107,368 research outputs found
Coherent energy and force uncertainty in deep learning force fields
In machine learning energy potentials for atomic systems, forces are commonly
obtained as the negative derivative of the energy function with respect to
atomic positions. To quantify aleatoric uncertainty in the predicted energies,
a widely used modeling approach involves predicting both a mean and variance
for each energy value. However, this model is not differentiable under the
usual white noise assumption, so energy uncertainty does not naturally
translate to force uncertainty. In this work we propose a machine learning
potential energy model in which energy and force aleatoric uncertainty are
linked through a spatially correlated noise process. We demonstrate our
approach on an equivariant messages passing neural network potential trained on
energies and forces on two out-of-equilibrium molecular datasets. Furthermore,
we also show how to obtain epistemic uncertainties in this setting based on a
Bayesian interpretation of deep ensemble models.Comment: Presented at Advancing Molecular Machine Learning - Overcoming
Limitations [ML4Molecules], ELLIS workshop, VIRTUAL, December 8, 2023,
unofficial NeurIPS 2023 side-even
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
This work introduces a number of algebraic topology approaches, such as
multicomponent persistent homology, multi-level persistent homology and
electrostatic persistence for the representation, characterization, and
description of small molecules and biomolecular complexes. Multicomponent
persistent homology retains critical chemical and biological information during
the topological simplification of biomolecular geometric complexity.
Multi-level persistent homology enables a tailored topological description of
inter- and/or intra-molecular interactions of interest. Electrostatic
persistence incorporates partial charge information into topological
invariants. These topological methods are paired with Wasserstein distance to
characterize similarities between molecules and are further integrated with a
variety of machine learning algorithms, including k-nearest neighbors, ensemble
of trees, and deep convolutional neural networks, to manifest their descriptive
and predictive powers for chemical and biological problems. Extensive numerical
experiments involving more than 4,000 protein-ligand complexes from the PDBBind
database and near 100,000 ligands and decoys in the DUD database are performed
to test respectively the scoring power and the virtual screening power of the
proposed topological approaches. It is demonstrated that the present approaches
outperform the modern machine learning based methods in protein-ligand binding
affinity predictions and ligand-decoy discrimination
An Overview on Application of Machine Learning Techniques in Optical Networks
Today's telecommunication networks have become sources of enormous amounts of
widely heterogeneous data. This information can be retrieved from network
traffic traces, network alarms, signal quality indicators, users' behavioral
data, etc. Advanced mathematical tools are required to extract meaningful
information from these data and take decisions pertaining to the proper
functioning of the networks from the network-generated data. Among these
mathematical tools, Machine Learning (ML) is regarded as one of the most
promising methodological approaches to perform network-data analysis and enable
automated network self-configuration and fault management. The adoption of ML
techniques in the field of optical communication networks is motivated by the
unprecedented growth of network complexity faced by optical networks in the
last few years. Such complexity increase is due to the introduction of a huge
number of adjustable and interdependent system parameters (e.g., routing
configurations, modulation format, symbol rate, coding schemes, etc.) that are
enabled by the usage of coherent transmission/reception technologies, advanced
digital signal processing and compensation of nonlinear effects in optical
fiber propagation. In this paper we provide an overview of the application of
ML to optical communications and networking. We classify and survey relevant
literature dealing with the topic, and we also provide an introductory tutorial
on ML for researchers and practitioners interested in this field. Although a
good number of research papers have recently appeared, the application of ML to
optical networks is still in its infancy: to stimulate further work in this
area, we conclude the paper proposing new possible research directions
Computing server power modeling in a data center: survey,taxonomy and performance evaluation
Data centers are large scale, energy-hungry infrastructure serving the
increasing computational demands as the world is becoming more connected in
smart cities. The emergence of advanced technologies such as cloud-based
services, internet of things (IoT) and big data analytics has augmented the
growth of global data centers, leading to high energy consumption. This upsurge
in energy consumption of the data centers not only incurs the issue of surging
high cost (operational and maintenance) but also has an adverse effect on the
environment. Dynamic power management in a data center environment requires the
cognizance of the correlation between the system and hardware level performance
counters and the power consumption. Power consumption modeling exhibits this
correlation and is crucial in designing energy-efficient optimization
strategies based on resource utilization. Several works in power modeling are
proposed and used in the literature. However, these power models have been
evaluated using different benchmarking applications, power measurement
techniques and error calculation formula on different machines. In this work,
we present a taxonomy and evaluation of 24 software-based power models using a
unified environment, benchmarking applications, power measurement technique and
error formula, with the aim of achieving an objective comparison. We use
different servers architectures to assess the impact of heterogeneity on the
models' comparison. The performance analysis of these models is elaborated in
the paper
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