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.
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Over the last few decades, numerous LiDAR-inertial odometry (LIO) algorithms have been developed, demonstrating satisfactory performance across diverse environments. Most of these algorithms have predominantly been validated in open outdoor environments, however they often encounter challenges in confined indoor settings. In such indoor environments, reliable point cloud registration becomes problematic due to the rapid changes in LiDAR scans and repetitive structural features like walls and stairs, particularly in multifloor buildings. In this paper, we present NV-LIO, a normal vector based LIO framework, designed for simultaneous localization and mapping (SLAM) in indoor environments with multifloor structures. Our approach extracts the normal vectors from the LiDAR scans and utilizes them for correspondence search to enhance the point cloud registration performance. To ensure robust registration, the distribution of the normal vector directions is analyzed, and situations of degeneracy are examined to adjust the matching uncertainty. Additionally, a viewpoint based loop closure module is implemented to avoid wrong correspondences that are blocked by the walls. The propsed method is validated through public datasets and our own dataset. To contribute to the community, the code will be made public on //github.com/dhchung/nv_lio.
Industry 5.0 and beyond networks have driven the emergence of numerous mission-critical applications, prompting contemplation of the neXt-generation ultra-reliable low-latency communication (xURLLC). To guarantee low-latency requirements, xURLLC heavily relies on short-blocklength packets with sporadic arrival traffic. As a disruptive multi-access technique, rate-splitting multiple access (RSMA) has emerged as a promising avenue to enhance quality of service (QoS) and flexibly manage interference for next-generation communication networks. In this paper, we investigate an innovative RSMA-assisted uplink xURLLC industrial internet-of-things (IIoT) (RSMA-xURLLC-IIoT) network. To unveil reliable insights into the statistical QoS provisioning (SQP) for our proposed network with sporadic arrival traffic, we leverage stochastic network calculus (SNC) to develop a dependable theoretical framework. Building upon this theoretical framework, we formulate the SQP-driven short-packet size maximization problem and the SQP-driven transmit power minimization problem, aiming to guarantee the SQP performance to latency, decoding, and reliability while maximizing the short-packet size and minimizing the transmit power, respectively. By exploiting Monte-Carlo methods, we have thoroughly validated the dependability of the developed theoretical framework. Moreover, through extensive comparison analysis with state-of-the-art multi-access techniques, including non-orthogonal multiple access (NOMA) and orthogonal multiple access (OMA), we have demonstrated the superior performance gains achieved by the proposed RSMA-xURLLC-IIoT networks.
Large scale machine learning-based Raga identification continues to be a nontrivial issue in the computational aspects behind Carnatic music. Each raga consists of many unique and intrinsic melodic patterns that can be used to easily identify them from others. These ragas can also then be used to cluster songs within the same raga, as well as identify songs in other closely related ragas. In this case, the input sound is analyzed using a combination of steps including using a Discrete Fourier transformation and using Triangular Filtering to create custom bins of possible notes, extracting features from the presence of particular notes or lack thereof. Using a combination of Neural Networks including 1D Convolutional Neural Networks conventionally known as Time-Delay Neural Networks) and Long Short-Term Memory (LSTM), which are a form of Recurrent Neural Networks, the backbone of the classification strategy to build the model can be created. In addition, to help with variations in shruti, a long-time attention-based mechanism will be implemented to determine the relative changes in frequency rather than the absolute differences. This will provide a much more meaningful data point when training audio clips in different shrutis. To evaluate the accuracy of the classifier, a dataset of 676 recordings is used. The songs are distributed across the list of ragas. The goal of this program is to be able to effectively and efficiently label a much wider range of audio clips in more shrutis, ragas, and with more background noise.
Targetless IMU-LiDAR extrinsic calibration methods are gaining significant attention as the importance of the IMU-LiDAR fusion system increases. Notably, existing calibration methods derive calibration parameters under the assumption that the methods require full motion in all axes. When IMU and LiDAR are mounted on a ground robot the motion of which is restricted to planar motion, existing calibration methods are likely to exhibit degraded performance. To address this issue, we present GRIL-Calib: a novel targetless Ground Robot IMU-LiDAR Calibration method. Our proposed method leverages ground information to compensate for the lack of unrestricted full motion. First, we propose LiDAR Odometry (LO) using ground plane residuals to enhance calibration accuracy. Second, we propose the Ground Plane Motion (GPM) constraint and incorporate it into the optimization for calibration, enabling the determination of full 6-DoF extrinsic parameters, including theoretically unobservable direction. Finally, unlike baseline methods, we formulate the calibration not as sequential two optimizations but as a single optimization (SO) problem, solving all calibration parameters simultaneously and improving accuracy. We validate our GRIL-Calib by applying it to various real-world datasets and comparing its performance with that of existing state-of-the-art methods in terms of accuracy and robustness. Our code is available at //github.com/Taeyoung96/GRIL-Calib.
Efficient sampling of the Boltzmann distribution of molecular systems is a long-standing challenge. Recently, instead of generating long molecular dynamics simulations, generative machine learning methods such as normalizing flows have been used to learn the Boltzmann distribution directly, without samples. However, this approach is susceptible to mode collapse and thus often does not explore the full configurational space. In this work, we address this challenge by separating the problem into two levels, the fine-grained and coarse-grained degrees of freedom. A normalizing flow conditioned on the coarse-grained space yields a probabilistic connection between the two levels. To explore the configurational space, we employ coarse-grained simulations with active learning which allows us to update the flow and make all-atom potential energy evaluations only when necessary. Using alanine dipeptide as an example, we show that our methods obtain a speedup to molecular dynamics simulations of approximately 15.9 to 216.2 compared to the speedup of 4.5 of the current state-of-the-art machine learning approach.
