ICLR 2023 论文列表

Large pre-trained language models (PLMs) have demonstrated strong performance on natural language understanding (NLU) tasks through fine-tuning. However, fine-tuned models still suffer from overconfident predictions, especially in out-of-domain settings. In this paper, we tackle the problem of calibrating fine-tuned language models. We demonstrate that the PLMs are well-calibrated on the masked language modeling task with robust predictive confidence under domain shift, yet the fine-tuned models fail to retain such property due to catastrophic forgetting, which impacts the calibration on the downstream classification task. In light of these observations, we evaluate the calibration of several methods that preserve pre-trained features and show that preserving pre-trained features can improve the calibration of fine-tuned language models. Among these methods, our proposed method that encourages the fine-tuned model to learn generative representations with auxiliary language modeling objective achieves competitive accuracy and the lowest expected calibration error compared to several strong baselines under both in-domain and out-of-domain settings on three downstream NLU tasks.

Deep generative models (DGMs) are data-eager because learning a complex model on limited data suffers from a large variance and easily overfits. Inspired by the classical perspective of the bias-variance tradeoff, we propose regularized deep generative model (Reg-DGM), which leverages a nontransferable pre-trained model to reduce the variance of generative modeling with limited data. Formally, Reg-DGM optimizes a weighted sum of a certain divergence and the expectation of an energy function, where the divergence is between the data and the model distributions, and the energy function is defined by the pre-trained model w.r.t. the model distribution. We analyze a simple yet representative Gaussian-fitting case to demonstrate how the weighting hyperparameter trades off the bias and the variance. Theoretically, we characterize the existence and the uniqueness of the global minimum of Reg-DGM in a non-parametric setting and prove its convergence with neural networks trained by gradient-based methods. Empirically, with various pre-trained feature extractors and a data-dependent energy function, Reg-DGM consistently improves the generation performance of strong DGMs with limited data and achieves competitive results to the state-of-the-art methods. Our implementation is available at https://github.com/ML-GSAI/Reg-ADA-APA.

We propose Adaptive Deep Kernel Fitting with Implicit Function Theorem (ADKF-IFT), a novel framework for learning deep kernel Gaussian processes (GPs) by interpolating between meta-learning and conventional deep kernel learning. Our approach employs a bilevel optimization objective where we meta-learn generally useful feature representations across tasks, in the sense that task-specific GP models estimated on top of such features achieve the lowest possible predictive loss on average. We solve the resulting nested optimization problem using the implicit function theorem (IFT). We show that our ADKF-IFT framework contains previously proposed Deep Kernel Learning (DKL) and Deep Kernel Transfer (DKT) as special cases. Although ADKF-IFT is a completely general method, we argue that it is especially well-suited for drug discovery problems and demonstrate that it significantly outperforms previous state-of-the-art methods on a variety of real-world few-shot molecular property prediction tasks and out-of-domain molecular property prediction and optimization tasks.

Sequence modeling has important applications in natural language processing and computer vision. Recently, the transformer-based models have shown strong performance on various sequence modeling tasks, which rely on attention to capture pairwise token relations, and position embedding to inject positional information. While showing good performance, the transformer models are inefficient to scale to long input sequences, mainly due to the quadratic space-time complexity of attention. To overcome this inefficiency, we propose to model sequences with a relative position encoded Toeplitz matrix and use a Toeplitz matrix-vector production trick to reduce the space-time complexity of the sequence modeling to log linear. A lightweight sub-network called relative position encoder is proposed to generate relative position coefficients with a fixed budget of parameters, enabling the proposed Toeplitz neural network to deal with varying sequence lengths. In addition, despite being trained on 512-token sequences, our model can extrapolate input sequence length up to 14K tokens in inference with consistent performance. Extensive experiments on autoregressive and bidirectional language modeling, image modeling, and the challenging Long-range Arena Benchmark show that our method achieves better performance than its competitors in most downstream tasks while being significantly faster.

The long runtime of high-fidelity partial differential equation (PDE) solvers makes them unsuitable for time-critical applications. We propose to accelerate PDE solvers using reduced-order modeling (ROM). Whereas prior ROM approaches reduce the dimensionality of discretized vector fields, our continuous reduced-order modeling (CROM) approach builds a low-dimensional embedding of the continuous vector fields themselves, not their discretization. We represent this reduced manifold using continuously differentiable neural fields, which may train on any and all available numerical solutions of the continuous system, even when they are obtained using diverse methods or discretizations. We validate our approach on an extensive range of PDEs with training data from voxel grids, meshes, and point clouds. Compared to prior discretization-dependent ROM methods, such as linear subspace proper orthogonal decomposition (POD) and nonlinear manifold neural-network-based autoencoders, CROM features higher accuracy, lower memory consumption, dynamically adaptive resolutions, and applicability to any discretization. For equal latent space dimension, CROM exhibits 79$\times$ and 49$\times$ better accuracy, and 39$\times$ and 132$\times$ smaller memory footprint, than POD and autoencoder methods, respectively. Experiments demonstrate 109$\times$ and 89$\times$ wall-clock speedups over unreduced models on CPUs and GPUs, respectively. Videos and codes are available on the project page: https://crom-pde.github.io

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.

