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Hongyu Guo

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ICLR Conference 2025 Conference Paper

AssembleFlow: Rigid Flow Matching with Inertial Frames for Molecular Assembly

  • Hongyu Guo
  • Yoshua Bengio
  • Shengchao Liu

Molecular assembly, where a cluster of rigid molecules aggregated into strongly correlated forms, is fundamental to determining the properties of materials. However, traditional numerical methods for simulating this process are computationally expensive, and existing generative models on material generation overlook the rigidity inherent in molecular structures, leading to unwanted distortions and invalid internal structures in molecules. To address this, we introduce AssembleFlow. AssembleFlow leverages inertial frames to establish reference coordinate systems at the molecular level for tracking the orientation and motion of molecules within the cluster. It further decomposes molecular $\text{SE}(3)$ transformations into translations in $\mathbb{R}^3$ and rotations in $\text{SO}(3)$, enabling explicit enforcement of both translational and rotational rigidity during each generation step within the flow matching framework. This decomposition also empowers distinct probability paths for each transformation group, effectively allowing for the separate learning of their velocity functions: the former, moving in Euclidean space, uses linear interpolation (LERP), while the latter, evolving in spherical space, employs spherical linear interpolation (SLERP) with a closed-form solution. Empirical validation on the benchmarking data COD-Cluster17 shows that AssembleFlow significantly outperforms six competitive deep learning baselines by at least 45\% in assembly matching scores while maintaining 100\% molecular integrity. Also, it matches the assembly performance of a widely used domain-specific simulation tool while reducing computational cost by 25-fold.

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ICLR Conference 2025 Conference Paper

Structure Language Models for Protein Conformation Generation

  • Jiarui Lu
  • Xiaoyin Chen
  • Stephen Zhewen Lu
  • Chence Shi
  • Hongyu Guo
  • Yoshua Bengio
  • Jian Tang 0005

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally expensive. Recently, deep generative models have shown promise in generating protein conformations as a more efficient alternative. However, these methods predominantly rely on the diffusion process within a 3D geometric space, which typically centers around the vicinity of metastable states and is often inefficient in terms of runtime. In this paper, we introduce Structure Language Modeling (SLM) as a novel framework for efficient protein conformation generation. Specifically, the protein structures are first encoded into a compact latent space using a discrete variational auto-encoder, followed by conditional language modeling that effectively captures sequence-specific conformation distributions. This enables a more efficient and interpretable exploration of diverse ensemble modes compared to existing methods. Based on this general framework, we instantiate SLM with various popular LM architectures as well as proposing the ESMDiff, a novel BERT-like structure language model fine-tuned from ESM3 with masked diffusion. We verify our approach in various scenarios, including the equilibrium dynamics of BPTI, conformational change pairs, and intrinsically disordered proteins. SLM provides a highly efficient solution, offering a 20-100x speedup than existing methods in generating diverse conformations, shedding light on promising avenues for future research.

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TMLR Journal 2024 Journal Article

Calibration Attacks: A Comprehensive Study of Adversarial Attacks on Model Confidence

  • Stephen Obadinma
  • Xiaodan Zhu
  • Hongyu Guo

In this work, we highlight and perform a comprehensive study on calibration attacks, a form of adversarial attacks that aim to trap victim models to be heavily miscalibrated without altering their predicted labels, hence endangering the trustworthiness of the models and follow-up decision making based on their confidence. We propose four typical forms of calibration attacks: underconfidence, overconfidence, maximum miscalibration, and random confidence attacks, conducted in both the black-box and white-box setups. We demonstrate that the attacks are highly effective on both convolutional and attention-based models: with a small number of queries, they seriously skew confidence without changing the predictive performance. Given the potential danger, we further investigate the effectiveness of a wide range of adversarial defence and recalibration methods, including our proposed defences specifically designed for calibration attacks to mitigate the harm. From the ECE and KS scores, we observe that there are still significant limitations in handling calibration attacks. To the best of our knowledge, this is the first dedicated study that provides a comprehensive investigation on calibration-focused attacks. We hope this study helps attract more attention to these types of attacks and hence hamper their potential serious damages. To this end, this work also provides detailed analyses to understand the characteristics of the attacks.

