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Deep Reinforcement Learning (DRL) is regarded as a promising tool for optical network optimization. However, the flexibility and efficiency of current DRL-based solutions for optical network optimization require further improvement. Currently, generative models have showcased their significant performance advantages across various domains. In this paper, we introduce OpticGAI, the AI-generated policy design paradigm for optical networks. In detail, it is implemented as a novel DRL framework that utilizes generative models to learn the optimal policy network. Furthermore, we assess the performance of OpticGAI on two NP-hard optical network problems, Routing and Wavelength Assignment (RWA) and dynamic Routing, Modulation, and Spectrum Allocation (RMSA), to show the feasibility of the AI-generated policy paradigm. Simulation results have shown that OpticGAI achieves the highest reward and the lowest blocking rate of both RWA and RMSA problems. OpticGAI poses a promising direction for future research on generative AI-enhanced flexible optical network optimization., Comment: Accepted by ACM SIGCOMM 2024 Workshop on Hot Topics in Optical Technologies and Applications in Networking

Unmanned Combat Aerial Vehicle (UCAV) dogfight, which refers to a fight between two or more UCAVs usually at close quarters, plays a decisive role on the aerial battlefields. With the evolution of artificial intelligence, dogfight progressively transits towards intelligent and autonomous modes. However, the development of autonomous dogfight policy learning is hindered by challenges such as weak exploration capabilities, low learning efficiency, and unrealistic simulated environments. To overcome these challenges, this paper proposes a novel imitative reinforcement learning framework, which efficiently leverages expert data while enabling autonomous exploration. The proposed framework not only enhances learning efficiency through expert imitation, but also ensures adaptability to dynamic environments via autonomous exploration with reinforcement learning. Therefore, the proposed framework can learn a successful dogfight policy of 'pursuit-lock-launch' for UCAVs. To support data-driven learning, we establish a dogfight environment based on the Harfang3D sandbox, where we conduct extensive experiments. The results indicate that the proposed framework excels in multistage dogfight, significantly outperforms state-of-the-art reinforcement learning and imitation learning methods. Thanks to the ability of imitating experts and autonomous exploration, our framework can quickly learn the critical knowledge in complex aerial combat tasks, achieving up to a 100% success rate and demonstrating excellent robustness.

Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative heterogeneous graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements various cutting-edge methods. Secondly, a single task on \textit{de novo} molecule generation can hardly reflect their capabilities. To broaden the scope, we have adapted these models to a range of tasks essential in drug design, which are considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of \textit{de novo} molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide the pre-trained versions of the state-of-the-art models and deep insights with analysis from empirical studies. The codebase for CBGBench is publicly accessible at \url{https://github.com/Edapinenut/CBGBench}., Comment: 9 pages main context

To mitigate the computational complexity in the self-attention mechanism on long sequences, linear attention utilizes computation tricks to achieve linear complexity, while state space models (SSMs) popularize a favorable practice of using non-data-dependent memory pattern, i.e., emphasize the near and neglect the distant, to processing sequences. Recent studies have shown the priorities by combining them as one. However, the efficiency of linear attention remains only at the theoretical level in a causal setting, and SSMs require various designed constraints to operate effectively on specific data. Therefore, in order to unveil the true power of the hybrid design, the following two issues need to be addressed: (1) hardware-efficient implementation for linear attention and (2) stabilization of SSMs. To achieve this, we leverage the thought of tiling and hierarchy to propose CHELA (short-long Convolutions with Hardware-Efficient Linear Attention), which replaces SSMs with short-long convolutions and implements linear attention in a divide-and-conquer manner. This approach enjoys global abstraction and data-dependent selection from stable SSM and linear attention while maintaining real linear complexity. Our comprehensive experiments on the Long Range Arena benchmark and language modeling tasks demonstrate the effectiveness of the proposed method., Comment: ICML 2024 camera ready

