arXiv subjects

Hongyu Guo

Publications and source records attributed to Hongyu Guo.

At least 55 records · Page 3Linked to original sources

arXiv2023

GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow

Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these models cannot effectively generate 3D molecules with 2D skeletal curtailments and property constraints, which are pivotal to drug potency and development. To tackle this challenge, we propose GraphVF, a variational flow-based framework that combines 2D topology and 3D geometry, for controllable generation of binding 3D molecules. Empirically, our method achieves state-of-the-art binding affinity and realistic sub-structural layouts for protein-specific generation. In particular, GraphVF represents the first controllable geometry-aware, protein-specific molecule generation method, which can generate binding 3D molecules with tailored sub-structures and physio-chemical properties. Our code is available at https://github.com/Franco-Solis/GraphVF-code.

q-bio.BM↗

arXiv2022

ifMixup: Interpolating Graph Pair to Regularize Graph Classification

We present a simple and yet effective interpolation-based regularization technique, aiming to improve the generalization of Graph Neural Networks (GNNs) on supervised graph classification. We leverage Mixup, an effective regularizer for vision, where random sample pairs and their labels are interpolated to create synthetic images for training. Unlike images with grid-like coordinates, graphs have arbitrary structure and topology, which can be very sensitive to any modification that alters the graph's semantic meanings. This posts two unanswered questions for Mixup-like regularization schemes: Can we directly mix up a pair of graph inputs? If so, how well does such mixing strategy regularize the learning of GNNs? To answer these two questions, we propose ifMixup, which first adds dummy nodes to make two graphs have the same input size and then simultaneously performs linear interpolation between the aligned node feature vectors and the aligned edge representations of the two graphs. We empirically show that such simple mixing schema can effectively regularize the classification learning, resulting in superior predictive accuracy to popular graph augmentation and GNN methods.

cs.LG↗

arXiv2022

Modeling driver's evasive behavior during safety-critical lane changes:Two-dimensional time-to-collision and deep reinforcement learning

Lane changes are complex driving behaviors and frequently involve safety-critical situations. This study aims to develop a lane-change-related evasive behavior model, which can facilitate the development of safety-aware traffic simulations and predictive collision avoidance systems. Large-scale connected vehicle data from the Safety Pilot Model Deployment (SPMD) program were used for this study. A new surrogate safety measure, two-dimensional time-to-collision (2D-TTC), was proposed to identify the safety-critical situations during lane changes. The validity of 2D-TTC was confirmed by showing a high correlation between the detected conflict risks and the archived crashes. A deep deterministic policy gradient (DDPG) algorithm, which could learn the sequential decision-making process over continuous action spaces, was used to model the evasive behaviors in the identified safety-critical situations. The results showed the superiority of the proposed model in replicating both the longitudinal and lateral evasive behaviors.

cs.AI↗

arXiv2022

SoftEdge: Regularizing Graph Classification with Random Soft Edges

Augmented graphs play a vital role in regularizing Graph Neural Networks (GNNs), which leverage information exchange along edges in graphs, in the form of message passing, for learning. Due to their effectiveness, simple edge and node manipulations (e.g., addition and deletion) have been widely used in graph augmentation. Nevertheless, such common augmentation techniques can dramatically change the semantics of the original graph, causing overaggressive augmentation and thus under-fitting in the GNN learning. To address this problem arising from dropping or adding graph edges and nodes, we propose SoftEdge, which assigns random weights to a portion of the edges of a given graph for augmentation. The synthetic graph generated by SoftEdge maintains the same nodes and their connectivities as the original graph, thus mitigating the semantic changes of the original graph. We empirically show that this simple method obtains superior accuracy to popular node and edge manipulation approaches and notable resilience to the accuracy degradation with the GNN depth.

cs.LG↗

arXiv2022

Pre-training Molecular Graph Representation with 3D Geometry

Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric information plays a more vital role in predicting molecular functionalities. However, the lack of 3D information in real-world scenarios has significantly impeded the learning of geometric graph representation. To cope with this challenge, we propose the Graph Multi-View Pre-training (GraphMVP) framework where self-supervised learning (SSL) is performed by leveraging the correspondence and consistency between 2D topological structures and 3D geometric views. GraphMVP effectively learns a 2D molecular graph encoder that is enhanced by richer and more discriminative 3D geometry. We further provide theoretical insights to justify the effectiveness of GraphMVP. Finally, comprehensive experiments show that GraphMVP can consistently outperform existing graph SSL methods.

cs.LG↗

arXiv2021

A Graph to Graphs Framework for Retrosynthesis Prediction

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive and also suffer from the problem of coverage. In this paper, we propose a novel template-free approach called G2Gs by transforming a target molecular graph into a set of reactant molecular graphs. G2Gs first splits the target molecular graph into a set of synthons by identifying the reaction centers, and then translates the synthons to the final reactant graphs via a variational graph translation framework. Experimental results show that G2Gs significantly outperforms existing template-free approaches by up to 63% in terms of the top-1 accuracy and achieves a performance close to that of state-of-the-art template based approaches, but does not require domain knowledge and is much more scalable.

