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Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical calculations is the most commonly used method. However, this way is heavily dependent on individual experience and chemical intuition. In our previous study, we proposed a research paradigm that uses enhanced sampling in molecular dynamics simulations to study chemical reactions. This approach can directly simulate the entire process of a chemical reaction. However, the computational speed limits the use of high-precision potential energy functions for simulations. To address this issue, we present a scheme for training high-precision force fields for molecular modeling using a previously developed graph-neural-network-based molecular model, molecular configuration transformer. This potential energy function allows for highly accurate simulations at a low computational cost, leading to more precise calculations of the mechanism of chemical reactions. We applied this approach to study a Claisen rearrangement reaction and a Carbonyl insertion reaction catalyzed by Manganese.

The NeuroEvolution of Augmenting Topologies (NEAT) algorithm has received considerable recognition in the field of neuroevolution. Its effectiveness is derived from initiating with simple networks and incrementally evolving both their topologies and weights. Although its capability across various challenges is evident, the algorithm's computational efficiency remains an impediment, limiting its scalability potential. In response, this paper introduces a tensorization method for the NEAT algorithm, enabling the transformation of its diverse network topologies and associated operations into uniformly shaped tensors for computation. This advancement facilitates the execution of the NEAT algorithm in a parallelized manner across the entire population. Furthermore, we develop TensorNEAT, a library that implements the tensorized NEAT algorithm and its variants, such as CPPN and HyperNEAT. Building upon JAX, TensorNEAT promotes efficient parallel computations via automated function vectorization and hardware acceleration. Moreover, the TensorNEAT library supports various benchmark environments including Gym, Brax, and gymnax. Through evaluations across a spectrum of robotics control environments in Brax, TensorNEAT achieves up to 500x speedups compared to the existing implementations such as NEAT-Python. Source codes are available at: //github.com/EMI-Group/tensorneat.

Generative Flow Networks (GFlowNets) are probabilistic models predicated on Markov flows, employing specific amortization algorithms to learn stochastic policies that generate compositional substances including biomolecules, chemical materials, and more. Demonstrating formidable prowess in generating high-performance biochemical molecules, GFlowNets accelerate the discovery of scientific substances, effectively circumventing the time-consuming, labor-intensive, and costly shortcomings intrinsic to conventional material discovery. However, previous work often struggles to accumulate exploratory experience and is prone to becoming disoriented within expansive sampling spaces. Attempts to address this issue, such as LS-GFN, are limited to local greedy searches and lack broader global adjustments. This paper introduces a novel GFlowNets variant, the Dynamic Backtracking GFN (DB-GFN), which enhances the adaptability of decision-making steps through a reward-based dynamic backtracking mechanism. DB-GFN permits backtracking during the network construction process according to the current state's reward value, thus correcting disadvantageous decisions and exploring alternative pathways during the exploration process. Applied to generative tasks of biochemical molecules and genetic material sequences, DB-GFN surpasses existing GFlowNets models and traditional reinforcement learning methods in terms of sample quality, exploration sample quantity, and training convergence speed. Furthermore, the orthogonal nature of DB-GFN suggests its potential as a powerful tool for future improvements in GFlowNets, with the promise of integrating with other strategies to achieve more efficient search performance.

The rapid evolution of Integrated Circuit (IC) development necessitates innovative methodologies such as code generation to manage complexity and increase productivity. Using the right methodology for generator development to maximize the capability and, most notably, the feasibility of generators is a crucial part of this work. Meta-Modeling-based approaches drawing on the principles of Model Driven Architecture (MDA) are a promising methodology for generator development. The goal of this paper is to show why such an MDA-based approach can provide extremely powerful generators with minimal implementation effort and to demonstrate that this approach is a superior alternative to the most advanced hardware generation languages such as SpinalHDL and Chisel. For this purpose, this paper provides an in-depth comparison of the Meta-Modeling approach against these hardware generation languages, highlighting the unique advantages of a Meta-Modeling-based approach and summarizes the benefits.

Diagnosis of hematological malignancies depends on accurate identification of white blood cells in peripheral blood smears. Deep learning techniques are emerging as a viable solution to scale and optimize this process by automatic identification of cells in laboratories. However, these techniques face several challenges such as limited generalizability, sensitivity to domain shifts and lack of explainability. Here, we are introducing a novel approach based on neural cellular automata (NCA) for white blood cell classification. We test our approach on three datasets of white blood cell images and show that we achieve competitive performance compared to conventional methods. Our NCA-based method is significantly smaller in terms of parameters and exhibits robustness to domain shifts. Furthermore, the architecture is inherently explainable, providing insights into the decision process for each classification, helping experts understand and validate model predictions. Results demonstrate that NCA not only can be used for image classification, but also address key challenges of conventional methods, indicating a high potential for applicability in clinical practice.