Large Language Models (LLMs) have demonstrated wide-ranging applications across various fields and have shown significant potential in the academic peer-review process. However, existing applications are primarily limited to static review generation based on submitted papers, which fail to capture the dynamic and iterative nature of real-world peer reviews. In this paper, we reformulate the peer-review process as a multi-turn, long-context dialogue, incorporating distinct roles for authors, reviewers, and decision makers. We construct a comprehensive dataset containing over 26,841 papers with 92,017 reviews collected from multiple sources, including the top-tier conference and prestigious journal. This dataset is meticulously designed to facilitate the applications of LLMs for multi-turn dialogues, effectively simulating the complete peer-review process. Furthermore, we propose a series of metrics to evaluate the performance of LLMs for each role under this reformulated peer-review setting, ensuring fair and comprehensive evaluations. We believe this work provides a promising perspective on enhancing the LLM-driven peer-review process by incorporating dynamic, role-based interactions. It aligns closely with the iterative and interactive nature of real-world academic peer review, offering a robust foundation for future research and development in this area. We open-source the dataset at https://github.com/chengtan9907/ReviewMT., Comment: Under review

The robust association of the same objects across video frames in complex scenes is crucial for many applications, especially Multiple Object Tracking (MOT). Current methods predominantly rely on labeled domain-specific video datasets, which limits the cross-domain generalization of learned similarity embeddings. We propose MASA, a novel method for robust instance association learning, capable of matching any objects within videos across diverse domains without tracking labels. Leveraging the rich object segmentation from the Segment Anything Model (SAM), MASA learns instance-level correspondence through exhaustive data transformations. We treat the SAM outputs as dense object region proposals and learn to match those regions from a vast image collection. We further design a universal MASA adapter which can work in tandem with foundational segmentation or detection models and enable them to track any detected objects. Those combinations present strong zero-shot tracking ability in complex domains. Extensive tests on multiple challenging MOT and MOTS benchmarks indicate that the proposed method, using only unlabeled static images, achieves even better performance than state-of-the-art methods trained with fully annotated in-domain video sequences, in zero-shot association. Project Page: https://matchinganything.github.io/, Comment: CVPR 2024 Highlight. code at: https://github.com/siyuanliii/masa

The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite advancements, a lack of evaluation framework makes it difficult to ensure equitable assessment due to experimental settings, model intricacy, benchmark datasets, and reproducibility challenges. In the absence of standardization, comparative analyses risk becoming biased and unreliable. To surmount this impasse, we introduce GenBench, a comprehensive benchmarking suite specifically tailored for evaluating the efficacy of Genomic Foundation Models. GenBench offers a modular and expandable framework that encapsulates a variety of state-of-the-art methodologies. Through systematic evaluations of datasets spanning diverse biological domains with a particular emphasis on both short-range and long-range genomic tasks, firstly including the three most important DNA tasks covering Coding Region, Non-Coding Region, Genome Structure, etc. Moreover, We provide a nuanced analysis of the interplay between model architecture and dataset characteristics on task-specific performance. Our findings reveal an interesting observation: independent of the number of parameters, the discernible difference in preference between the attention-based and convolution-based models on short- and long-range tasks may provide insights into the future design of GFM.

Large language models equipped with retrieval-augmented generation (RAG) represent a burgeoning field aimed at enhancing answering capabilities by leveraging external knowledge bases. Although the application of RAG with language-only models has been extensively explored, its adaptation into multimodal vision-language models remains nascent. Going beyond mere answer generation, the primary goal of multimodal RAG is to cultivate the models' ability to reason in response to relevant queries. To this end, we introduce a novel multimodal RAG framework named RMR (Retrieval Meets Reasoning). The RMR framework employs a bi-modal retrieval module to identify the most relevant question-answer pairs, which then serve as scaffolds for the multimodal reasoning process. This training-free approach not only encourages the model to engage deeply with the reasoning processes inherent in the retrieved content but also facilitates the generation of answers that are precise and richly interpretable. Surprisingly, utilizing solely the ScienceQA dataset, collected from elementary and high school science curricula, RMR significantly boosts the performance of various vision-language models across a spectrum of benchmark datasets, including A-OKVQA, MMBench, and SEED. These outcomes highlight the substantial potential of our multimodal retrieval and reasoning mechanism to improve the reasoning capabilities of vision-language models., Comment: Under review

