DeepNLP/ICLR-2023-Accepted-Papers huggingface dataset:
Conditional Positional Encodings for Vision Transformers
Authors: Xiangxiang Chu,Zhi Tian,Bo Zhang,Xinlong Wang,Chunhua Shen

We propose a conditional positional encoding (CPE) scheme for vision Transformers. Unlike previous fixed or learnable positional encodings that are predefined and independent of input tokens, CPE is dynamically generated and conditioned on the local neighborhood of the input tokens. As a result, CPE can easily generalize to the input sequences that are longer than what the model has ever seen during the training. Besides, CPE can keep the desired translation equivalence in vision tasks, resulting in improved performance. We implement CPE with a simple Position Encoding Generator (PEG) to get seamlessly incorporated into the current Transformer framework. Built on PEG, we present Conditional Position encoding Vision Transformer (CPVT). We demonstrate that CPVT has visually similar attention maps compared to those with learned positional encodings and delivers outperforming results.
ManiSkill2: A Unified Benchmark for Generalizable Manipulation Skills
Authors: Jiayuan Gu,Fanbo Xiang,Xuanlin Li,Zhan Ling,Xiqiang Liu,Tongzhou Mu,Yihe Tang,Stone Tao,Xinyue Wei,Yunchao Yao,Xiaodi Yuan,Pengwei Xie,Zhiao Huang,Rui Chen,Hao Su

Generalizable manipulation skills, which can be composed to tackle long-horizon and complex daily chores, are one of the cornerstones of Embodied AI. However, existing benchmarks, mostly composed of a suite of simulatable environments, are insufficient to push cutting-edge research works because they lack object-level topological and geometric variations, are not based on fully dynamic simulation, or are short of native support for multiple types of manipulation tasks. To this end, we present ManiSkill2, the next generation of the SAPIEN ManiSkill benchmark, to address critical pain points often encountered by researchers when using benchmarks for generalizable manipulation skills. ManiSkill2 includes 20 manipulation task families with 2000+ object models and 4M+ demonstration frames, which cover stationary/mobile-base, single/dual-arm, and rigid/soft-body manipulation tasks with 2D/3D-input data simulated by fully dynamic engines. It defines a unified interface and evaluation protocol to support a wide range of algorithms (e.g., classic sense-plan-act, RL, IL), visual observations (point cloud, RGBD), and controllers (e.g., action type and parameterization). Moreover, it empowers fast visual input learning algorithms so that a CNN-based policy can collect samples at about 2000 FPS with 1 GPU and 16 processes on a regular workstation. It implements a render server infrastructure to allow sharing rendering resources across all environments, thereby significantly reducing memory usage. We open-source all codes of our benchmark (simulator, environments, and baselines) and host an online challenge open to interdisciplinary researchers.
Deja Vu: Continual Model Generalization for Unseen Domains
Authors: Chenxi Liu,Lixu Wang,Lingjuan Lyu,Chen Sun,Xiao Wang,Qi Zhu

In real-world applications, deep learning models often run in non-stationary environments where the target data distribution continually shifts over time. There have been numerous domain adaptation (DA) methods in both online and offline modes to improve cross-domain adaptation ability. However, these DA methods typically only provide good performance after a long period of adaptation, and perform poorly on new domains before and during adaptation – in what we call the “Unfamiliar Period”, especially when domain shifts happen suddenly and significantly. On the other hand, domain generalization (DG) methods have been proposed to improve the model generalization ability on unadapted domains. However, existing DG works are ineffective for continually changing domains due to severe catastrophic forgetting of learned knowledge. To overcome these limitations of DA and DG in handling the Unfamiliar Period during continual domain shift, we propose RaTP, a framework that focuses on improving models’ target domain generalization (TDG) capability, while also achieving effective target domain adaptation (TDA) capability right after training on certain domains and forgetting alleviation (FA) capability on past domains. RaTP includes a training-free data augmentation module to prepare data for TDG, a novel pseudo-labeling mechanism to provide reliable supervision for TDA, and a prototype contrastive alignment algorithm to align different domains for achieving TDG, TDA and FA. Extensive experiments on Digits, PACS, and DomainNet demonstrate that RaTP significantly outperforms state-of-the-art works from Continual DA, Source-Free DA, Test-Time/Online DA, Single DG, Multiple DG and Unified DA&DG in TDG, and achieves comparable TDA and FA capabilities.
A Graph Neural Network Approach to Automated Model Building in Cryo-EM Maps
Authors: Kiarash Jamali,Dari Kimanius,Sjors HW Scheres

Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. At sufficient resolution, the cryo-EM maps, along with some knowledge about the imaged molecules, allow de novo atomic modelling. Typically, this is done through a laborious manual process. Recent advances in machine learning applications to protein structure prediction show potential for automating this process. Taking inspiration from these techniques, we have built ModelAngelo for automated model building of proteins in cryo-EM maps. ModelAngelo first uses a residual convolutional neural network (CNN) to initialize a graph representation with nodes assigned to individual amino acids of the proteins in the map and edges representing the protein chain. The graph is then refined with a graph neural network (GNN) that combines the cryo-EM data, the amino acid sequence data and prior knowledge about protein geometries. The GNN refines the geometry of the protein chain and classifies the amino acids for each of its nodes. The final graph is post-processed with a hidden Markov model (HMM) search to map each protein chain to entries in a user provided sequence file. Application to 28 test cases shows that ModelAngelo outperforms state-of-the-art and approximates manual building for cryo-EM maps with resolutions better than 3.5 A.
Distilling Cognitive Backdoor Patterns within an Image
Authors: Hanxun Huang,Xingjun Ma,Sarah Monazam Erfani,James Bailey

This paper proposes a simple method to distill and detect backdoor patterns within an image: \emph{Cognitive Distillation} (CD). The idea is to extract the ``minimal essence" from an input image responsible for the model's prediction. CD optimizes an input mask to extract a small pattern from the input image that can lead to the same model output (i.e., logits or deep features). The extracted pattern can help understand the cognitive mechanism of a model on clean vs. backdoor images and is thus called a \emph{Cognitive Pattern} (CP). Using CD and the distilled CPs, we uncover an interesting phenomenon of backdoor attacks: despite the various forms and sizes of trigger patterns used by different attacks, the CPs of backdoor samples are all surprisingly and suspiciously small. 
One thus can leverage the learned mask to detect and remove backdoor examples from poisoned training datasets. 
We conduct extensive experiments to show that CD can robustly detect a wide range of advanced backdoor attacks.
We also show that CD can potentially be applied to help detect potential biases from face datasets.
Code is available at https://github.com/HanxunH/CognitiveDistillation.
Revocable Deep Reinforcement Learning with Affinity Regularization for Outlier-Robust Graph Matching
Authors: Chang Liu,Zetian Jiang,Runzhong Wang,Lingxiao Huang,Pinyan Lu,Junchi Yan

Graph matching (GM) has been a building block in various areas including computer vision and pattern recognition. Despite recent impressive progress, existing deep GM methods often have obvious difficulty in handling outliers, which are ubiquitous in practice. We propose a deep reinforcement learning based approach RGM, whose sequential node matching scheme naturally fits the strategy for selective inlier matching against outliers. A revocable action framework is devised to improve the agent's flexibility against the complex constrained GM. Moreover, we propose a quadratic approximation technique to regularize the affinity score, in the presence of outliers. As such, the agent can finish inlier matching timely when the affinity score stops growing, for which otherwise an additional parameter i.e. the number of inliers is needed to avoid matching outliers. In this paper, we focus on learning the back-end solver under the most general form of GM: the Lawler's QAP, whose input is the affinity matrix. Especially, our approach can also boost existing GM methods that use such input. Experiments on multiple real-world datasets demonstrate its performance regarding both accuracy and robustness.
One Transformer Can Understand Both 2D & 3D Molecular Data
Authors: Shengjie Luo,Tianlang Chen,Yixian Xu,Shuxin Zheng,Tie-Yan Liu,Liwei Wang,Di He

