-size/dense matrix inversion/multiplication, thereby, significantly speeding up the simulation time with improved convergence property. We theoretically show that the solution of our framework is consistent with that of the original problem and, further, elucidate mathematical conditions for the convergence of our proposed solver. Performance and properties of our proposed simulation framework are also demonstrated and experimentally-validated for various large-dimensional/multi-contact scenarios including deformable objects.