This paper investigates Support Vector Regression (SVR) in the context of the fundamental risk quadrangle paradigm. It is shown that both formulations of SVR, $\varepsilon$-SVR and $\nu$-SVR, correspond to the minimization of equivalent regular error measures (Vapnik error and superquantile (CVaR) norm, respectively) with a regularization penalty. These error measures, in turn, give rise to corresponding risk quadrangles. Additionally, the technique used for the construction of quadrangles serves as a powerful tool in proving the equivalence between $\varepsilon$-SVR and $\nu$-SVR. By constructing the fundamental risk quadrangle, which corresponds to SVR, we show that SVR is the asymptotically unbiased estimator of the average of two symmetric conditional quantiles. Additionally, SVR is formulated as a regular deviation minimization problem with a regularization penalty by invoking Error Shaping Decomposition of Regression. Finally, the dual formulation of SVR in the risk quadrangle framework is derived.

Face Anti-spoofing (FAS) is essential to secure face recognition systems from various physical attacks. However, recent research generally focuses on short-distance applications (i.e., phone unlocking) while lacking consideration of long-distance scenes (i.e., surveillance security checks). In order to promote relevant research and fill this gap in the community, we collect a large-scale Surveillance High-Fidelity Mask (SuHiFiMask) dataset captured under 40 surveillance scenes, which has 101 subjects from different age groups with 232 3D attacks (high-fidelity masks), 200 2D attacks (posters, portraits, and screens), and 2 adversarial attacks. In this scene, low image resolution and noise interference are new challenges faced in surveillance FAS. Together with the SuHiFiMask dataset, we propose a Contrastive Quality-Invariance Learning (CQIL) network to alleviate the performance degradation caused by image quality from three aspects: (1) An Image Quality Variable module (IQV) is introduced to recover image information associated with discrimination by combining the super-resolution network. (2) Using generated sample pairs to simulate quality variance distributions to help contrastive learning strategies obtain robust feature representation under quality variation. (3) A Separate Quality Network (SQN) is designed to learn discriminative features independent of image quality. Finally, a large number of experiments verify the quality of the SuHiFiMask dataset and the superiority of the proposed CQIL.

Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of sequence-structure data. With the development of Artificial Intelligence (AI) techniques, Protein Representation Learning (PRL) has recently emerged as a promising research topic for extracting informative knowledge from massive protein sequences or structures. To pave the way for AI researchers with little bioinformatics background, we present a timely and comprehensive review of PRL formulations and existing PRL methods from the perspective of model architectures, pretext tasks, and downstream applications. We first briefly introduce the motivations for protein representation learning and formulate it in a general and unified framework. Next, we divide existing PRL methods into three main categories: sequence-based, structure-based, and sequence-structure co-modeling. Finally, we discuss some technical challenges and potential directions for improving protein representation learning. The latest advances in PRL methods are summarized in a GitHub repository https://github.com/LirongWu/awesome-protein-representation-learning.

We introduce MegaPose, a method to estimate the 6D pose of novel objects, that is, objects unseen during training. At inference time, the method only assumes knowledge of (i) a region of interest displaying the object in the image and (ii) a CAD model of the observed object. The contributions of this work are threefold. First, we present a 6D pose refiner based on a render&compare strategy which can be applied to novel objects. The shape and coordinate system of the novel object are provided as inputs to the network by rendering multiple synthetic views of the object's CAD model. Second, we introduce a novel approach for coarse pose estimation which leverages a network trained to classify whether the pose error between a synthetic rendering and an observed image of the same object can be corrected by the refiner. Third, we introduce a large-scale synthetic dataset of photorealistic images of thousands of objects with diverse visual and shape properties and show that this diversity is crucial to obtain good generalization performance on novel objects. We train our approach on this large synthetic dataset and apply it without retraining to hundreds of novel objects in real images from several pose estimation benchmarks. Our approach achieves state-of-the-art performance on the ModelNet and YCB-Video datasets. An extensive evaluation on the 7 core datasets of the BOP challenge demonstrates that our approach achieves performance competitive with existing approaches that require access to the target objects during training. Code, dataset and trained models are available on the project page: https://megapose6d.github.io/.

Solving partial differential equations is difficult. Recently proposed neural resolution-invariant models, despite their effectiveness and efficiency, usually require equispaced spatial points of data. However, sampling in spatial domain is sometimes inevitably non-equispaced in real-world systems, limiting their applicability. In this paper, we propose a Non-equispaced Fourier PDE Solver (\textsc{NFS}) with adaptive interpolation on resampled equispaced points and a variant of Fourier Neural Operators as its components. Experimental results on complex PDEs demonstrate its advantages in accuracy and efficiency. Compared with the spatially-equispaced benchmark methods, it achieves superior performance with $42.85\%$ improvements on MAE, and is able to handle non-equispaced data with a tiny loss of accuracy. Besides, to our best knowledge, \textsc{NFS} is the first ML-based method with mesh invariant inference ability to successfully model turbulent flows in non-equispaced scenarios, with a minor deviation of the error on unseen spatial points.