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ICLR Conference 2024 Conference Paper

Conversational Drug Editing Using Retrieval and Domain Feedback

  • Shengchao Liu
  • Jiongxiao Wang
  • Yijin Yang
  • Chengpeng Wang
  • Ling Liu 0001
  • Hongyu Guo
  • Chaowei Xiao

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reactions and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on all 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making.

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TMLR Journal 2023 Journal Article

$f$-MICL: Understanding and Generalizing InfoNCE-based Contrastive Learning

  • Yiwei Lu
  • Guojun Zhang
  • Sun Sun
  • Hongyu Guo
  • Yaoliang Yu

In self-supervised contrastive learning, a widely-adopted objective function is InfoNCE, which uses the heuristic cosine similarity for the representation comparison, and is closely related to maximizing the Kullback-Leibler (KL)-based mutual information. In this paper, we aim at answering two intriguing questions: (1) Can we go beyond the KL-based objective? (2) Besides the popular cosine similarity, can we design a better similarity function? We provide answers to both questions by generalizing the KL-based mutual information to the $f$-Mutual Information in Contrastive Learning ($f$-MICL) using the $f$-divergences. To answer the first question, we provide a wide range of $f$-MICL objectives which share the nice properties of InfoNCE (e.g., alignment and uniformity), and meanwhile result in similar or even superior performance. For the second question, assuming that the joint feature distribution is proportional to the Gaussian kernel, we derive an $f$-Gaussian similarity with better interpretability and empirical performance. Finally, we identify close relationships between the $f$-MICL objective and several popular InfoNCE-based objectives. Using benchmark tasks from both vision and natural language, we empirically evaluate $f$-MICL with different $f$-divergences on various architectures (SimCLR, MoCo, and MoCo v3) and datasets. We observe that $f$-MICL generally outperforms the benchmarks and the best-performing $f$-divergence is task and dataset dependent.

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ICML Conference 2023 Conference Paper

A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining

  • Shengchao Liu
  • Weitao Du
  • Zhiming Ma
  • Hongyu Guo
  • Jian Tang 0005

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e. g. , SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

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NeurIPS Conference 2023 Conference Paper

Disentangled Wasserstein Autoencoder for T-Cell Receptor Engineering

  • Tianxiao Li
  • Hongyu Guo
  • Filippo Grazioli
  • Mark Gerstein
  • Martin Renqiang Min

In protein biophysics, the separation between the functionally important residues (forming the active site or binding surface) and those that create the overall structure (the fold) is a well-established and fundamental concept. Identifying and modifying those functional sites is critical for protein engineering but computationally non-trivial, and requires significant domain knowledge. To automate this process from a data-driven perspective, we propose a disentangled Wasserstein autoencoder with an auxiliary classifier, which isolates the function-related patterns from the rest with theoretical guarantees. This enables one-pass protein sequence editing and improves the understanding of the resulting sequences and editing actions involved. To demonstrate its effectiveness, we apply it to T-cell receptors (TCRs), a well-studied structure-function case. We show that our method can be used to alter the function of TCRs without changing the structural backbone, outperforming several competing methods in generation quality and efficiency, and requiring only 10\% of the running time needed by baseline models. To our knowledge, this is the first approach that utilizes disentangled representations for TCR engineering.

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AAAI Conference 2023 Conference Paper

Interpolating Graph Pair to Regularize Graph Classification

  • Hongyu Guo
  • Yongyi Mao

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.

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ICLR Conference 2023 Conference Paper

Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching

  • Shengchao Liu
  • Hongyu Guo
  • Jian Tang 0005

Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the power of pretraining on 3D geometric structures has been less explored. This is owing to the difficulty of finding a sufficient proxy task that can empower the pretraining to effectively extract essential features from the geometric structures. Motivated by the dynamic nature of 3D molecules, where the continuous motion of a molecule in the 3D Euclidean space forms a smooth potential energy surface, we propose GeoSSL, a 3D coordinate denoising pretraining framework to model such an energy landscape. Further by leveraging an SE(3)-invariant score matching method, we propose GeoSSL-DDM in which the coordinate denoising proxy task is effectively boiled down to denoising the pairwise atomic distances in a molecule. Our comprehensive experiments confirm the effectiveness and robustness of our proposed method.