Peer prediction mechanisms motivate high-quality feedback with provable guarantees. However, current methods only apply to rather simple reports, like multiple-choice or scalar numbers. We aim to broaden these techniques to the larger domain of text-based reports, drawing on the recent developments in large language models. This vastly increases the applicability of peer prediction mechanisms as textual feedback is the norm in a large variety of feedback channels: peer reviews, e-commerce customer reviews, and comments on social media. We introduce two mechanisms, the Generative Peer Prediction Mechanism (GPPM) and the Generative Synopsis Peer Prediction Mechanism (GSPPM). These mechanisms utilize LLMs as predictors, mapping from one agent's report to a prediction of her peer's report. Theoretically, we show that when the LLM prediction is sufficiently accurate, our mechanisms can incentivize high effort and truth-telling as an (approximate) Bayesian Nash equilibrium. Empirically, we confirm the efficacy of our mechanisms through experiments conducted on two real datasets: the Yelp review dataset and the ICLR OpenReview dataset. We highlight the results that on the ICLR dataset, our mechanisms can differentiate three quality levels -- human-written reviews, GPT-4-generated reviews, and GPT-3.5-generated reviews in terms of expected scores. Additionally, GSPPM penalizes LLM-generated reviews more effectively than GPPM.
The intersection of chemistry and Artificial Intelligence (AI) is an active area of research focused on accelerating scientific discovery. While using large language models (LLMs) with scientific modalities has shown potential, there are significant challenges to address, such as improving training efficiency and dealing with the out-of-distribution problem. Focussing on the task of automated language-molecule translation, we are the first to use state-of-the art (SOTA) human-centric optimisation algorithms in the cross-modal setting, successfully aligning cross-language-molecule modals. We empirically show that we can augment the capabilities of scientific LLMs without the need for extensive data or large models. We conduct experiments using only 10% of the available data to mitigate memorisation effects associated with training large models on extensive datasets. We achieve significant performance gains, surpassing the best benchmark model trained on extensive in-distribution data by a large margin and reach new SOTA levels. Additionally we are the first to propose employing non-linear fusion for mixing cross-modal LLMs which further boosts performance gains without increasing training costs or data needs. Finally, we introduce a fine-grained, domain-agnostic evaluation method to assess hallucination in LLMs and promote responsible use.
We initiate the study of counting Markov Equivalence Classes (MEC) under logical constraints. MECs are equivalence classes of Directed Acyclic Graphs (DAGs) that encode the same conditional independence structure among the random variables of a DAG model. Observational data can only allow to infer a DAG model up to Markov Equivalence. However, Markov equivalent DAGs can represent different causal structures, potentially super-exponentially many. Hence, understanding MECs combinatorially is critical to understanding the complexity of causal inference. In this paper, we focus on analysing MECs of size one, with logical constraints on the graph topology. We provide a polynomial-time algorithm (w.r.t. the number of nodes) for enumerating essential DAGs (the only members of an MEC of size one) with arbitrary logical constraints expressed in first-order logic with two variables and counting quantifiers (C^2). Our work brings together recent developments in tractable first-order model counting and combinatorics of MECs.
Addressing the statistical challenge of computing the multivariate normal (MVN) probability in high dimensions holds significant potential for enhancing various applications. One common way to compute high-dimensional MVN probabilities is the Separation-of-Variables (SOV) algorithm. This algorithm is known for its high computational complexity of O(n^3) and space complexity of O(n^2), mainly due to a Cholesky factorization operation for an n X n covariance matrix, where $n$ represents the dimensionality of the MVN problem. This work proposes a high-performance computing framework that allows scaling the SOV algorithm and, subsequently, the confidence region detection algorithm. The framework leverages parallel linear algebra algorithms with a task-based programming model to achieve performance scalability in computing process probabilities, especially on large-scale systems. In addition, we enhance our implementation by incorporating Tile Low-Rank (TLR) approximation techniques to reduce algorithmic complexity without compromising the necessary accuracy. To evaluate the performance and accuracy of our framework, we conduct assessments using simulated data and a wind speed dataset. Our proposed implementation effectively handles high-dimensional multivariate normal (MVN) probability computations on shared and distributed-memory systems using finite precision arithmetics and TLR approximation computation. Performance results show a significant speedup of up to 20X in solving the MVN problem using TLR approximation compared to the reference dense solution without sacrificing the application's accuracy. The qualitative results on synthetic and real datasets demonstrate how we maintain high accuracy in detecting confidence regions even when relying on TLR approximation to perform the underlying linear algebra operations.
Graph Neural Networks (GNNs) have shown promising results on a broad spectrum of applications. Most empirical studies of GNNs directly take the observed graph as input, assuming the observed structure perfectly depicts the accurate and complete relations between nodes. However, graphs in the real world are inevitably noisy or incomplete, which could even exacerbate the quality of graph representations. In this work, we propose a novel Variational Information Bottleneck guided Graph Structure Learning framework, namely VIB-GSL, in the perspective of information theory. VIB-GSL advances the Information Bottleneck (IB) principle for graph structure learning, providing a more elegant and universal framework for mining underlying task-relevant relations. VIB-GSL learns an informative and compressive graph structure to distill the actionable information for specific downstream tasks. VIB-GSL deduces a variational approximation for irregular graph data to form a tractable IB objective function, which facilitates training stability. Extensive experimental results demonstrate that the superior effectiveness and robustness of VIB-GSL.
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