Unlike vision and language data which usually has a unique format, molecules can naturally be characterized using different chemical formulations. One can view a molecule as a 2D graph or define it as a collection of atoms located in a 3D space. For molecular representation learning, most previous works designed neural networks only for a particular data format, making the learned models likely to fail for other data formats. We believe a general-purpose neural network model for chemistry should be able to handle molecular tasks across data modalities. To achieve this goal, in this work, we develop a novel Transformer-based Molecular model called Transformer-M, which can take molecular data of 2D or 3D formats as input and generate meaningful semantic representations. Using the standard Transformer as the backbone architecture, Transformer-M develops two separated channels to encode 2D and 3D structural information and incorporate them with the atom features in the network modules. When the input data is in a particular format, the corresponding channel will be activated, and the other will be disabled. By training on 2D and 3D molecular data with properly designed supervised signals, Transformer-M automatically learns to leverage knowledge from different data modalities and correctly capture the representations. We conducted extensive experiments for Transformer-M. All empirical results show that Transformer-M can simultaneously achieve strong performance on 2D and 3D tasks, suggesting its broad applicability. The code and models will be made publicly available at https://github.com/lsj2408/Transformer-M.
Mind the Gap: Offline Policy Optimization for Imperfect Rewards
Authors: Jianxiong Li,Xiao Hu,Haoran Xu,Jingjing Liu,Xianyuan Zhan,Qing-Shan Jia,Ya-Qin Zhang

Reward function is essential in reinforcement learning (RL), serving as the guiding signal to incentivize agents to solve given tasks, however, is also notoriously difficult to design. In many cases, only imperfect rewards are available, which inflicts substantial performance loss for RL agents. In this study, we propose a unified offline policy optimization approach, \textit{RGM (Reward Gap Minimization)}, which can smartly handle diverse types of imperfect rewards. RGM is formulated as a bi-level optimization problem: the upper layer optimizes a reward correction term that performs visitation distribution matching w.r.t. some expert data; the lower layer solves a pessimistic RL problem with the corrected rewards. By exploiting the duality of the lower layer, we derive a tractable algorithm that enables sampled-based learning without any online interactions.  Comprehensive experiments demonstrate that RGM achieves superior performance to existing methods under diverse settings of imperfect rewards. Further, RGM can effectively correct wrong or inconsistent rewards against expert preference and retrieve useful information from biased rewards. Code is available at https://github.com/Facebear-ljx/RGM.
Learning to Compose Soft Prompts for Compositional Zero-Shot Learning
Authors: Nihal V. Nayak,Peilin Yu,Stephen Bach

We introduce compositional soft prompting (CSP), a parameter-efficient learning technique to improve the zero-shot compositionality of large-scale pretrained vision-language models (VLMs) like CLIP. We develop CSP for compositional zero-shot learning, the task of predicting unseen attribute-object compositions (e.g., old cat and young tiger). VLMs have a flexible text encoder that can represent arbitrary classes as natural language prompts but they often underperform task-specific architectures on the compositional zero-shot benchmark datasets. CSP treats the attributes and objects that define classes as learnable tokens of vocabulary. During training, the vocabulary is tuned to recognize classes that compose tokens in multiple ways (e.g., old cat and white cat). At test time, we recompose the learned attribute-object vocabulary in new combinations to recognize novel classes. We show that CSP outperforms the CLIP on benchmark datasets by an average of 10.9 percentage points on AUC. CSP also outperforms CoOp, a soft prompting method that fine-tunes the prefix context tokens, by an average of 5.8 percentage points on AUC. We perform additional experiments to show that CSP improves generalization to higher-order attribute-attribute-object compositions (e.g., old white cat) and combinations of pretrained attributes and fine-tuned objects. The code is available at https://github.com/BatsResearch/csp.
SQA3D: Situated Question Answering in 3D Scenes
Authors: Xiaojian Ma,Silong Yong,Zilong Zheng,Qing Li,Yitao Liang,Song-Chun Zhu,Siyuan Huang