cs.LG↗

arXiv2021

Midpoint Regularization: from High Uncertainty Training to Conservative Classification

Label Smoothing (LS) improves model generalization through penalizing models from generating overconfident output distributions. For each training sample the LS strategy smooths the one-hot encoded training signal by distributing its distribution mass over the non-ground truth classes. We extend this technique by considering example pairs, coined PLS. PLS first creates midpoint samples by averaging random sample pairs and then learns a smoothing distribution during training for each of these midpoint samples, resulting in midpoints with high uncertainty labels for training. We empirically show that PLS significantly outperforms LS, achieving up to 30% of relative classification error reduction. We also visualize that PLS produces very low winning softmax scores for both in and out of distribution samples.

cs.LG↗

arXiv2021

Symmetric Wasserstein Autoencoders

Leveraging the framework of Optimal Transport, we introduce a new family of generative autoencoders with a learnable prior, called Symmetric Wasserstein Autoencoders (SWAEs). We propose to symmetrically match the joint distributions of the observed data and the latent representation induced by the encoder and the decoder. The resulting algorithm jointly optimizes the modelling losses in both the data and the latent spaces with the loss in the data space leading to the denoising effect. With the symmetric treatment of the data and the latent representation, the algorithm implicitly preserves the local structure of the data in the latent space. To further improve the quality of the latent representation, we incorporate a reconstruction loss into the objective, which significantly benefits both the generation and reconstruction. We empirically show the superior performance of SWAEs over the state-of-the-art generative autoencoders in terms of classification, reconstruction, and generation.

cs.LG↗

arXiv2021

Self-supervised Graph-level Representation Learning with Local and Global Structure

This paper studies unsupervised/self-supervised whole-graph representation learning, which is critical in many tasks such as molecule properties prediction in drug and material discovery. Existing methods mainly focus on preserving the local similarity structure between different graph instances but fail to discover the global semantic structure of the entire data set. In this paper, we propose a unified framework called Local-instance and Global-semantic Learning (GraphLoG) for self-supervised whole-graph representation learning. Specifically, besides preserving the local similarities, GraphLoG introduces the hierarchical prototypes to capture the global semantic clusters. An efficient online expectation-maximization (EM) algorithm is further developed for learning the model. We evaluate GraphLoG by pre-training it on massive unlabeled graphs followed by fine-tuning on downstream tasks. Extensive experiments on both chemical and biological benchmark data sets demonstrate the effectiveness of the proposed approach.

cs.LG↗

arXiv2021

Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction

Reliably predicting the products of chemical reactions presents a fundamental challenge in synthetic chemistry. Existing machine learning approaches typically produce a reaction product by sequentially forming its subparts or intermediate molecules. Such autoregressive methods, however, not only require a pre-defined order for the incremental construction but preclude the use of parallel decoding for efficient computation. To address these issues, we devise a non-autoregressive learning paradigm that predicts reaction in one shot. Leveraging the fact that chemical reactions can be described as a redistribution of electrons in molecules, we formulate a reaction as an arbitrary electron flow and predict it with a novel multi-pointer decoding network. Experiments on the USPTO-MIT dataset show that our approach has established a new state-of-the-art top-1 accuracy and achieves at least 27 times inference speedup over the state-of-the-art methods. Also, our predictions are easier for chemists to interpret owing to predicting the electron flows.

physics.chem-ph↗

arXiv2021

Aggregated Learning: A Vector-Quantization Approach to Learning Neural Network Classifiers

We consider the problem of learning a neural network classifier. Under the information bottleneck (IB) principle, we associate with this classification problem a representation learning problem, which we call "IB learning". We show that IB learning is, in fact, equivalent to a special class of the quantization problem. The classical results in rate-distortion theory then suggest that IB learning can benefit from a "vector quantization" approach, namely, simultaneously learning the representations of multiple input objects. Such an approach assisted with some variational techniques, result in a novel learning framework, "Aggregated Learning", for classification with neural network models. In this framework, several objects are jointly classified by a single neural network. The effectiveness of this framework is verified through extensive experiments on standard image recognition and text classification tasks.

cs.LG↗

arXiv2020

Regularization via Adaptive Pairwise Label Smoothing

Label Smoothing (LS) is an effective regularizer to improve the generalization of state-of-the-art deep models. For each training sample the LS strategy smooths the one-hot encoded training signal by distributing its distribution mass over the non ground-truth classes, aiming to penalize the networks from generating overconfident output distributions. This paper introduces a novel label smoothing technique called Pairwise Label Smoothing (PLS). The PLS takes a pair of samples as input. Smoothing with a pair of ground-truth labels enables the PLS to preserve the relative distance between the two truth labels while further soften that between the truth labels and the other targets, resulting in models producing much less confident predictions than the LS strategy. Also, unlike current LS methods, which typically require to find a global smoothing distribution mass through cross-validation search, PLS automatically learns the distribution mass for each input pair during training. We empirically show that PLS significantly outperforms LS and the baseline models, achieving up to 30% of relative classification error reduction. We also visually show that when achieving such accuracy gains the PLS tends to produce very low winning softmax scores.