Federated learning has been predominantly concerned with collaborative training of deep networks from scratch, and especially the many challenges that arise, such as communication cost, robustness to heterogeneous data, and support for diverse device capabilities. However, there is no unified framework that addresses all these problems together. This paper studies the challenges and opportunities of exploiting pre-trained Transformer models in FL. In particular, we propose to efficiently adapt such pre-trained models by injecting a novel attention-based adapter module at each transformer block that both modulates the forward pass and makes an early prediction. Training only the lightweight adapter by FL leads to fast and communication-efficient learning even in the presence of heterogeneous data and devices. Extensive experiments on standard FL benchmarks, including CIFAR-100, FEMNIST and SpeechCommandsv2 demonstrate that this simple framework provides fast and accurate FL while supporting heterogenous device capabilities, efficient personalization, and scalable-cost anytime inference.

The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have proved the power of language models (LMs) in processing the protein sequence databases, which inherit the advantages of attention networks and capture useful information in learning representations for proteins. The past two years have witnessed remarkable success in tertiary protein structure prediction (PSP), including evolution-based and single-sequence-based PSP. It seems that instead of using energy-based models and sampling procedures, protein language model (pLM)-based pipelines have emerged as mainstream paradigms in PSP. Despite the fruitful progress, the PSP community needs a systematic and up-to-date survey to help bridge the gap between LMs in the natural language processing (NLP) and PSP domains and introduce their methodologies, advancements and practical applications. To this end, in this paper, we first introduce the similarities between protein and human languages that allow LMs extended to pLMs, and applied to protein databases. Then, we systematically review recent advances in LMs and pLMs from the perspectives of network architectures, pre-training strategies, applications, and commonly-used protein databases. Next, different types of methods for PSP are discussed, particularly how the pLM-based architectures function in the process of protein folding. Finally, we identify challenges faced by the PSP community and foresee promising research directions along with the advances of pLMs. This survey aims to be a hands-on guide for researchers to understand PSP methods, develop pLMs and tackle challenging problems in this field for practical purposes.

Modern deep neural networks tend to be evaluated on static test sets. One shortcoming of this is the fact that these deep neural networks cannot be easily evaluated for robustness issues with respect to specific scene variations. For example, it is hard to study the robustness of these networks to variations of object scale, object pose, scene lighting and 3D occlusions. The main reason is that collecting real datasets with fine-grained naturalistic variations of sufficient scale can be extremely time-consuming and expensive. In this work, we present Counterfactual Simulation Testing, a counterfactual framework that allows us to study the robustness of neural networks with respect to some of these naturalistic variations by building realistic synthetic scenes that allow us to ask counterfactual questions to the models, ultimately providing answers to questions such as "Would your classification still be correct if the object were viewed from the top?" or "Would your classification still be correct if the object were partially occluded by another object?". Our method allows for a fair comparison of the robustness of recently released, state-of-the-art Convolutional Neural Networks and Vision Transformers, with respect to these naturalistic variations. We find evidence that ConvNext is more robust to pose and scale variations than Swin, that ConvNext generalizes better to our simulated domain and that Swin handles partial occlusion better than ConvNext. We also find that robustness for all networks improves with network scale and with data scale and variety. We release the Naturalistic Variation Object Dataset (NVD), a large simulated dataset of 272k images of everyday objects with naturalistic variations such as object pose, scale, viewpoint, lighting and occlusions. Project page: https://counterfactualsimulation.github.io

Unsupervised domain adaptation (UDA) has been highly successful in transferring knowledge acquired from a label-rich source domain to a label-scarce target domain. Open-set domain adaptation (ODA) and universal domain adaptation (UNDA) have been proposed as solutions to the problem concerning the presence of additional novel categories in the target domain. Existing ODA and UNDA approaches treat all novel categories as one unified unknown class and attempt to detect this unknown class during the training process. We find that domain variance leads to more significant view-noise in unsupervised data augmentation, affecting the further applications of contrastive learning~(CL), as well as the current closed-set classifier and open-set classifier causing the model to be overconfident in novel class discovery. To address the above two issues, we propose Soft-contrastive All-in-one Network~(SAN) for ODA and UNDA tasks. SAN includes a novel data-augmentation-based CL loss, which is used to improve the representational capability, and a more human-intuitive classifier, which is used to improve the new class discovery capability. The soft contrastive learning~(SCL) loss is used to weaken the adverse effects of the data-augmentation label noise problem, which is amplified in domain transfer. The All-in-One~(AIO) classifier overcomes the overconfidence problem of the current mainstream closed-set classifier and open-set classifier in a more human-intuitive way. The visualization results and ablation experiments demonstrate the importance of the two proposed innovations. Moreover, extensive experimental results on ODA and UNDA show that SAN has advantages over the existing state-of-the-art methods.

Generating molecules that bind to specific proteins is an important but challenging task in drug discovery. Previous works usually generate atoms in an auto-regressive way, where element types and 3D coordinates of atoms are generated one by one. However, in real-world molecular systems, the interactions among atoms in an entire molecule are global, leading to the energy function pair-coupled among atoms. With such energy-based consideration, the modeling of probability should be based on joint distributions, rather than sequentially conditional ones. Thus, the unnatural sequentially auto-regressive modeling of molecule generation is likely to violate the physical rules, thus resulting in poor properties of the generated molecules. In this work, a generative diffusion model for molecular 3D structures based on target proteins as contextual constraints is established, at a full-atom level in a non-autoregressive way. Given a designated 3D protein binding site, our model learns the generative process that denoises both element types and 3D coordinates of an entire molecule, with an equivariant network. Experimentally, the proposed method shows competitive performance compared with prevailing works in terms of high affinity with proteins and appropriate molecule sizes as well as other drug properties such as drug-likeness of the generated molecules.