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ICLR Conference 2023 Conference Paper

Over-Training with Mixup May Hurt Generalization

  • Zixuan Liu
  • Ziqiao Wang
  • Hongyu Guo
  • Yongyi Mao

Mixup, which creates synthetic training instances by linearly interpolating random sample pairs, is a simple and yet effective regularization technique to boost the performance of deep models trained with SGD. In this work, we report a previously unobserved phenomenon in Mixup raining: on a number of standard datasets, the performance of Mixup-trained models starts to decay after training for a large number of epochs, giving rise to a U-shaped generalization curve. This behavior is further aggravated when the size of original dataset is reduced. To help understand such a behavior of Mixup, we show theoretically that Mixup training may introduce undesired data-dependent label noises to the synthesized data. Via analyzing a least-square regression problem with a random feature model, we explain why noisy labels may cause the U-shaped curve to occur: Mixup improves generalization through fitting the clean patterns at the early training stage, but as training progresses, Mixup becomes over-fitting to the noise in the synthetic data. Extensive experiments are performed on a variety of benchmark datasets, validating this explanation.

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NeurIPS Conference 2023 Conference Paper

Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials

  • Shengchao Liu
  • Weitao Du
  • Yanjing Li
  • Zhuoxinran Li
  • Zhiling Zheng
  • Chenru Duan
  • Zhi-Ming Ma
  • Omar Yaghi

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science ({\eg}, physics, chemistry, & biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 52 diverse tasks, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications. The source code is available on \href{https: //github. com/chao1224/Geom3D}{the GitHub repository}.

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ICLR Conference 2022 Conference Paper

Pre-training Molecular Graph Representation with 3D Geometry

  • Shengchao Liu
  • Hanchen Wang 0002
  • Weiyang Liu
  • Joan Lasenby
  • Hongyu Guo
  • Jian Tang 0005

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. Code is available on GitHub: https://github.com/chao1224/GraphMVP.

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ICML Conference 2021 Conference Paper

Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction

  • Hangrui Bi
  • Hengyi Wang
  • Chence Shi
  • Connor W. Coley
  • Jian Tang 0005
  • Hongyu Guo

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.

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ICML Conference 2021 Conference Paper

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

  • Minghao Xu
  • Hang Wang
  • Bingbing Ni
  • Hongyu Guo
  • Jian Tang 0005

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.

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UAI Conference 2021 Conference Paper

Symmetric Wasserstein autoencoders

  • Sun Sun 0002
  • Hongyu Guo

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.

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ICML Conference 2020 Conference Paper

A Graph to Graphs Framework for Retrosynthesis Prediction

  • Chence Shi
  • Minkai Xu
  • Hongyu Guo
  • Ming Zhang 0004
  • Jian Tang 0005

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.

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AAAI Conference 2020 Conference Paper

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

  • Masoumeh Soflaei
  • Hongyu Guo
  • Ali Al-Bashabsheh
  • Yongyi Mao
  • Richong Zhang

We consider the problem of learning a neural network classi- fier. 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.

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AAAI Conference 2020 Conference Paper

Nonlinear Mixup: Out-Of-Manifold Data Augmentation for Text Classification

  • Hongyu Guo

Data augmentation with Mixup (Zhang et al. 2018) has shown to be an effective model regularizer for current art deep classification networks. It generates out-of-manifold samples through linearly interpolating inputs and their corresponding labels of random sample pairs. Despite its great successes, Mixup requires convex combination of the inputs as well as the modeling targets of a sample pair, thus significantly limits the space of its synthetic samples and consequently its regularization effect. To cope with this limitation, we propose ”nonlinear Mixup”. Unlike Mixup where the input and label pairs share the same, linear, scalar mixing policy, our approach embraces nonlinear interpolation policy for both the input and label pairs, where the mixing policy for the labels is adaptively learned based on the mixed input. Experiments on benchmark sentence classification datasets indicate that our approach significantly improves upon Mixup. Our empirical studies also show that the out-of-manifold samples generated by our strategy encourage training samples in each class to form a tight representation cluster that is far from others.

