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Add to EdgePredicting Polymer Properties Based on Multimodal Multitask Pretraining
Jun 07, 2024
In the past few decades, polymers, high-molecular-weight compounds formed by bonding numerous identical or similar monomers covalently, have played an essential role in various scientific fields. In this context, accurate prediction of their properties is becoming increasingly crucial. Typically, the properties of a polymer, such as plasticity, conductivity, bio-compatibility, and so on, are highly correlated with its 3D structure. However, current methods for predicting polymer properties heavily rely on information from polymer SMILES sequences (P-SMILES strings) while ignoring crucial 3D structural information, leading to sub-optimal performance. In this work, we propose MMPolymer, a novel multimodal multitask pretraining framework incorporating both polymer 1D sequential information and 3D structural information to enhance downstream polymer property prediction tasks. Besides, to overcome the limited availability of polymer 3D data, we further propose the "Star Substitution" strategy to extract 3D structural information effectively. During pretraining, MMPolymer not only predicts masked tokens and recovers 3D coordinates but also achieves the cross-modal alignment of latent representation. Subsequently, we further fine-tune the pretrained MMPolymer for downstream polymer property prediction tasks in the supervised learning paradigm. Experimental results demonstrate that MMPolymer achieves state-of-the-art performance in various polymer property prediction tasks. Moreover, leveraging the pretrained MMPolymer and using only one modality (either P-SMILES string or 3D conformation) during fine-tuning can also surpass existing polymer property prediction methods, highlighting the exceptional capability of MMPolymer in polymer feature extraction and utilization. Our online platform for polymer property prediction is available at https://app.bohrium.dp.tech/mmpolymer.
Bridging The Gap between Low-rank and Orthogonal Adaptation via Householder Reflection Adaptation
May 24, 2024While following different technical routes, both low-rank and orthogonal adaptation techniques can efficiently adapt large-scale pre-training models in specific tasks or domains based on a small piece of trainable parameters. In this study, we bridge the gap between these two techniques, proposing a simple but effective adaptation method based on Householder reflections. Given a pre-trained model, our method fine-tunes its layers by multiplying each frozen weight matrix with an orthogonal matrix constructed by a chain of learnable Householder reflections (HRs). This HR-based orthogonal fine-tuning is equivalent to an adaptive low-rank adaptation. Moreover, we show that the orthogonality of the reflection planes corresponding to the HRs impacts the model capacity and regularity. The analysis motivates us to regularize the orthogonality of the HRs, leading to different implementations of the proposed Householder reflection adaptation (HRA) method. Compared with state-of-the-art methods, HRA achieves superior performance with fewer learnable parameters when adapting large language models and conditional image generators. The code is available at https://github.com/DaShenZi721/HRA
Revisiting Counterfactual Regression through the Lens of Gromov-Wasserstein Information Bottleneck
May 24, 2024As a promising individualized treatment effect (ITE) estimation method, counterfactual regression (CFR) maps individuals' covariates to a latent space and predicts their counterfactual outcomes. However, the selection bias between control and treatment groups often imbalances the two groups' latent distributions and negatively impacts this method's performance. In this study, we revisit counterfactual regression through the lens of information bottleneck and propose a novel learning paradigm called Gromov-Wasserstein information bottleneck (GWIB). In this paradigm, we learn CFR by maximizing the mutual information between covariates' latent representations and outcomes while penalizing the kernelized mutual information between the latent representations and the covariates. We demonstrate that the upper bound of the penalty term can be implemented as a new regularizer consisting of $i)$ the fused Gromov-Wasserstein distance between the latent representations of different groups and $ii)$ the gap between the transport cost generated by the model and the cross-group Gromov-Wasserstein distance between the latent representations and the covariates. GWIB effectively learns the CFR model through alternating optimization, suppressing selection bias while avoiding trivial latent distributions. Experiments on ITE estimation tasks show that GWIB consistently outperforms state-of-the-art CFR methods. To promote the research community, we release our project at https://github.com/peteryang1031/Causal-GWIB.
