Protein inverse folding has attracted increasing attention in recent years. However, we observe that current methods are usually limited to the CATH dataset and the recovery metric. The lack of a unified framework for ensembling and comparing different methods hinders the comprehensive investigation. In this paper, we propose ProteinInvBench, a new benchmark for protein design, which comprises extended protein design tasks, integrated models, and diverse evaluation metrics. We broaden the application of methods originally designed for single-chain protein design to new scenarios of multi-chain and de novo protein design. Recent impressive methods, including GraphTrans, StructGNN, GVP, GCA, AlphaDesign, ProteinMPNN, PiFold and KWDesign are integrated into our framework. In addition to the recovery, we also evaluate the confidence, diversity, sc-TM, efficiency, and robustness to thoroughly revisit current protein design approaches and inspire future work. As a result, we establish the first comprehensive benchmark for protein design, which is publicly available at https://github.com/A4Bio/OpenCPD.

Learning binary classifiers from positive and unlabeled data (PUL) is vital in many real-world applications, especially when verifying negative examples is difficult. Despite the impressive empirical performance of recent PUL methods, challenges like accumulated errors and increased estimation bias persist due to the absence of negative labels. In this paper, we unveil an intriguing yet long-overlooked observation in PUL: resampling the positive data in each training iteration to ensure a balanced distribution between positive and unlabeled examples results in strong early-stage performance. Furthermore, predictive trends for positive and negative classes display distinctly different patterns. Specifically, the scores (output probability) of unlabeled negative examples consistently decrease, while those of unlabeled positive examples show largely chaotic trends. Instead of focusing on classification within individual time frames, we innovatively adopt a holistic approach, interpreting the scores of each example as a temporal point process (TPP).

While deep reinforcement learning (RL) has been demonstrated effective in solving complex control tasks, sample efficiency remains a key challenge due to the large amounts of data required for remarkable performance. Existing research explores the application of representation learning for data-efficient RL, e.g., learning predictive representations by predicting long-term future states. However, many existing methods do not fully exploit the structural information inherent in sequential state signals, which can potentially improve the quality of long-term decision-making but is difficult to discern in the time domain. To tackle this problem, we propose State Sequences Prediction via Fourier Transform (SPF), a novel method that exploits the frequency domain of state sequences to extract the underlying patterns in time series data for learning expressive representations efficiently. Specifically, we theoretically analyze the existence of structural information in state sequences, which is closely related to policy performance and signal regularity, and then propose to predict the Fourier transform of infinite-step future state sequences to extract such information. One of the appealing features of SPF is that it is simple to implement while not requiring storage of infinite-step future states as prediction targets. Experiments demonstrate that the proposed method outperforms several state-of-the-art algorithms in terms of both sample efficiency and performance.2

We present a volume rendering-based neural surface reconstruction method that takes as few as three disparate RGB images as input. Our key idea is to regularize the reconstruction, which is severely ill-posed and leaving significant gaps between the sparse views, by learning a set of neural templates to act as surface priors. Our method, coined DiViNet, operates in two stages. It first learns the templates, in the form of 3DGaussian functions, across different scenes, without 3D supervision. In the reconstruction stage, our predicted templates serve as anchors to help "stitch" the surfaces over sparse regions. We demonstrate that our approach is not only able to complete the surface geometry but also reconstructs surface details to a reasonable extent from a few disparate input views. On the DTU and BlendedMVS datasets, our approach achieves the best reconstruction quality among existing methods in the presence of such sparse views and performs on par, if not better, with competing methods when dense views are employed as inputs.

Particle-based variational inference methods (ParVIs) such as Stein variational gradient descent (SVGD) update the particles based on the kernelized Wasserstein gradient flow for the Kullback-Leibler (KL) divergence. However, the design of kernels is often non-trivial and can be restrictive for the flexibility of the method. Recent works show that functional gradient flow approximations with quadratic form regularization terms can improve performance. In this paper, we propose a ParVI framework, called generalized Wasserstein gradient descent (GWG), based on a generalized Wasserstein gradient flow of the KL divergence, which can be viewed as a functional gradient method with a broader class of regularizers induced by convex functions. We show that GWG exhibits strong convergence guarantees. We also provide an adaptive version that automatically chooses Wasserstein metric to accelerate convergence. In experiments, we demonstrate the effectiveness and efficiency of the proposed framework on both simulated and real data problems.

Particle-based variational inference methods (ParVIs) such as Stein variational gradient descent (SVGD) update the particles based on the kernelized Wasserstein gradient flow for the Kullback-Leibler (KL) divergence. However, the design of kernels is often non-trivial and can be restrictive for the flexibility of the method. Recent works show that functional gradient flow approximations with quadratic form regularization terms can improve performance. In this paper, we propose a ParVI framework, called generalized Wasserstein gradient descent (GWG), based on a generalized Wasserstein gradient flow of the KL divergence, which can be viewed as a functional gradient method with a broader class of regularizers induced by convex functions. We show that GWG exhibits strong convergence guarantees. We also provide an adaptive version that automatically chooses Wasserstein metric to accelerate convergence. In experiments, we demonstrate the effectiveness and efficiency of the proposed framework on both simulated and real data problems.