Zhen Zhang

Zhen Zhang, Zongren Zou, Ellen Kuhl et al.

Misfolded tau proteins play a critical role in the progression and pathology of Alzheimer's disease. Recent studies suggest that the spatio-temporal pattern of misfolded tau follows a reaction-diffusion type equation. However, the precise mathematical model and parameters that characterize the progression of misfolded protein across the brain remain incompletely understood. Here, we use deep learning and artificial intelligence to discover a mathematical model for the progression of Alzheimer's disease using longitudinal tau positron emission tomography from the Alzheimer's Disease Neuroimaging Initiative database. Specifically, we integrate physics informed neural networks (PINNs) and symbolic regression to discover a reaction-diffusion type partial differential equation for tau protein misfolding and spreading. First, we demonstrate the potential of our model and parameter discovery on synthetic data. Then, we apply our method to discover the best model and parameters to explain tau imaging data from 46 individuals who are likely to develop Alzheimer's disease and 30 healthy controls. Our symbolic regression discovers different misfolding models $f(c)$ for two groups, with a faster misfolding for the Alzheimer's group, $f(c) = 0.23c^3 - 1.34c^2 + 1.11c$, than for the healthy control group, $f(c) = -c^3 +0.62c^2 + 0.39c$. Our results suggest that PINNs, supplemented by symbolic regression, can discover a reaction-diffusion type model to explain misfolded tau protein concentrations in Alzheimer's disease. We expect our study to be the starting point for a more holistic analysis to provide image-based technologies for early diagnosis, and ideally early treatment of neurodegeneration in Alzheimer's disease and possibly other misfolding-protein based neurodegenerative disorders.

Vivek Oommen, Aniruddha Bora, Zhen Zhang et al.

We integrate neural operators with diffusion models to address the spectral limitations of neural operators in surrogate modeling of turbulent flows. While neural operators offer computational efficiency, they exhibit deficiencies in capturing high-frequency flow dynamics, resulting in overly smooth approximations. To overcome this, we condition diffusion models on neural operators to enhance the resolution of turbulent structures. Our approach is validated for different neural operators on diverse datasets, including a high Reynolds number jet flow simulation and experimental Schlieren velocimetry. The proposed method significantly improves the alignment of predicted energy spectra with true distributions compared to neural operators alone. This enables the diffusion models to stabilize longer forecasts through diffusion-corrected autoregressive rollouts, as we demonstrate in this work. Additionally, proper orthogonal decomposition analysis demonstrates enhanced spectral fidelity in space-time. This work establishes a new paradigm for combining generative models with neural operators to advance surrogate modeling of turbulent systems, and it can be used in other scientific applications that involve microstructure and high-frequency content. See our project page: vivekoommen.github.io/NO_DM

Yangning Li, Yinghui Li, Xinyu Wang et al.

Multimodal Retrieval Augmented Generation (mRAG) plays an important role in mitigating the "hallucination" issue inherent in multimodal large language models (MLLMs). Although promising, existing heuristic mRAGs typically predefined fixed retrieval processes, which causes two issues: (1) Non-adaptive Retrieval Queries. (2) Overloaded Retrieval Queries. However, these flaws cannot be adequately reflected by current knowledge-seeking visual question answering (VQA) datasets, since the most required knowledge can be readily obtained with a standard two-step retrieval. To bridge the dataset gap, we first construct Dyn-VQA dataset, consisting of three types of "dynamic" questions, which require complex knowledge retrieval strategies variable in query, tool, and time: (1) Questions with rapidly changing answers. (2) Questions requiring multi-modal knowledge. (3) Multi-hop questions. Experiments on Dyn-VQA reveal that existing heuristic mRAGs struggle to provide sufficient and precisely relevant knowledge for dynamic questions due to their rigid retrieval processes. Hence, we further propose the first self-adaptive planning agent for multimodal retrieval, OmniSearch. The underlying idea is to emulate the human behavior in question solution which dynamically decomposes complex multimodal questions into sub-question chains with retrieval action. Extensive experiments prove the effectiveness of our OmniSearch, also provide direction for advancing mRAG. The code and dataset will be open-sourced at https://github.com/Alibaba-NLP/OmniSearch.

Zhen Zhang, Yeonjong Shin, George Em Karniadakis

We propose the GENERIC formalism informed neural networks (GFINNs) that obey the symmetric degeneracy conditions of the GENERIC formalism. GFINNs comprise two modules, each of which contains two components. We model each component using a neural network whose architecture is designed to satisfy the required conditions. The component-wise architecture design provides flexible ways of leveraging available physics information into neural networks. We prove theoretically that GFINNs are sufficiently expressive to learn the underlying equations, hence establishing the universal approximation theorem. We demonstrate the performance of GFINNs in three simulation problems: gas containers exchanging heat and volume, thermoelastic double pendulum and the Langevin dynamics. In all the examples, GFINNs outperform existing methods, hence demonstrating good accuracy in predictions for both deterministic and stochastic systems.

Pengzhan Jin, Zhen Zhang, Aiqing Zhu et al.

We propose new symplectic networks (SympNets) for identifying Hamiltonian systems from data based on a composition of linear, activation and gradient modules. In particular, we define two classes of SympNets: the LA-SympNets composed of linear and activation modules, and the G-SympNets composed of gradient modules. Correspondingly, we prove two new universal approximation theorems that demonstrate that SympNets can approximate arbitrary symplectic maps based on appropriate activation functions. We then perform several experiments including the pendulum, double pendulum and three-body problems to investigate the expressivity and the generalization ability of SympNets. The simulation results show that even very small size SympNets can generalize well, and are able to handle both separable and non-separable Hamiltonian systems with data points resulting from short or long time steps. In all the test cases, SympNets outperform the baseline models, and are much faster in training and prediction. We also develop an extended version of SympNets to learn the dynamics from irregularly sampled data. This extended version of SympNets can be thought of as a universal model representing the solution to an arbitrary Hamiltonian system.

Jun Zhang, Yao-Kun Lei, Xing Che et al.

In this paper we first analyzed the inductive bias underlying the data scattered across complex free energy landscapes (FEL), and exploited it to train deep neural networks which yield reduced and clustered representation for the FEL. Our parametric method, called Information Distilling of Metastability (IDM), is end-to-end differentiable thus scalable to ultra-large dataset. IDM is also a clustering algorithm and is able to cluster the samples in the meantime of reducing the dimensions. Besides, as an unsupervised learning method, IDM differs from many existing dimensionality reduction and clustering methods in that it neither requires a cherry-picked distance metric nor the ground-true number of clusters, and that it can be used to unroll and zoom-in the hierarchical FEL with respect to different timescales. Through multiple experiments, we show that IDM can achieve physically meaningful representations which partition the FEL into well-defined metastable states hence are amenable for downstream tasks such as mechanism analysis and kinetic modeling.