Generalizable Face Landmarking Guided by Conditional Face Warping
Apr 18, 2024As a significant step for human face modeling, editing, and generation, face landmarking aims at extracting facial keypoints from images. A generalizable face landmarker is required in practice because real-world facial images, e.g., the avatars in animations and games, are often stylized in various ways. However, achieving generalizable face landmarking is challenging due to the diversity of facial styles and the scarcity of labeled stylized faces. In this study, we propose a simple but effective paradigm to learn a generalizable face landmarker based on labeled real human faces and unlabeled stylized faces. Our method learns the face landmarker as the key module of a conditional face warper. Given a pair of real and stylized facial images, the conditional face warper predicts a warping field from the real face to the stylized one, in which the face landmarker predicts the ending points of the warping field and provides us with high-quality pseudo landmarks for the corresponding stylized facial images. Applying an alternating optimization strategy, we learn the face landmarker to minimize $i)$ the discrepancy between the stylized faces and the warped real ones and $ii)$ the prediction errors of both real and pseudo landmarks. Experiments on various datasets show that our method outperforms existing state-of-the-art domain adaptation methods in face landmarking tasks, leading to a face landmarker with better generalizability. Code is available at https://plustwo0.github.io/project-face-landmarker}{https://plustwo0.github.io/project-face-landmarker.
To Search or to Recommend: Predicting Open-App Motivation with Neural Hawkes Process
Apr 04, 2024
Incorporating Search and Recommendation (S&R) services within a singular application is prevalent in online platforms, leading to a new task termed open-app motivation prediction, which aims to predict whether users initiate the application with the specific intent of information searching, or to explore recommended content for entertainment. Studies have shown that predicting users' motivation to open an app can help to improve user engagement and enhance performance in various downstream tasks. However, accurately predicting open-app motivation is not trivial, as it is influenced by user-specific factors, search queries, clicked items, as well as their temporal occurrences. Furthermore, these activities occur sequentially and exhibit intricate temporal dependencies. Inspired by the success of the Neural Hawkes Process (NHP) in modeling temporal dependencies in sequences, this paper proposes a novel neural Hawkes process model to capture the temporal dependencies between historical user browsing and querying actions. The model, referred to as Neural Hawkes Process-based Open-App Motivation prediction model (NHP-OAM), employs a hierarchical transformer and a novel intensity function to encode multiple factors, and open-app motivation prediction layer to integrate time and user-specific information for predicting users' open-app motivations. To demonstrate the superiority of our NHP-OAM model and construct a benchmark for the Open-App Motivation Prediction task, we not only extend the public S&R dataset ZhihuRec but also construct a new real-world Open-App Motivation Dataset (OAMD). Experiments on these two datasets validate NHP-OAM's superiority over baseline models. Further downstream application experiments demonstrate NHP-OAM's effectiveness in predicting users' Open-App Motivation, highlighting the immense application value of NHP-OAM.
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications
Mar 01, 2024
Geometric graph is a special kind of graph with geometric features, which is 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 tackle this issue, researchers proposed a variety of Geometric Graph Neural Networks 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 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.
Sliceformer: Make Multi-head Attention as Simple as Sorting in Discriminative Tasks
Oct 26, 2023
As one of the most popular neural network modules, Transformer plays a central role in many fundamental deep learning models, e.g., the ViT in computer vision and the BERT and GPT in natural language processing. The effectiveness of the Transformer is often attributed to its multi-head attention (MHA) mechanism. In this study, we discuss the limitations of MHA, including the high computational complexity due to its ``query-key-value'' architecture and the numerical issue caused by its softmax operation. Considering the above problems and the recent development tendency of the attention layer, we propose an effective and efficient surrogate of the Transformer, called Sliceformer. Our Sliceformer replaces the classic MHA mechanism with an extremely simple ``slicing-sorting'' operation, i.e., projecting inputs linearly to a latent space and sorting them along different feature dimensions (or equivalently, called channels). For each feature dimension, the sorting operation implicitly generates an implicit attention map with sparse, full-rank, and doubly-stochastic structures. We consider different implementations of the slicing-sorting operation and analyze their impacts on the Sliceformer. We test the Sliceformer in the Long-Range Arena benchmark, image classification, text classification, and molecular property prediction, demonstrating its advantage in computational complexity and universal effectiveness in discriminative tasks. Our Sliceformer achieves comparable or better performance with lower memory cost and faster speed than the Transformer and its variants. Moreover, the experimental results reveal that applying our Sliceformer can empirically suppress the risk of mode collapse when representing data. The code is available at \url{https://github.com/SDS-Lab/sliceformer}.
