Hong Xu

Qingyu Song, Wei Lin, Juncheng Wang et al.

Learning to optimize (L2O) is an emerging technique to solve mathematical optimization problems with learning-based methods. Although with great success in many real-world scenarios such as wireless communications, computer networks, and electronic design, existing L2O works lack theoretical demonstration of their performance and robustness in out-of-distribution (OOD) scenarios. We address this gap by providing comprehensive proofs. First, we prove a sufficient condition for a robust L2O model with homogeneous convergence rates over all In-Distribution (InD) instances. We assume an L2O model achieves robustness for an InD scenario. Based on our proposed methodology of aligning OOD problems to InD problems, we also demonstrate that the L2O model's convergence rate in OOD scenarios will deteriorate by an equation of the L2O model's input features. Moreover, we propose an L2O model with a concise gradient-only feature construction and a novel gradient-based history modeling method. Numerical simulation demonstrates that our proposed model outperforms the state-of-the-art baseline in both InD and OOD scenarios and achieves up to 10 $\times$ convergence speedup. The code of our method can be found from https://github.com/NetX-lab/GoMathL2O-Official.

Alex Bozarth, Brendan Dwyer, Fei Hu et al.

A recent trend observed in traditionally challenging fields such as computer vision and natural language processing has been the significant performance gains shown by deep learning (DL). In many different research fields, DL models have been evolving rapidly and become ubiquitous. Despite researchers' excitement, unfortunately, most software developers are not DL experts and oftentimes have a difficult time following the booming DL research outputs. As a result, it usually takes a significant amount of time for the latest superior DL models to prevail in industry. This issue is further exacerbated by the common use of sundry incompatible DL programming frameworks, such as Tensorflow, PyTorch, Theano, etc. To address this issue, we propose a system, called Model Asset Exchange (MAX), that avails developers of easy access to state-of-the-art DL models. Regardless of the underlying DL programming frameworks, it provides an open source Python library (called the MAX framework) that wraps DL models and unifies programming interfaces with our standardized RESTful APIs. These RESTful APIs enable developers to exploit the wrapped DL models for inference tasks without the need to fully understand different DL programming frameworks. Using MAX, we have wrapped and open-sourced more than 30 state-of-the-art DL models from various research fields, including computer vision, natural language processing and signal processing, etc. In the end, we selectively demonstrate two web applications that are built on top of MAX, as well as the process of adding a DL model to MAX.

Hong Xu, Shireen Y. Elhabian

Particle-based shape modeling (PSM) is a popular approach to automatically quantify shape variability in populations of anatomies. The PSM family of methods employs optimization to automatically populate a dense set of corresponding particles (as pseudo landmarks) on 3D surfaces to allow subsequent shape analysis. A recent deep learning approach leverages implicit radial basis function representations of shapes to better adapt to the underlying complex geometry of anatomies. Here, we propose an adaptation of this method using a traditional optimization approach that allows more precise control over the desired characteristics of models by leveraging both an eigenshape and a correspondence loss. Furthermore, the proposed approach avoids using a black-box model and allows more freedom for particles to navigate the underlying surfaces, yielding more informative statistical models. We demonstrate the efficacy of the proposed approach to state-of-the-art methods on two real datasets and justify our choice of losses empirically.

Hong Xu, Alan Morris, Shireen Y. Elhabian

Statistical Shape Modeling (SSM) is a quantitative method for analyzing morphological variations in anatomical structures. These analyses often necessitate building models on targeted anatomical regions of interest to focus on specific morphological features. We propose an extension to \particle-based shape modeling (PSM), a widely used SSM framework, to allow shape modeling to arbitrary regions of interest. Existing methods to define regions of interest are computationally expensive and have topological limitations. To address these shortcomings, we use mesh fields to define free-form constraints, which allow for delimiting arbitrary regions of interest on shape surfaces. Furthermore, we add a quadratic penalty method to the model optimization to enable computationally efficient enforcement of any combination of cutting-plane and free-form constraints. We demonstrate the effectiveness of this method on a challenging synthetic dataset and two medical datasets.

Hong Xu, Shireen Y. Elhabian

Statistical shape modeling (SSM) is an essential tool for analyzing variations in anatomical morphology. In a typical SSM pipeline, 3D anatomical images, gone through segmentation and rigid registration, are represented using lower-dimensional shape features, on which statistical analysis can be performed. Various methods for constructing compact shape representations have been proposed, but they involve laborious and costly steps. We propose Image2SSM, a novel deep-learning-based approach for SSM that leverages image-segmentation pairs to learn a radial-basis-function (RBF)-based representation of shapes directly from images. This RBF-based shape representation offers a rich self-supervised signal for the network to estimate a continuous, yet compact representation of the underlying surface that can adapt to complex geometries in a data-driven manner. Image2SSM can characterize populations of biological structures of interest by constructing statistical landmark-based shape models of ensembles of anatomical shapes while requiring minimal parameter tuning and no user assistance. Once trained, Image2SSM can be used to infer low-dimensional shape representations from new unsegmented images, paving the way toward scalable approaches for SSM, especially when dealing with large cohorts. Experiments on synthetic and real datasets show the efficacy of the proposed method compared to the state-of-art correspondence-based method for SSM.

Hong Xu, David E. Timm, Shireen Y. Elhabian

Cryogenic electron microscopy (cryo-EM) has become an enabling technology in drug discovery and in understanding molecular bases of disease by producing near-atomic resolution (less than 0.4 nm) 3D reconstructions of biological macromolecules. The imaging process required for 3D reconstructions involves a highly iterative and empirical screening process, starting with the acquisition of low magnification images of the cryo-EM grids. These images are inspected for squares that are likely to contain useful molecular signals. Potentially useful squares within the grid are then imaged at progressively higher magnifications, with the goal of identifying sub-micron areas within circular holes (bounded by the squares) for imaging at high magnification. This arduous, multi-step data acquisition process represents a bottleneck for obtaining a high throughput data collection. Here, we focus on automating the early decision making for the microscope operator, scoring low magnification images of squares, and proposing the first deep learning framework, XCryoNet, for automated cryo-EM grid screening. XCryoNet is a semi-supervised, attention-guided deep learning approach that provides explainable scoring of automatically extracted square images using limited amounts of labeled data. Results show up to 8% and 37% improvements over a fully supervised and a no-attention solution, respectively, when labeled data is scarce.