We propose a new task to benchmark scene understanding of embodied agents: Situated Question Answering in 3D Scenes (SQA3D). Given a scene context (e.g., 3D scan), SQA3D requires the tested agent to first understand its situation (position, orientation, etc.) in the 3D scene as described by text, then reason about its surrounding environment and answer a question under that situation. Based upon 650 scenes from ScanNet, we provide a dataset centered around 6.8k unique situations, along with 20.4k descriptions and 33.4k diverse reasoning questions for these situations. These questions examine a wide spectrum of reasoning capabilities for an intelligent agent, ranging from spatial relation comprehension to commonsense understanding, navigation, and multi-hop reasoning. SQA3D imposes a significant challenge to current multi-modal especially 3D reasoning models. We evaluate various state-of-the-art approaches and find that the best one only achieves an overall score of 47.20%, while amateur human participants can reach 90.06%. We believe SQA3D could facilitate future embodied AI research with stronger situation understanding and reasoning capability.
Empowering Networks With Scale and Rotation Equivariance Using A Similarity Convolution
Authors: Zikai Sun,Thierry Blu

The translational equivariant nature of Convolutional Neural Networks (CNNs) is a reason for its great success in computer vision. However, networks do not enjoy more general equivariance properties such as rotation or scaling, ultimately limiting their generalization performance. To address this limitation, we devise a method that endows CNNs with simultaneous equivariance with respect to translation, rotation, and scaling.  Our approach defines a convolution-like operation and ensures equivariance based on our proposed scalable Fourier-Argand representation. The method maintains similar efficiency as a traditional network and hardly introduces any additional learnable parameters, since it does not face the computational issue that often occurs in group-convolution operators. We validate the efficacy of our approach in the image classification task, demonstrating its robustness and the generalization ability to both scaled and rotated inputs.
Robust and Controllable Object-Centric Learning through Energy-based Models
Authors: Ruixiang ZHANG,Tong Che,Boris Ivanovic,Renhao Wang,Marco Pavone,Yoshua Bengio,Liam Paull

Humans are remarkably good at understanding and reasoning about complex visual scenes. The capability of decomposing low-level observations into discrete objects allows us to build a grounded abstract representation and identify the compositional structure of the world. Thus it is a crucial step for machine learning models to be capable of inferring objects and their properties from visual scene without explicit supervision. However, existing works on object-centric representation learning are either relying on tailor-made neural network modules or assuming sophisticated models of underlying generative and inference processes. In this work, we present EGO, a conceptually simple and general approach to learning object-centric representation through energy-based model. By forming a permutation-invariant energy function using vanilla attention blocks that are readily available in Transformers, we can infer object-centric latent variables via gradient-based MCMC methods where permutation equivariance is automatically guaranteed. We show that EGO can be easily integrated into existing architectures, and can effectively extract high-quality object-centric representations, leading to better segmentation accuracy and competitive downstream task performance. We empirically evaluate the robustness of the learned representation from EGO against distribution shift. Finally, we demonstrate the effectiveness of EGO in systematic compositional generalization, by recomposing learned energy functions for novel scene generation and manipulation.
Topology-aware Robust Optimization for Out-of-Distribution Generalization
Authors: Fengchun Qiao,Xi Peng

Out-of-distribution (OOD) generalization is a challenging machine learning problem yet highly desirable in many high-stake applications. 
Existing methods suffer from overly pessimistic modeling with low generalization confidence. As generalizing to arbitrary test distributions is impossible, we hypothesize that further structure on the topology of distributions is crucial in developing strong OOD resilience. To this end, we propose topology-aware robust optimization (TRO) that seamlessly integrates distributional topology in a principled optimization framework. More specifically, TRO solves two optimization objectives: (1) Topology Learning which explores data manifold to uncover the distributional topology; (2) Learning on Topology which exploits the topology to constrain robust optimization for tightly-bounded generalization risks. We theoretically demonstrate the effectiveness of our approach, and empirically show that it significantly outperforms the state of the arts in a wide range of tasks including classification, regression, and semantic segmentation. Moreover, we empirically find the data-driven distributional topology is consistent with domain knowledge, enhancing the explainability of our approach.
EAGLE: Large-scale Learning of Turbulent Fluid Dynamics with Mesh Transformers
Authors: Steeven JANNY,Aurélien Bénéteau,Madiha Nadri,Julie Digne,Nicolas THOME,Christian Wolf

