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Register a new userHamNet: Conformation-Guided Molecular Representation with Hamiltonian Neural Networks
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Ziyao Li
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Well-designed molecular representations (fingerprints) are vital to combine medical chemistry and deep learning. Whereas incorporating 3D geometry of molecules (i.e. conformations) in their representations seems beneficial, current 3D algorithms are still in infancy. In this paper, we propose a novel molecular representation algorithm which preserves 3D conformations of molecules with a Molecular Hamiltonian Network (HamNet). In HamNet, implicit positions and momentums of atoms in a molecule interact in the Hamiltonian Engine following the discretized Hamiltonian equations. These implicit coordinations are supervised with real conformations with translation- & rotation-invariant losses, and further used as inputs to the Fingerprint Generator, a message-passing neural network. Experiments show that the Hamiltonian Engine can well preserve molecular conformations, and that the fingerprints generated by HamNet achieve state-of-the-art performances on MoleculeNet, a standard molecular machine learning benchmark.
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We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning methods have shown great potential by training on a large collection of conformation data. Challenges arise from the limited model capacity for capturing complex distributions of conformations and the difficulty in modeling long-range dependencies between atoms. Inspired by the recent progress in deep generative models, in this paper, we propose a novel probabilistic framework to generate valid and diverse conformations given a molecular graph. We propose a method combining the advantages of both flow-based and energy-based models, enjoying: (1) a high model capacity to estimate the multimodal conformation distribution; (2) explicitly capturing the complex long-range dependencies between atoms in the observation space. Extensive experiments demonstrate the superior performance of the proposed method on several benchmarks, including conformation generation and distance modeling tasks, with a significant improvement over existing generative models for molecular conformation sampling.
The rapid growth of research in exploiting machine learning to predict chaotic systems has revived a recent interest in Hamiltonian Neural Networks (HNNs) with physical constraints defined by the Hamiltons equations of motion, which represent a major class of physics-enhanced neural networks. We introduce a class of HNNs capable of adaptable prediction of nonlinear physical systems: by training the neural network based on time series from a small number of bifurcation-parameter values of the target Hamiltonian system, the HNN can predict the dynamical states at other parameter values, where the network has not been exposed to any information about the system at these parameter values. The architecture of the HNN differs from the previous ones in that we incorporate an input parameter channel, rendering the HNN parameter--cognizant. We demonstrate, using paradigmatic Hamiltonian systems, that training the HNN using time series from as few as four parameter values bestows the neural machine with the ability to predict the state of the target system in an entire parameter interval. Utilizing the ensemble maximum Lyapunov exponent and the alignment index as indicators, we show that our parameter-cognizant HNN can successfully predict the route of transition to chaos. Physics-enhanced machine learning is a forefront area of research, and our adaptable HNNs provide an approach to understanding machine learning with broad applications.
Heterogeneous presentation of a neurological disorder suggests potential differences in the underlying pathophysiological changes that occur in the brain. We propose to model heterogeneous patterns of functional network differences using a demographic-guided attention (DGA) mechanism for recurrent neural network models for prediction from functional magnetic resonance imaging (fMRI) time-series data. The context computed from the DGA head is used to help focus on the appropriate functional networks based on individual demographic information. We demonstrate improved classification on 3 subsets of the ABIDE I dataset used in published studies that have previously produced state-of-the-art results, evaluating performance under a leave-one-site-out cross-validation framework for better generalizeability to new data. Finally, we provide examples of interpreting functional network differences based on individual demographic variables.
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it are consistent with the conclusions we would draw from a model at a finer level of detail. It has been proven that a force matching scheme defines a thermodynamically consistent coarse-grained model for an atomistic system in the variational limit. Wang et al. [ACS Cent. Sci. 5, 755 (2019)] demonstrated that the existence of such a variational limit enables the use of a supervised machine learning framework to generate a coarse-grained force field, which can then be used for simulation in the coarse-grained space. Their framework, however, requires the manual input of molecular features upon which to machine learn the force field. In the present contribution, we build upon the advance of Wang et al.and introduce a hybrid architecture for the machine learning of coarse-grained force fields that learns their own features via a subnetwork that leverages continuous filter convolutions on a graph neural network architecture. We demonstrate that this framework succeeds at reproducing the thermodynamics for small biomolecular systems. Since the learned molecular representations are inherently transferable, the architecture presented here sets the stage for the development of machine-learned, coarse-grained force fields that are transferable across molecular systems.
As neural networks get widespread adoption in resource-constrained embedded devices, there is a growing need for low-power neural systems. Spiking Neural Networks (SNNs)are emerging to be an energy-efficient alternative to the traditional Artificial Neural Networks (ANNs) which are known to be computationally intensive. From an application perspective, as federated learning involves multiple energy-constrained devices, there is a huge scope to leverage energy efficiency provided by SNNs. Despite its importance, there has been little attention on training SNNs on a large-scale distributed system like federated learning. In this paper, we bring SNNs to a more realistic federated learning scenario. Specifically, we propose a federated learning framework for decentralized and privacy-preserving training of SNNs. To validate the proposed federated learning framework, we experimentally evaluate the advantages of SNNs on various aspects of federated learning with CIFAR10 and CIFAR100 benchmarks. We observe that SNNs outperform ANNs in terms of overall accuracy by over 15% when the data is distributed across a large number of clients in the federation while providing up to5.3x energy efficiency. In addition to efficiency, we also analyze the sensitivity of the proposed federated SNN framework to data distribution among the clients, stragglers, and gradient noise and perform a comprehensive comparison with ANNs.
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