cs.LG↗

arXiv2019

Weighted graphlets and deep neural networks for protein structure classification

As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally classifies the structures of proteins into pre-defined groups. We develop a weighted network that depicts the protein structures, and more importantly, we propose the first graphlet-based measure that applies to weighted networks. Further, we develop a deep neural network (DNN) composed of both convolutional and recurrent layers to use this measure for classification. Put together, our approach shows dramatic improvements in performance over existing graphlet-based approaches on 36 real datasets. Even comparing with the state-of-the-art approach, it almost halves the classification error. In addition to protein structure networks, our weighted-graphlet measure and DNN classifier can potentially be applied to classification of other weighted networks in computational biology as well as in other domains.

stat.ML↗

arXiv2019

Uncover the Ground-Truth Relations in Distant Supervision: A Neural Expectation-Maximization Framework

Distant supervision for relation extraction enables one to effectively acquire structured relations out of very large text corpora with less human efforts. Nevertheless, most of the prior-art models for such tasks assume that the given text can be noisy, but their corresponding labels are clean. Such unrealistic assumption is contradictory with the fact that the given labels are often noisy as well, thus leading to significant performance degradation of those models on real-world data. To cope with this challenge, we propose a novel label-denoising framework that combines neural network with probabilistic modelling, which naturally takes into account the noisy labels during learning. We empirically demonstrate that our approach significantly improves the current art in uncovering the ground-truth relation labels.

cs.CL↗

arXiv2019

MixUp as Directional Adversarial Training

In this work, we explain the working mechanism of MixUp in terms of adversarial training. We introduce a new class of adversarial training schemes, which we refer to as directional adversarial training, or DAT. In a nutshell, a DAT scheme perturbs a training example in the direction of another example but keeps its original label as the training target. We prove that MixUp is equivalent to a special subclass of DAT, in that it has the same expected loss function and corresponds to the same optimization problem asymptotically. This understanding not only serves to explain the effectiveness of MixUp, but also reveals a more general family of MixUp schemes, which we call Untied MixUp. We prove that the family of Untied MixUp schemes is equivalent to the entire class of DAT schemes. We establish empirically the existence of Untied Mixup schemes which improve upon MixUp.

cs.LG↗

arXiv2019

Augmenting Data with Mixup for Sentence Classification: An Empirical Study

Mixup, a recent proposed data augmentation method through linearly interpolating inputs and modeling targets of random samples, has demonstrated its capability of significantly improving the predictive accuracy of the state-of-the-art networks for image classification. However, how this technique can be applied to and what is its effectiveness on natural language processing (NLP) tasks have not been investigated. In this paper, we propose two strategies for the adaption of Mixup on sentence classification: one performs interpolation on word embeddings and another on sentence embeddings. We conduct experiments to evaluate our methods using several benchmark datasets. Our studies show that such interpolation strategies serve as an effective, domain independent data augmentation approach for sentence classification, and can result in significant accuracy improvement for both CNN and LSTM models.

cs.CL↗

arXiv2019

Aggregated Learning: A Deep Learning Framework Based on Information-Bottleneck Vector Quantization

Based on the notion of information bottleneck (IB), we formulate a quantization problem called "IB quantization". We show that IB quantization is equivalent to learning based on the IB principle. Under this equivalence, the standard neural network models can be viewed as scalar (single sample) IB quantizers. It is known, from conventional rate-distortion theory, that scalar quantizers are inferior to vector (multi-sample) quantizers. Such a deficiency then inspires us to develop a novel learning framework, AgrLearn, that corresponds to vector IB quantizers for learning with neural networks. Unlike standard networks, AgrLearn simultaneously optimizes against multiple data samples. We experimentally verify that AgrLearn can result in significant improvements when applied to several current deep learning architectures for image recognition and text classification. We also empirically show that AgrLearn can reduce up to 80% of the training samples needed for ResNet training.

cs.LG↗

arXiv2018

MixUp as Locally Linear Out-Of-Manifold Regularization

MixUp is a recently proposed data-augmentation scheme, which linearly interpolates a random pair of training examples and correspondingly the one-hot representations of their labels. Training deep neural networks with such additional data is shown capable of significantly improving the predictive accuracy of the current art. The power of MixUp, however, is primarily established empirically and its working and effectiveness have not been explained in any depth. In this paper, we develop an understanding for MixUp as a form of "out-of-manifold regularization", which imposes certain "local linearity" constraints on the model's input space beyond the data manifold. This analysis enables us to identify a limitation of MixUp, which we call "manifold intrusion". In a nutshell, manifold intrusion in MixUp is a form of under-fitting resulting from conflicts between the synthetic labels of the mixed-up examples and the labels of original training data. Such a phenomenon usually happens when the parameters controlling the generation of mixing policies are not sufficiently fine-tuned on the training data. To address this issue, we propose a novel adaptive version of MixUp, where the mixing policies are automatically learned from the data using an additional network and objective function designed to avoid manifold intrusion. The proposed regularizer, AdaMixUp, is empirically evaluated on several benchmark datasets. Extensive experiments demonstrate that AdaMixUp improves upon MixUp when applied to the current art of deep classification models.

cs.LG↗