Estimating fluid dynamics is classically done through the simulation and integration of numerical models solving the Navier-Stokes equations, which is computationally complex and time-consuming even on high-end hardware. This is a notoriously hard problem to solve, which has recently been addressed with machine learning, in particular graph neural networks (GNN) and variants trained and evaluated on datasets of static objects in static scenes with fixed geometry. We attempt to go beyond existing work in complexity and introduce a new model, method and benchmark. We propose EAGLE: a large-scale dataset of ∼1.1 million 2D meshes resulting from simulations of unsteady fluid dynamics caused by a moving flow source interacting with nonlinear scene structure of varying geometries, with 600 different scenes of three different types in total. To perform future forecasting of pressure and velocity on the challenging EAGLE dataset, we introduce a new mesh transformer. It leverages node clustering, graph pooling and global attention to learn long-range dependencies between spatially distant data points without needing a large number of iterations, as existing GNN methods do. We show that our transformer outperforms state-of-the-art performance on, both, existing synthetic and real datasets and on EAGLE. Finally, we highlight that our approach learns to attend to airflow, integrating complex information in a single iteration.
Limitless Stability for Graph Convolutional Networks 
Authors: Christian Koke

This work establishes rigorous, novel and widely applicable stability guarantees and transferability bounds for general graph convolutional networks  -- without reference to any underlying limit object or statistical distribution. Crucially, utilized graph-shift operators are not necessarily assumed to be normal, allowing for the treatment of networks on both directed- and undirected graphs within the developed framework. In the undirected setting, stability to node-level perturbations is related to an 'adequate spectral covering' property of the filters in each layer. Stability to edge-level perturbations is discussed and related to properties of the utilized filters such as their Lipschitz constants. Results on stability to  vertex-set non-preserving perturbations are obtained by utilizing recently developed mathematical-physics based tools. As an exemplifying application of the developed theory, it is showcased that
general graph convolutional networks utilizing the un-normalized graph Laplacian as graph-shift-operator  can be rendered stable to collapsing strong edges in the underlying graph if filters are mandated to be constant at infinity. These theoretical results are supported by corresponding numerical investigations showcasing the response of filters and networks to such perturbations.
De Novo Molecular Generation via Connection-aware Motif Mining
Authors: Zijie Geng,Shufang Xie,Yingce Xia,Lijun Wu,Tao Qin,Jie Wang,Yongdong Zhang,Feng Wu,Tie-Yan Liu

De novo molecular generation is an essential task for science discovery. Recently, fragment-based deep generative models have attracted much research attention due to their flexibility in generating novel molecules based on existing molecule fragments. However, the motif vocabulary, i.e., the collection of frequent fragments, is usually built upon heuristic rules, which brings difficulties to capturing common substructures from large amounts of molecules. In this work, we propose MiCaM to generate molecules based on mined connection-aware motifs. Specifically, it leverages a data-driven algorithm to automatically discover motifs from a molecule library by iteratively merging subgraphs based on their frequency. The obtained motif vocabulary consists of not only molecular motifs (i.e., the frequent fragments), but also their connection information, indicating how the motifs are connected with each other. Based on the mined connection-aware motifs, MiCaM builds a connection-aware generator, which simultaneously picks up motifs and determines how they are connected. We test our method on distribution-learning benchmarks (i.e., generating novel molecules to resemble the distribution of a given training set) and goal-directed benchmarks (i.e., generating molecules with target properties), and achieve significant improvements over previous fragment-based baselines. Furthermore, we demonstrate that our method can effectively mine domain-specific motifs for different tasks.