State space models (SSMs) have demonstrated state-of-the-art sequence modeling performance in some modalities, but underperform attention in language modeling. Moreover, despite scaling nearly linearly in sequence length instead of quadratically, SSMs are still slower than Transformers due to poor hardware utilization. In this paper, we make progress on understanding the expressivity gap between SSMs and attention in language modeling, and on reducing the hardware barrier between SSMs and attention. First, we use synthetic language modeling tasks to understand the gap between SSMs and attention. We find that existing SSMs struggle with two capabilities: recalling earlier tokens in the sequence and comparing tokens across the sequence. To understand the impact on language modeling, we propose a new SSM layer, H3, that is explicitly designed for these abilities. H3 matches attention on the synthetic languages and comes within 0.4 PPL of Transformers on OpenWebText. Furthermore, a hybrid 125M-parameter H3-attention model that retains two attention layers surprisingly outperforms Transformers on OpenWebText by 1.0 PPL. Next, to improve the efficiency of training SSMs on modern hardware, we propose FlashConv. FlashConv uses a fused block FFT algorithm to improve efficiency on sequences up to 8K, and introduces a novel state passing algorithm that exploits the recurrent properties of SSMs to scale to longer sequences. FlashConv yields 2$\times$ speedup on the long-range arena benchmark and allows hybrid language models to generate text 2.4$\times$ faster than Transformers. Using FlashConv, we scale hybrid H3-attention language models up to 2.7B parameters on the Pile and find promising initial results, achieving lower perplexity than Transformers and outperforming Transformers in zero- and few-shot learning on a majority of tasks in the SuperGLUE benchmark.

Models using structured state space sequence (S4) layers have achieved state-of-the-art performance on long-range sequence modeling tasks. An S4 layer combines linear state space models (SSMs), the HiPPO framework, and deep learning to achieve high performance. We build on the design of the S4 layer and introduce a new state space layer, the S5 layer. Whereas an S4 layer uses many independent single-input, single-output SSMs, the S5 layer uses one multi-input, multi-output SSM. We establish a connection between S5 and S4, and use this to develop the initialization and parameterization used by the S5 model. The result is a state space layer that can leverage efficient and widely implemented parallel scans, allowing S5 to match the computational efficiency of S4, while also achieving state-of-the-art performance on several long-range sequence modeling tasks. S5 averages $87.4\%$ on the long range arena benchmark, and $98.5\%$ on the most difficult Path-X task.

Neural networks with physics-based inductive biases such as Lagrangian neural networks (LNNs), and Hamiltonian neural networks (HNNs) learn the dynamics of physical systems by encoding strong inductive biases. Alternatively, Neural ODEs with appropriate inductive biases have also been shown to give similar performances. However, these models, when applied to particle-based systems, are transductive in nature and hence, do not generalize to large system sizes. In this paper, we present a graph-based neural ODE, GNODE, to learn the time evolution of dynamical systems. Further, we carefully analyze the role of different inductive biases on the performance of GNODE. We show that similar to LNN and HNN, encoding the constraints explicitly can significantly improve the training efficiency and performance of GNODE significantly. Our experiments also assess the value of additional inductive biases, such as Newton’s third law, on the final performance of the model. We demonstrate that inducing these biases can enhance the performance of the model by orders of magnitude in terms of both energy violation and rollout error. Interestingly, we observe that the GNODE trained with the most effective inductive biases, namely MCGNODE, outperforms the graph versions of LNN and HNN, namely, Lagrangian graph networks (LGN) and Hamiltonian graph networks (HGN) in terms of energy violation error by ∼4 orders of magnitude for a pendulum system, and ∼2 orders of magnitude for spring systems. These results suggest that NODE-based systems can give competitive performances with energy-conserving neural networks by employing appropriate inductive biases.

