Nicholas E. Charron

Maciej Majewski, Adrià Pérez, Philipp Thölke et al.

A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.

Xiaqing Pan, Nicholas Charron, Yongqian Yang et al.

We introduce the Aria Digital Twin (ADT) - an egocentric dataset captured using Aria glasses with extensive object, environment, and human level ground truth. This ADT release contains 200 sequences of real-world activities conducted by Aria wearers in two real indoor scenes with 398 object instances (324 stationary and 74 dynamic). Each sequence consists of: a) raw data of two monochrome camera streams, one RGB camera stream, two IMU streams; b) complete sensor calibration; c) ground truth data including continuous 6-degree-of-freedom (6DoF) poses of the Aria devices, object 6DoF poses, 3D eye gaze vectors, 3D human poses, 2D image segmentations, image depth maps; and d) photo-realistic synthetic renderings. To the best of our knowledge, there is no existing egocentric dataset with a level of accuracy, photo-realism and comprehensiveness comparable to ADT. By contributing ADT to the research community, our mission is to set a new standard for evaluation in the egocentric machine perception domain, which includes very challenging research problems such as 3D object detection and tracking, scene reconstruction and understanding, sim-to-real learning, human pose prediction - while also inspiring new machine perception tasks for augmented reality (AR) applications. To kick start exploration of the ADT research use cases, we evaluated several existing state-of-the-art methods for object detection, segmentation and image translation tasks that demonstrate the usefulness of ADT as a benchmarking dataset.

Zhaoyang Lv, Nicholas Charron, Pierre Moulon et al.

We present Aria Everyday Activities (AEA) Dataset, an egocentric multimodal open dataset recorded using Project Aria glasses. AEA contains 143 daily activity sequences recorded by multiple wearers in five geographically diverse indoor locations. Each of the recording contains multimodal sensor data recorded through the Project Aria glasses. In addition, AEA provides machine perception data including high frequency globally aligned 3D trajectories, scene point cloud, per-frame 3D eye gaze vector and time aligned speech transcription. In this paper, we demonstrate a few exemplar research applications enabled by this dataset, including neural scene reconstruction and prompted segmentation. AEA is an open source dataset that can be downloaded from https://www.projectaria.com/datasets/aea/. We are also providing open-source implementations and examples of how to use the dataset in Project Aria Tools https://github.com/facebookresearch/projectaria_tools.

Jiang Wang, Simon Olsson, Christoph Wehmeyer et al.

Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such computationally expensive simulations is the definition of coarse-grained molecular models. Existing coarse-graining approaches define an effective interaction potential to match defined properties of high-resolution models or experimental data. In this paper, we reformulate coarse-graining as a supervised machine learning problem. We use statistical learning theory to decompose the coarse-graining error and cross-validation to select and compare the performance of different models. We introduce CGnets, a deep learning approach, that learns coarse-grained free energy functions and can be trained by a force matching scheme. CGnets maintain all physically relevant invariances and allow one to incorporate prior physics knowledge to avoid sampling of unphysical structures. We show that CGnets can capture all-atom explicit-solvent free energy surfaces with models using only a few coarse-grained beads and no solvent, while classical coarse-graining methods fail to capture crucial features of the free energy surface. Thus, CGnets are able to capture multi-body terms that emerge from the dimensionality reduction.