In recent years, large language models (LLMs) have made remarkable achievements in various domains. However, the untimeliness and cost of knowledge updates coupled with hallucination issues of LLMs have curtailed their applications in knowledge intensive tasks, where retrieval augmented generation (RAG) can be of help. Nevertheless, existing retrieval augmented models typically use similarity as a bridge between queries and documents and follow a retrieve then read procedure. In this work, we argue that similarity is not always the panacea and totally relying on similarity would sometimes degrade the performance of retrieval augmented generation. To this end, we propose MetRag, a Multi layEred Thoughts enhanced Retrieval Augmented Generation framework. To begin with, beyond existing similarity oriented thought, we embrace a small scale utility model that draws supervision from an LLM for utility oriented thought and further come up with a smarter model by comprehensively combining the similarity and utility oriented thoughts. Furthermore, given the fact that the retrieved document set tends to be huge and using them in isolation makes it difficult to capture the commonalities and characteristics among them, we propose to make an LLM as a task adaptive summarizer to endow retrieval augmented generation with compactness-oriented thought. Finally, with multi layered thoughts from the precedent stages, an LLM is called for knowledge augmented generation. Extensive experiments on knowledge-intensive tasks have demonstrated the superiority of MetRag., Comment: 12 pages

Molecule inverse folding has been a long-standing challenge in chemistry and biology, with the potential to revolutionize drug discovery and material science. Despite specified models have been proposed for different small- or macro-molecules, few have attempted to unify the learning process, resulting in redundant efforts. Complementary to recent advancements in molecular structure prediction, such as RoseTTAFold All-Atom and AlphaFold3, we propose the unified model UniIF for the inverse folding of all molecules. We do such unification in two levels: 1) Data-Level: We propose a unified block graph data form for all molecules, including the local frame building and geometric feature initialization. 2) Model-Level: We introduce a geometric block attention network, comprising a geometric interaction, interactive attention and virtual long-term dependency modules, to capture the 3D interactions of all molecules. Through comprehensive evaluations across various tasks such as protein design, RNA design, and material design, we demonstrate that our proposed method surpasses state-of-the-art methods on all tasks. UniIF offers a versatile and effective solution for general molecule inverse folding.

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data, pre-training with massive unlabeled data has emerged as a promising solution. However, this process faces a series of challenges: (1) complex higher-order dependencies among multiple (more than paired) structural scales have not yet been fully captured; (2) it is rarely explored how mutations alter the local conformation of the surrounding microenvironment; (3) pre-training is costly, both in data size and computational burden. In this paper, we first construct a hierarchical prompt codebook to record common microenvironmental patterns at different structural scales independently. Then, we develop a novel codebook pre-training task, namely masked microenvironment modeling, to model the joint distribution of each mutation with their residue types, angular statistics, and local conformational changes in the microenvironment. With the constructed prompt codebook, we encode the microenvironment around each mutation into multiple hierarchical prompts and combine them to flexibly provide information to wild-type and mutated protein complexes about their microenvironmental differences. Such a hierarchical prompt learning framework has demonstrated superior performance and training efficiency over state-of-the-art pre-training-based methods in mutation effect prediction and a case study of optimizing human antibodies against SARS-CoV-2.