A Quasi-Wasserstein Loss for Learning Graph Neural Networks
Oct 19, 2023When learning graph neural networks (GNNs) in node-level prediction tasks, most existing loss functions are applied for each node independently, even if node embeddings and their labels are non-i.i.d. because of their graph structures. To eliminate such inconsistency, in this study we propose a novel Quasi-Wasserstein (QW) loss with the help of the optimal transport defined on graphs, leading to new learning and prediction paradigms of GNNs. In particular, we design a "Quasi-Wasserstein" distance between the observed multi-dimensional node labels and their estimations, optimizing the label transport defined on graph edges. The estimations are parameterized by a GNN in which the optimal label transport may determine the graph edge weights optionally. By reformulating the strict constraint of the label transport to a Bregman divergence-based regularizer, we obtain the proposed Quasi-Wasserstein loss associated with two efficient solvers learning the GNN together with optimal label transport. When predicting node labels, our model combines the output of the GNN with the residual component provided by the optimal label transport, leading to a new transductive prediction paradigm. Experiments show that the proposed QW loss applies to various GNNs and helps to improve their performance in node-level classification and regression tasks.
DHOT-GM: Robust Graph Matching Using A Differentiable Hierarchical Optimal Transport Framework
Oct 18, 2023Graph matching is one of the most significant graph analytic tasks in practice, which aims to find the node correspondence across different graphs. Most existing approaches rely on adjacency matrices or node embeddings when matching graphs, whose performances are often sub-optimal because of not fully leveraging the multi-modal information hidden in graphs, such as node attributes, subgraph structures, etc. In this study, we propose a novel and effective graph matching method based on a differentiable hierarchical optimal transport (HOT) framework, called DHOT-GM. Essentially, our method represents each graph as a set of relational matrices corresponding to the information of different modalities. Given two graphs, we enumerate all relational matrix pairs and obtain their matching results, and accordingly, infer the node correspondence by the weighted averaging of the matching results. This method can be implemented as computing the HOT distance between the two graphs -- each matching result is an optimal transport plan associated with the Gromov-Wasserstein (GW) distance between two relational matrices, and the weights of all matching results are the elements of an upper-level optimal transport plan defined on the matrix sets. We propose a bi-level optimization algorithm to compute the HOT distance in a differentiable way, making the significance of the relational matrices adjustable. Experiments on various graph matching tasks demonstrate the superiority and robustness of our method compared to state-of-the-art approaches.
Decentralized Entropic Optimal Transport for Privacy-preserving Distributed Distribution Comparison
Jan 28, 2023
Privacy-preserving distributed distribution comparison measures the distance between the distributions whose data are scattered across different agents in a distributed system and cannot be shared among the agents. In this study, we propose a novel decentralized entropic optimal transport (EOT) method, which provides a privacy-preserving and communication-efficient solution to this problem with theoretical guarantees. In particular, we design a mini-batch randomized block-coordinate descent (MRBCD) scheme to optimize the decentralized EOT distance in its dual form. The dual variables are scattered across different agents and updated locally and iteratively with limited communications among partial agents. The kernel matrix involved in the gradients of the dual variables is estimated by a distributed kernel approximation method, and each agent only needs to approximate and store a sub-kernel matrix by one-shot communication and without sharing raw data. We analyze our method's communication complexity and provide a theoretical bound for the approximation error caused by the convergence error, the approximated kernel, and the mismatch between the storage and communication protocols. Experiments on synthetic data and real-world distributed domain adaptation tasks demonstrate the effectiveness of our method.