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IJCAI Conference 2019 Conference Paper

Learning K-way D-dimensional Discrete Embedding for Hierarchical Data Visualization and Retrieval

  • Xiaoyuan Liang
  • Martin Renqiang Min
  • Hongyu Guo
  • Guiling Wang

Traditional embedding approaches associate a real-valued embedding vector with each symbol or data point, which is equivalent to applying a linear transformation to ``one-hot" encoding of discrete symbols or data objects. Despite simplicity, these methods generate storage-inefficient representations and fail to effectively encode the internal semantic structure of data, especially when the number of symbols or data points and the dimensionality of the real-valued embedding vectors are large. In this paper, we propose a regularized autoencoder framework to learn compact Hierarchical K-way D-dimensional (HKD) discrete embedding of symbols or data points, aiming at capturing essential semantic structures of data. Experimental results on synthetic and real-world datasets show that our proposed HKD embedding can effectively reveal the semantic structure of data via hierarchical data visualization and greatly reduce the search space of nearest neighbor retrieval while preserving high accuracy.

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AAAI Conference 2019 Conference Paper

MixUp as Locally Linear Out-of-Manifold Regularization

  • Hongyu Guo
  • Yongyi Mao
  • Richong Zhang

MixUp (Zhang et al. 2017) is a recently proposed dataaugmentation 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.

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IJCAI Conference 2019 Conference Paper

Modeling Noisy Hierarchical Types in Fine-Grained Entity Typing: A Content-Based Weighting Approach

  • Junshuang Wu
  • Richong Zhang
  • Yongyi Mao
  • Hongyu Guo
  • Jinpeng Huai

Fine-grained entity typing (FET), which annotates the entities in a sentence with a set of finely specified type labels, often serves as the first and critical step towards many natural language processing tasks. Despite great processes have been made, current FET methods have difficulty to cope with the noisy labels which naturally come with the data acquisition processes. Existing FET approaches either pre-process to clean the noise or simply focus on one of the noisy labels, sidestepping the fact that those noises are related and content dependent. In this paper, we directly model the structured, noisy labels with a novel content-sensitive weighting schema. Coupled with a newly devised cost function and a hierarchical type embedding strategy, our method leverages a random walk process to effectively weight out noisy labels during training. Experiments on several benchmark datasets validate the effectiveness of the proposed framework and establish it as a new state of the art strategy for noisy entity typing problem.

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IJCAI Conference 2017 Conference Paper

Exemplar-centered Supervised Shallow Parametric Data Embedding

  • Martin Renqiang Min
  • Hongyu Guo
  • Dongjin Song

Metric learning methods for dimensionality reduction in combination with k-Nearest Neighbors (kNN) have been extensively deployed in many classification, data embedding, and information retrieval applications. However, most of these approaches involve pairwise training data comparisons, and thus have quadratic computational complexity with respect to the size of training set, preventing them from scaling to fairly big datasets. Moreover, during testing, comparing test data against all the training data points is also expensive in terms of both computational cost and resources required. Furthermore, previous metrics are either too constrained or too expressive to be well learned. To effectively solve these issues, we present an exemplar-centered supervised shallow parametric data embedding model, using a Maximally Collapsing Metric Learning (MCML) objective. Our strategy learns a shallow high-order parametric embedding function and compares training/test data only with learned or precomputed exemplars, resulting in a cost function with linear computational complexity for both training and testing. We also empirically demonstrate, using several benchmark datasets, that for classification in two-dimensional embedding space, our approach not only gains speedup of kNN by hundreds of times, but also outperforms state-of-the-art supervised embedding approaches.

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ICML Conference 2015 Conference Paper

Long Short-Term Memory Over Recursive Structures

  • Xiaodan Zhu 0001
  • Parinaz Sobhani
  • Hongyu Guo

The chain-structured long short-term memory (LSTM) has showed to be effective in a wide range of problems such as speech recognition and machine translation. In this paper, we propose to extend it to tree structures, in which a memory cell can reflect the history memories of multiple child cells or multiple descendant cells in a recursive process. We call the model S-LSTM, which provides a principled way of considering long-distance interaction over hierarchies, e. g. , language or image parse structures. We leverage the models for semantic composition to understand the meaning of text, a fundamental problem in natural language understanding, and show that it outperforms a state-of-the-art recursive model by replacing its composition layers with the S-LSTM memory blocks. We also show that utilizing the given structures is helpful in achieving a performance better than that without considering the structures.

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