Liming Wu

Pierre Del Moral, Peng Hu, Liming Wu

These lecture notes present some new concentration inequalities for Feynman-Kac particle processes. We analyze different types of stochastic particle models, including particle profile occupation measures, genealogical tree based evolution models, particle free energies, as well as backward Markov chain particle models. We illustrate these results with a series of topics related to computational physics and biology, stochastic optimization, signal processing and bayesian statistics, and many other probabilistic machine learning algorithms. Special emphasis is given to the stochastic modeling and the quantitative performance analysis of a series of advanced Monte Carlo methods, including particle filters, genetic type island models, Markov bridge models, interacting particle Markov chain Monte Carlo methodologies.

Jiaqi Han, Jiacheng Cen, Liming Wu et al.

Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

Liming Wu, Zhichao Hou, Jirui Yuan et al.

Learning to represent and simulate the dynamics of physical systems is a crucial yet challenging task. Existing equivariant Graph Neural Network (GNN) based methods have encapsulated the symmetry of physics, \emph{e.g.}, translations, rotations, etc, leading to better generalization ability. Nevertheless, their frame-to-frame formulation of the task overlooks the non-Markov property mainly incurred by unobserved dynamics in the environment. In this paper, we reformulate dynamics simulation as a spatio-temporal prediction task, by employing the trajectory in the past period to recover the Non-Markovian interactions. We propose Equivariant Spatio-Temporal Attentive Graph Networks (ESTAG), an equivariant version of spatio-temporal GNNs, to fulfill our purpose. At its core, we design a novel Equivariant Discrete Fourier Transform (EDFT) to extract periodic patterns from the history frames, and then construct an Equivariant Spatial Module (ESM) to accomplish spatial message passing, and an Equivariant Temporal Module (ETM) with the forward attention and equivariant pooling mechanisms to aggregate temporal message. We evaluate our model on three real datasets corresponding to the molecular-, protein- and macro-level. Experimental results verify the effectiveness of ESTAG compared to typical spatio-temporal GNNs and equivariant GNNs.

Liming Wu, Shuo Han, Alain Chen et al.

Robust and accurate nuclei centroid detection is important for the understanding of biological structures in fluorescence microscopy images. Existing automated nuclei localization methods face three main challenges: (1) Most of object detection methods work only on 2D images and are difficult to extend to 3D volumes; (2) Segmentation-based models can be used on 3D volumes but it is computational expensive for large microscopy volumes and they have difficulty distinguishing different instances of objects; (3) Hand annotated ground truth is limited for 3D microscopy volumes. To address these issues, we present a scalable approach for nuclei centroid detection of 3D microscopy volumes. We describe the RCNN-SliceNet to detect 2D nuclei centroids for each slice of the volume from different directions and 3D agglomerative hierarchical clustering (AHC) is used to estimate the 3D centroids of nuclei in a volume. The model was trained with the synthetic microscopy data generated using Spatially Constrained Cycle-Consistent Adversarial Networks (SpCycleGAN) and tested on different types of real 3D microscopy data. Extensive experimental results demonstrate that our proposed method can accurately count and detect the nuclei centroids in a 3D microscopy volume.

Tengteng Wen, Zhuofeng Mo, Jingshan Li et al.

Deep learning methods have been widely applied to visual and acoustic technology. In this paper, we proposed an odor labeling convolutional encoder-decoder (OLCE) for odor identification in machine olfaction. OLCE composes a convolutional neural network encoder and decoder where the encoder output is constrained to odor labels. An electronic nose was used for the data collection of gas responses followed by a normative experimental procedure. Several evaluation indexes were calculated to evaluate the algorithm effectiveness: accuracy 92.57%, precision 92.29%, recall rate 92.06%, F1-Score 91.96%, and Kappa coefficient 90.76%. We also compared the model with some algorithms used in machine olfaction. The comparison result demonstrated that OLCE had the best performance among these algorithms. In the paper, some perspectives of machine olfactions have been also discussed.