The neural process (NP) is a family of computationally efficient models for learning distributions over functions. However, it suffers from under-fitting and shows suboptimal performance in practice. Researchers have primarily focused on incorporating diverse structural inductive biases, e.g. attention or convolution, in modeling. The topic of inference suboptimality and an analysis of the NP from the optimization objective perspective has hardly been studied in earlier work. To fix this issue, we propose a surrogate objective of the target log-likelihood of the meta dataset within the expectation maximization framework. The resulting model, referred to as the Self-normalized Importance weighted Neural Process (SI-NP), can learn a more accurate functional prior and has an improvement guarantee concerning the target log-likelihood. Experimental results show the competitive performance of SI-NP over other NPs objectives and illustrate that structural inductive biases, such as attention modules, can also augment our method to achieve SOTA performance.

We present Masked Frequency Modeling (MFM), a unified frequency-domain-based approach for self-supervised pre-training of visual models. Instead of randomly inserting mask tokens to the input embeddings in the spatial domain, in this paper, we shift the perspective to the frequency domain. Specifically, MFM first masks out a portion of frequency components of the input image and then predicts the missing frequencies on the frequency spectrum. Our key insight is that predicting masked components in the frequency domain is more ideal to reveal underlying image patterns rather than predicting masked patches in the spatial domain, due to the heavy spatial redundancy. Our findings suggest that with the right configuration of mask-and-predict strategy, both the structural information within high-frequency components and the low-level statistics among low-frequency counterparts are useful in learning good representations. For the first time, MFM demonstrates that, for both ViT and CNN, a simple non-Siamese framework can learn meaningful representations even using none of the following: (i) extra data, (ii) extra model, (iii) mask token. Experimental results on image classification and semantic segmentation, as well as several robustness benchmarks show the competitive performance and advanced robustness of MFM compared with recent masked image modeling approaches. Furthermore, we also comprehensively investigate the effectiveness of classical image restoration tasks for representation learning from a unified frequency perspective and reveal their intriguing relations with our MFM approach. Project page: https://www.mmlab-ntu.com/project/mfm/index.html.

The sequence alignment problem is one of the most fundamental problems in bioinformatics and a plethora of methods were devised to tackle it. Here we introduce BetaAlign, a methodology for aligning sequences using an NLP approach. BetaAlign accounts for the possible variability of the evolutionary process among different datasets by using an ensemble of transformers, each trained on millions of samples generated from a different evolutionary model. Our approach leads to alignment accuracy that is similar and often better than commonly used methods, such as MAFFT, DIALIGN, ClustalW, T-Coffee, PRANK, and MUSCLE.

Construction of a scaffold structure that supports a desired motif, conferring protein function, shows promise for the design of vaccines and enzymes. But a general solution to this motif-scaffolding problem remains open. Current machine-learning techniques for scaffold design are either limited to unrealistically small scaffolds (up to length 20) or struggle to produce multiple diverse scaffolds. We propose to learn a distribution over diverse and longer protein backbone structures via an E(3)-equivariant graph neural network. We develop SMCDiff to efficiently sample scaffolds from this distribution conditioned on a given motif; our algorithm is the first to theoretically guarantee conditional samples from a diffusion model in the large-compute limit. We evaluate our designed backbones by how well they align with AlphaFold2-predicted structures. We show that our method can (1) sample scaffolds up to 80 residues and (2) achieve structurally diverse scaffolds for a fixed motif.

Molecular representation learning (MRL) has gained tremendous attention due to its critical role in learning from limited supervised data for applications like drug design. In most MRL methods, molecules are treated as 1D sequential tokens or 2D topology graphs, limiting their ability to incorporate 3D information for downstream tasks and, in particular, making it almost impossible for 3D geometry prediction/generation. In this paper, we propose a universal 3D MRL framework, called Uni-Mol, that significantly enlarges the representation ability and application scope of MRL schemes. Uni-Mol contains two pretrained models with the same SE(3) Transformer architecture: a molecular model pretrained by 209M molecular conformations; a pocket model pretrained by 3M candidate protein pocket data. Besides, Uni-Mol contains several finetuning strategies to apply the pretrained models to various downstream tasks. By properly incorporating 3D information, Uni-Mol outperforms SOTA in 14/15 molecular property prediction tasks. Moreover, Uni-Mol achieves superior performance in 3D spatial tasks, including protein-ligand binding pose prediction, molecular conformation generation, etc. The code, model, and data are made publicly available at https://github.com/dptech-corp/Uni-Mol.

Self-supervised learning aims to learn a embedding space where semantically similar samples are close. Contrastive learning methods pull views of samples together and push different samples away, which utilizes semantic invariance of augmentation but ignores the relationship between samples. To better exploit the power of augmentation, we observe that semantically similar samples are more likely to have similar augmented views. Therefore, we can take the augmented views as a special description of a sample. In this paper, we model such a description as the augmentation distribution, and we call it augmentation feature. The similarity in augmentation feature reflects how much the views of two samples overlap and is related to their semantical similarity. Without computational burdens to explicitly estimate values of the augmentation feature, we propose Augmentation Component Analysis (ACA) with a contrastive-like loss to learn principal components and an on-the-fly projection loss to embed data. ACA equals an efficient dimension reduction by PCA and extracts low-dimensional embeddings, theoretically preserving the similarity of augmentation distribution between samples. Empirical results show that our method can achieve competitive results against various traditional contrastive learning methods on different benchmarks.