As an emerging paradigm of content creation, AI-Generated Content (AIGC) has been widely adopted by a large number of edge end users. However, the requests for generated content from AIGC users have obvious diversity, and there remains a notable lack of research addressing the variance in user demands for AIGC services. This gap underscores a critical need for suitable AIGC service selection mechanisms satisfying various AIGC user requirements under resource-constrained edge environments. To address this challenge, this paper proposes a novel Attention-based Diffusion Soft Actor-Critic (ADSAC) algorithm to select the appropriate AIGC model in response to heterogeneous AIGC user requests. Specifically, the ADSAC algorithm integrates a diffusion model as the policy network in the off-policy reinforcement learning (RL) framework, to capture the intricate relationships between the characteristics of AIGC tasks and the integrated edge network states. Furthermore, an attention mechanism is utilized to harness the contextual long-range dependencies present in state feature vectors, enhancing the decision-making process. Extensive experiments validate the effectiveness of our algorithm in enhancing the overall user utility and reducing the crash rate of servers. Compared to the existing methods, the proposed ADSAC algorithm outperforms existing methods, reducing the overall user utility loss and the server crash rate by at least 58.3% and 58.4%, respectively. These results demonstrate our ADSAC algorithm is a robust solution to the challenges of diverse and dynamic user requirements in edge-based AIGC application environments.

Similar to natural language models, pre-trained genome language models are proposed to capture the underlying intricacies within genomes with unsupervised sequence modeling. They have become essential tools for researchers and practitioners in biology. However, the hand-crafted tokenization policies used in these models may not encode the most discriminative patterns from the limited vocabulary of genomic data. In this paper, we introduce VQDNA, a general-purpose framework that renovates genome tokenization from the perspective of genome vocabulary learning. By leveraging vector-quantized codebooks as learnable vocabulary, VQDNA can adaptively tokenize genomes into pattern-aware embeddings in an end-to-end manner. To further push its limits, we propose Hierarchical Residual Quantization (HRQ), where varying scales of codebooks are designed in a hierarchy to enrich the genome vocabulary in a coarse-to-fine manner. Extensive experiments on 32 genome datasets demonstrate VQDNA's superiority and favorable parameter efficiency compared to existing genome language models. Notably, empirical analysis of SARS-CoV-2 mutations reveals the fine-grained pattern awareness and biological significance of learned HRQ vocabulary, highlighting its untapped potential for broader applications in genomics., Comment: ICML 2024. Preprint V2 with 17 pages and 5 figures

AI-generated content (AIGC) models, represented by large language models (LLM), have brought revolutionary changes to the content generation fields. The high-speed and extensive 6G technology is an ideal platform for providing powerful AIGC mobile service applications, while future 6G mobile networks also need to support intelligent and personalized mobile generation services. However, the significant ethical and security issues of current AIGC models, such as adversarial attacks, privacy, and fairness, greatly affect the credibility of 6G intelligent networks, especially in ensuring secure, private, and fair AIGC applications. In this paper, we propose TrustGAIN, a novel paradigm for trustworthy AIGC in 6G networks, to ensure trustworthy large-scale AIGC services in future 6G networks. We first discuss the adversarial attacks and privacy threats faced by AIGC systems in 6G networks, as well as the corresponding protection issues. Subsequently, we emphasize the importance of ensuring the unbiasedness and fairness of the mobile generative service in future intelligent networks. In particular, we conduct a use case to demonstrate that TrustGAIN can effectively guide the resistance against malicious or generated false information. We believe that TrustGAIN is a necessary paradigm for intelligent and trustworthy 6G networks to support AIGC services, ensuring the security, privacy, and fairness of AIGC network services.

Currently, the generative model has garnered considerable attention due to its application in addressing the challenge of scarcity of abnormal samples in the industrial Internet of Things (IoT). However, challenges persist regarding the edge deployment of generative models and the optimization of joint edge AI-generated content (AIGC) tasks. In this paper, we focus on the edge optimization of AIGC task execution and propose GMEL, a generative model-driven industrial AIGC collaborative edge learning framework. This framework aims to facilitate efficient few-shot learning by leveraging realistic sample synthesis and edge-based optimization capabilities. First, a multi-task AIGC computational offloading model is presented to ensure the efficient execution of heterogeneous AIGC tasks on edge servers. Then, we propose an attention-enhanced multi-agent reinforcement learning (AMARL) algorithm aimed at refining offloading policies within the IoT system, thereby supporting generative model-driven edge learning. Finally, our experimental results demonstrate the effectiveness of the proposed algorithm in optimizing the total system latency of the edge-based AIGC task completion.