Generative Flow Networks (GFlowNets) are probabilistic models predicated on Markov flows, employing specific amortization algorithms to learn stochastic policies that generate compositional substances including biomolecules, chemical materials, and more. Demonstrating formidable prowess in generating high-performance biochemical molecules, GFlowNets accelerate the discovery of scientific substances, effectively circumventing the time-consuming, labor-intensive, and costly shortcomings intrinsic to conventional material discovery. However, previous work often struggles to accumulate exploratory experience and is prone to becoming disoriented within expansive sampling spaces. Attempts to address this issue, such as LS-GFN, are limited to local greedy searches and lack broader global adjustments. This paper introduces a novel GFlowNet variant, the Dynamic Backtracking GFN (DB-GFN), which enhances the adaptability of decision-making steps through a reward-based dynamic backtracking mechanism. DB-GFN permits backtracking during the network construction process according to the current state's reward value, thus correcting disadvantageous decisions and exploring alternative pathways during the exploration process. Applied to generative tasks of biochemical molecules and genetic material sequences, DB-GFN surpasses existing GFlowNet models and traditional reinforcement learning methods in terms of sample quality, exploration sample quantity, and training convergence speed. Furthermore, the orthogonal nature of DB-GFN suggests its potential as a powerful tool for future improvements in GFN networks, with the promise of integrating with other strategies to achieve more efficient search performance.

Mutual Coupling (MC) is an unavoidable feature in Reconfigurable Intelligent Surfaces (RISs) with sub-wavelength inter-element spacing. Its inherent presence naturally leads to non-local RIS structures, which can be efficiently described via non-diagonal phase shift matrices. In this paper, we focus on optimizing MC in RIS-assisted multi-user MIMO wireless communication systems. We particularly formulate a novel problem to jointly optimize active and passive beamforming as well as MC in a physically consistent manner. To characterize MC, we deploy scattering parameters and propose a novel approach to optimize them through an offline optimization method, rather than optimizing MC on the fly. Our numerical results showcase that the system performance increases with the proposed MC optimization, and this improvement is achievable without the need for optimizing MC on-the-fly, which can be rather cumbersome.

Using Non-negative Matrix Factorization (NMF), the observed matrix can be approximated by the product of the basis and coefficient matrices. Moreover, if the coefficient vectors are explained by the covariates for each individual, the coefficient matrix can be written as the product of the parameter matrix and the covariate matrix, and additionally described in the framework of Non-negative Matrix tri-Factorization (tri-NMF) with covariates. Consequently, this is equal to the mean structure of the Growth Curve Model (GCM). The difference is that the basis matrix for GCM is given by the analyst, whereas that for NMF with covariates is unknown and optimized. In this study, we applied NMF with covariance to longitudinal data and compared it with GCM. We have also published an R package that implements this method, and we show how to use it through examples of data analyses including longitudinal measurement, spatiotemporal data and text data. In particular, we demonstrate the usefulness of Gaussian kernel functions as covariates.

Cooperative molecular communication (MC) is a promising technology for facilitating communication between nanomachines in the Internet of Bio-Nano Things (IoBNT) field. However, the performance of IoBNT is limited by the availability of energy for cooperative MC. This paper presents a novel transmitter design scheme that utilizes molecule movement between reservoirs, creating concentration differences through the consumption of free energy, and encoding information on molecule types. The performance of the transmitter is primarily influenced by energy costs, which directly impact the overall IoBNT system performance. To address this, the paper focuses on optimizing energy allocation in cooperative MC for enhanced transmitter performance. Theoretical analysis is conducted for two transmitters. For scenarios with more than two users, a genetic algorithm is employed in the energy allocation to minimize the total bit error rate (BER). Finally, numerical results show the effectiveness of the proposed energy allocation strategies in the considered cooperative MC system.

The Gromov-Wasserstein (GW) distance is frequently used in machine learning to compare distributions across distinct metric spaces. Despite its utility, it remains computationally intensive, especially for large-scale problems. Recently, a novel Wasserstein distance specifically tailored for Gaussian mixture models and known as MW (mixture Wasserstein) has been introduced by several authors. In scenarios where data exhibit clustering, this approach simplifies to a small-scale discrete optimal transport problem, which complexity depends solely on the number of Gaussian components in the GMMs. This paper aims to extend MW by introducing new Gromov-type distances. These distances are designed to be isometry-invariant in Euclidean spaces and are applicable for comparing GMMs across different dimensional spaces. Our first contribution is the Mixture Gromov Wasserstein distance (MGW), which can be viewed as a Gromovized version of MW. This new distance has a straightforward discrete formulation, making it highly efficient for estimating distances between GMMs in practical applications. To facilitate the derivation of a transport plan between GMMs, we present a second distance, the Embedded Wasserstein distance (EW). This distance turns out to be closely related to several recent alternatives to Gromov-Wasserstein. We show that EW can be adapted to derive a distance as well as optimal transportation plans between GMMs. We demonstrate the efficiency of these newly proposed distances on medium to large-scale problems, including shape matching and hyperspectral image color transfer.