Cyclic compounds that contain at least one ring play an important role in drug design. Despite the recent success of molecular modeling with graph neural networks (GNNs), few models explicitly take rings in compounds into consideration, consequently limiting the expressiveness of the models. In this work, we design a new variant of GNN, ring-enhanced GNN ($\mathcal{O}$-GNN), that explicitly models rings in addition to atoms and bonds in compounds. In $\mathcal{O}$-GNN, each ring is represented by a latent vector, which contributes to and is iteratively updated by atom and bond representations. Theoretical analysis shows that $\mathcal{O}$-GNN is able to distinguish two isomorphic subgraphs lying on different rings using only one layer while conventional graph convolutional neural networks require multiple layers to distinguish, demonstrating that $\mathcal{O}$-GNN is more expressive. Through experiments, $\mathcal{O}$-GNN shows good performance on $\bf{11}$ public datasets. In particular, it achieves state-of-the-art validation result on the PCQM4Mv1 benchmark (outperforming the previous KDDCup champion solution) and the drug-drug interaction prediction task on DrugBank. Furthermore, $\mathcal{O}$-GNN outperforms strong baselines (without modeling rings) on the molecular property prediction and retrosynthesis prediction tasks.

State space models have shown to be effective at modeling long range dependencies, specially on sequence classification tasks. In this work we focus on autoregressive sequence modeling over English books, Github source code and ArXiv mathematics articles. Based on recent developments around the effectiveness of gated activation functions, we propose a new layer named \textit{Gated State Space} (GSS) and show that it trains significantly faster than the diagonal version of S4 (i.e. DSS) on TPUs, is fairly competitive with several well-tuned Transformer-based baselines and exhibits zero-shot generalization to longer inputs while being straightforward to implement. Finally, we show that leveraging self-attention to model local dependencies improves the performance of GSS even further.

Time series modeling is a well-established problem, which often requires that methods (1) expressively represent complicated dependencies, (2) forecast long horizons, and (3) efficiently train over long sequences. State-space models (SSMs) are classical models for time series, and prior works combine SSMs with deep learning layers for efficient sequence modeling. However, we find fundamental limitations with these prior approaches, proving their SSM representations cannot express autoregressive time series processes. We thus introduce SpaceTime, a new state-space time series architecture that improves all three criteria. For expressivity, we propose a new SSM parameterization based on the companion matrix---a canonical representation for discrete-time processes---which enables SpaceTime's SSM layers to learn desirable autoregressive processes. For long horizon forecasting, we introduce a "closed-loop" variation of the companion SSM, which enables SpaceTime to predict many future time-steps by generating its own layer-wise inputs. For efficient training and inference, we introduce an algorithm that reduces the memory and compute of a forward pass with the companion matrix. With sequence length $\ell$ and state-space size $d$, we go from $\tilde{O}(d \ell)$ naïvely to $\tilde{O}(d + \ell)$. In experiments, our contributions lead to state-of-the-art results on extensive and diverse benchmarks, with best or second-best AUROC on 6 / 7 ECG and speech time series classification, and best MSE on 14 / 16 Informer forecasting tasks. Furthermore, we find SpaceTime (1) fits AR($p$) processes that prior deep SSMs fail on, (2) forecasts notably more accurately on longer horizons than prior state-of-the-art, and (3) speeds up training on real-world ETTh1 data by 73% and 80% relative wall-clock time over Transformers and LSTMs.

Sequence modeling is a core problem in machine learning, and various neural networks have been designed to process different types of sequence data. However, few attempts have been made to understand the inherent data property of sequence data, neglecting the critical factor that may significantly affect the performance of sequence modeling. In this paper, we theoretically and empirically analyze a generic property of sequence data, i.e., continuity, and connect this property with the performance of deep models. First, we empirically observe that different kinds of models for sequence modeling prefer data with different continuity. Then, we theoretically analyze the continuity preference of different models in both time and frequency domains. To further utilize continuity to improve sequence modeling, we propose a simple yet effective Lipschitz Regularizer, that can flexibly adjust data continuity according to model preferences, and bring very little extra computational cost. Extensive experiments on various tasks demonstrate that altering data continuity via Lipschitz Regularizer can largely improve the performance of many deep models for sequence modeling.