Transformer models have been successful in various sequence processing tasks, but the self-attention mechanism's computational cost limits its practicality for long sequences. Although there are existing attention variants that improve computational efficiency, they have a limited ability to abstract global information effectively based on their hand-crafted mixing strategies. On the other hand, state-space models (SSMs) are tailored for long sequences but cannot capture complicated local information. Therefore, the combination of them as a unified token mixer is a trend in recent long-sequence models. However, the linearized attention degrades performance significantly even when equipped with SSMs. To address the issue, we propose a new method called LongVQ. LongVQ uses the vector quantization (VQ) technique to compress the global abstraction as a length-fixed codebook, enabling the linear-time computation of the attention matrix. This technique effectively maintains dynamic global and local patterns, which helps to complement the lack of long-range dependency issues. Our experiments on the Long Range Arena benchmark, autoregressive language modeling, and image and speech classification demonstrate the effectiveness of LongVQ. Our model achieves significant improvements over other sequence models, including variants of Transformers, Convolutions, and recent State Space Models., Comment: Published at IJCAI 2024

Offline batch inference is a common task in the industry for deep learning applications, but it can be challenging to ensure stability and performance when dealing with large amounts of data and complicated inference pipelines. This paper demonstrated AntBatchInfer, an elastic batch inference framework, which is specially optimized for the non-dedicated cluster. AntBatchInfer addresses these challenges by providing multi-level fault-tolerant capabilities, enabling the stable execution of versatile and long-running inference tasks. It also improves inference efficiency by pipelining, intra-node, and inter-node scaling. It further optimizes the performance in complicated multiple-model batch inference scenarios. Through extensive experiments and real-world statistics, we demonstrate the superiority of our framework in terms of stability and efficiency. In the experiment, it outperforms the baseline by at least $2\times$ and $6\times$ in the single-model or multiple-model batch inference. Also, it is widely used at Ant Group, with thousands of daily jobs from various scenarios, including DLRM, CV, and NLP, which proves its practicability in the industry.

Many distributed training techniques like Parameter Server and AllReduce have been proposed to take advantage of the increasingly large data and rich features. However, stragglers frequently occur in distributed training due to resource contention and hardware heterogeneity, which significantly hampers the training efficiency. Previous works only address part of the stragglers and could not adaptively solve various stragglers in practice. Additionally, it is challenging to use a systematic framework to address all stragglers because different stragglers require diverse data allocation and fault-tolerance mechanisms. Therefore, this paper proposes a unified distributed training framework called AntDT (Ant Distributed Training Framework) to adaptively solve the straggler problems. Firstly, the framework consists of four components, including the Stateful Dynamic Data Sharding service, Monitor, Controller, and Agent. These components work collaboratively to efficiently distribute workloads and provide a range of pre-defined straggler mitigation methods with fault tolerance, thereby hiding messy details of data allocation and fault handling. Secondly, the framework provides a high degree of flexibility, allowing for the customization of straggler mitigation solutions based on the specific circumstances of the cluster. Leveraging this flexibility, we introduce two straggler mitigation solutions, namely AntDT-ND for non-dedicated clusters and AntDT-DD for dedicated clusters, as practical examples to resolve various types of stragglers at Ant Group. Justified by our comprehensive experiments and industrial deployment statistics, AntDT outperforms other SOTA methods more than 3x in terms of training efficiency. Additionally, in Alipay's homepage recommendation scenario, using AntDT reduces the training duration of the ranking model from 27.8 hours to just 5.4 hours.

QCD bounds on the leading-order (LO) hadronic vacuum polarization (HVP) contribution to the anomalous magnetic moment of the muon ($a_\mu^{\mathrm{HVP,LO}}$, $a_\mu=\left(g-2\right)_\mu/2$) are determined by imposing H\"older inequalities and related inequality constraints on systems of Finite-Energy QCD sum-rules. This novel methodology is complementary to lattice QCD and data-driven approaches to determining $a_\mu^{\mathrm{HVP,LO}}$. For the light-quark ($u,d,s$) contributions up to five-loop order in perturbation theory in the chiral limit, LO in light-quark mass corrections, next-to-leading order in dimension-four QCD condensates, and to LO in dimension-six QCD condensates, we find that $\left(673.0\pm 40.0\right)\times 10^{-10}\leq a_\mu^{\mathrm{HVP,LO}} \leq \left(807.5\pm 48.0\right)\times10^{-10}\,$, bridging the range between lattice QCD and data-driven values., Comment: 16 pages, 4 figures

Unmanned aerial vehicle (UAV) techniques have developed rapidly within the past few decades. Using UAVs provides benefits in numerous applications such as site surveying, communication systems, parcel delivery, target tracking, etc. The high manoeuvrability of the drone and its ability to replace a certain amount of labour cost are the reasons why it can be widely chosen. There will be more applications of UAVs if they can have longer flight time, which is a very challenging hurdle because of the energy constraint of the onboard battery. One promising solution is to equip UAVs with some lightweight solar panels to maximize flight time. Therefore, more research is needed for solar-powered UAVs (SUAVs) in different environments., Comment: 31 Pages, master degree thesis

Accurate monocular metric depth estimation (MMDE) is crucial to solving downstream tasks in 3D perception and modeling. However, the remarkable accuracy of recent MMDE methods is confined to their training domains. These methods fail to generalize to unseen domains even in the presence of moderate domain gaps, which hinders their practical applicability. We propose a new model, UniDepth, capable of reconstructing metric 3D scenes from solely single images across domains. Departing from the existing MMDE methods, UniDepth directly predicts metric 3D points from the input image at inference time without any additional information, striving for a universal and flexible MMDE solution. In particular, UniDepth implements a self-promptable camera module predicting dense camera representation to condition depth features. Our model exploits a pseudo-spherical output representation, which disentangles camera and depth representations. In addition, we propose a geometric invariance loss that promotes the invariance of camera-prompted depth features. Thorough evaluations on ten datasets in a zero-shot regime consistently demonstrate the superior performance of UniDepth, even when compared with methods directly trained on the testing domains. Code and models are available at: https://github.com/lpiccinelli-eth/unidepth

In this paper, we abstract the process of people hearing speech, extracting meaningful cues, and creating various dynamically audio-consistent talking faces, termed Listening and Imagining, into the task of high-fidelity diverse talking faces generation from a single audio. Specifically, it involves two critical challenges: one is to effectively decouple identity, content, and emotion from entangled audio, and the other is to maintain intra-video diversity and inter-video consistency. To tackle the issues, we first dig out the intricate relationships among facial factors and simplify the decoupling process, tailoring a Progressive Audio Disentanglement for accurate facial geometry and semantics learning, where each stage incorporates a customized training module responsible for a specific factor. Secondly, to achieve visually diverse and audio-synchronized animation solely from input audio within a single model, we introduce the Controllable Coherent Frame generation, which involves the flexible integration of three trainable adapters with frozen Latent Diffusion Models (LDMs) to focus on maintaining facial geometry and semantics, as well as texture and temporal coherence between frames. In this way, we inherit high-quality diverse generation from LDMs while significantly improving their controllability at a low training cost. Extensive experiments demonstrate the flexibility and effectiveness of our method in handling this paradigm. The codes will be released at https://github.com/modelscope/facechain.

Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction. While existing methods rely heavily on protein sequence for PPI prediction, it is the protein structure that is the key to determine the interactions. To take both protein modalities into account, we define the microenvironment of an amino acid residue by its sequence and structural contexts, which describe the surrounding chemical properties and geometric features. In addition, microenvironments defined in previous work are largely based on experimentally assayed physicochemical properties, for which the "vocabulary" is usually extremely small. This makes it difficult to cover the diversity and complexity of microenvironments. In this paper, we propose Microenvironment-Aware Protein Embedding for PPI prediction (MPAE-PPI), which encodes microenvironments into chemically meaningful discrete codes via a sufficiently large microenvironment "vocabulary" (i.e., codebook). Moreover, we propose a novel pre-training strategy, namely Masked Codebook Modeling (MCM), to capture the dependencies between different microenvironments by randomly masking the codebook and reconstructing the input. With the learned microenvironment codebook, we can reuse it as an off-the-shelf tool to efficiently and effectively encode proteins of different sizes and functions for large-scale PPI prediction. Extensive experiments show that MAPE-PPI can scale to PPI prediction with millions of PPIs with superior trade-offs between effectiveness and computational efficiency than the state-of-the-art competitors.

Accurate prediction of protein-ligand binding structures, a task known as molecular docking is crucial for drug design but remains challenging. While deep learning has shown promise, existing methods often depend on holo-protein structures (docked, and not accessible in realistic tasks) or neglect pocket sidechain conformations, leading to limited practical utility and unrealistic conformation predictions. To fill these gaps, we introduce an under-explored task, named flexible docking to predict poses of ligand and pocket sidechains simultaneously and introduce Re-Dock, a novel diffusion bridge generative model extended to geometric manifolds. Specifically, we propose energy-to-geometry mapping inspired by the Newton-Euler equation to co-model the binding energy and conformations for reflecting the energy-constrained docking generative process. Comprehensive experiments on designed benchmark datasets including apo-dock and cross-dock demonstrate our model's superior effectiveness and efficiency over current methods.

Exponential Moving Average (EMA) is a widely used weight averaging (WA) regularization to learn flat optima for better generalizations without extra cost in deep neural network (DNN) optimization. Despite achieving better flatness, existing WA methods might fall into worse final performances or require extra test-time computations. This work unveils the full potential of EMA with a single line of modification, i.e., switching the EMA parameters to the original model after each epoch, dubbed as Switch EMA (SEMA). From both theoretical and empirical aspects, we demonstrate that SEMA can help DNNs to reach generalization optima that better trade-off between flatness and sharpness. To verify the effectiveness of SEMA, we conduct comparison experiments with discriminative, generative, and regression tasks on vision and language datasets, including image classification, self-supervised learning, object detection and segmentation, image generation, video prediction, attribute regression, and language modeling. Comprehensive results with popular optimizers and networks show that SEMA is a free lunch for DNN training by improving performances and boosting convergence speeds., Comment: Preprint V1. Source code and models at https://github.com/Westlake-AI/SEMA

Reinforcement learning (RL) has shown its strength in challenging sequential decision-making problems. The reward function in RL is crucial to the learning performance, as it serves as a measure of the task completion degree. In real-world problems, the rewards are predominantly human-designed, which requires laborious tuning, and is easily affected by human cognitive biases. To achieve automatic auxiliary reward generation, we propose a novel representation learning approach that can measure the ``transition distance'' between states. Building upon these representations, we introduce an auxiliary reward generation technique for both single-task and skill-chaining scenarios without the need for human knowledge. The proposed approach is evaluated in a wide range of manipulation tasks. The experiment results demonstrate the effectiveness of measuring the transition distance between states and the induced improvement by auxiliary rewards, which not only promotes better learning efficiency but also increases convergent stability.

Finite-temperature quantum field theory provides the foundation for many important phenomena in the Standard Model and extensions, including phase transitions, baryogenesis, and gravitational waves. Methods are developed to enable application of pySecDec (a Python-language-based package designed for numerical calculation of dimensionally-regulated loop integrals) to numerically evaluate finite-temperature loop integrals in the imaginary time (Matsubara) formalism. These methods consist of two main elements: an inverse Wick rotation that converts a finite-temperature loop integral into a form applicable to pySecDec, and asymptotic techniques to regulate and accelerate convergence of the Matsubara frequency summations. Numerical pySecDec evaluation of finite-temperature, two-point and three-point, one-loop topologies for scalar fields is used to illustrate and validate these new methodologies. Advantages of these finite-temperature pySecDec numerical methods are illustrated by the inclusion of multiple mass and external momentum scales., Comment: 16 pages, 9 figures

As the deep learning revolution marches on, self-supervised learning has garnered increasing attention in recent years thanks to its remarkable representation learning ability and the low dependence on labeled data. Among these varied self-supervised techniques, masked modeling has emerged as a distinctive approach that involves predicting parts of the original data that are proportionally masked during training. This paradigm enables deep models to learn robust representations and has demonstrated exceptional performance in the context of computer vision, natural language processing, and other modalities. In this survey, we present a comprehensive review of the masked modeling framework and its methodology. We elaborate on the details of techniques within masked modeling, including diverse masking strategies, recovering targets, network architectures, and more. Then, we systematically investigate its wide-ranging applications across domains. Furthermore, we also explore the commonalities and differences between masked modeling methods in different fields. Toward the end of this paper, we conclude by discussing the limitations of current techniques and point out several potential avenues for advancing masked modeling research. A paper list project with this survey is available at \url{https://github.com/Lupin1998/Awesome-MIM}., Comment: Preprint v2 (fix typos and citations). GitHub project at https://github.com/Lupin1998/Awesome-MIM

Protein design involves generating protein sequences based on their corresponding protein backbones. While deep generative models show promise for learning protein design directly from data, the lack of publicly available structure-sequence pairings limits their generalization capabilities. Previous efforts of generative protein design have focused on architectural improvements and pseudo-data augmentation to overcome this bottleneck. To further address this challenge, we propose a novel protein design paradigm called MMDesign, which leverages multi-modality transfer learning. To our knowledge, MMDesign is the first framework that combines a pretrained structural module with a pretrained contextual module, using an auto-encoder (AE) based language model to incorporate prior semantic knowledge of protein sequences. We also introduce a cross-layer cross-modal alignment algorithm to enable the structural module to learn long-term temporal information and ensure consistency between structural and contextual modalities. Experimental results, only training with the small CATH dataset, demonstrate that our MMDesign framework consistently outperforms other baselines on various public test sets. To further assess the biological plausibility of the generated protein sequences and data distribution, we present systematic quantitative analysis techniques that provide interpretability and reveal more about the laws of protein design.

Multimodal reasoning is a challenging task that requires models to reason across multiple modalities to answer questions. Existing approaches have made progress by incorporating language and visual modalities into a two-stage reasoning framework, separating rationale generation from answer inference. However, these approaches often fall short due to the inadequate quality of the generated rationales. In this work, we delve into the importance of rationales in model reasoning. We observe that when rationales are completely accurate, the model's accuracy significantly improves, highlighting the need for high-quality rationale generation. Motivated by this, we propose MC-CoT, a self-consistency training strategy that generates multiple rationales and answers, subsequently selecting the most accurate through a voting process. This approach not only enhances the quality of generated rationales but also leads to more accurate and robust answers. Through extensive experiments, we demonstrate that our approach significantly improves model performance across various benchmarks. Remarkably, we show that even smaller base models, when equipped with our proposed approach, can achieve results comparable to those of larger models, illustrating the potential of our approach in harnessing the power of rationales for improved multimodal reasoning. The code is available at https://github.com/chengtan9907/mc-cot., Comment: Accepted by ECCV 2024

Imitation learning (IL) has achieved considerable success in solving complex sequential decision-making problems. However, current IL methods mainly assume that the environment for learning policies is the same as the environment for collecting expert datasets. Therefore, these methods may fail to work when there are slight differences between the learning and expert environments, especially for challenging problems with high-dimensional image observations. However, in real-world scenarios, it is rare to have the chance to collect expert trajectories precisely in the target learning environment. To address this challenge, we propose a novel robust imitation learning approach, where we develop an inverse dynamics state representation learning objective to align the expert environment and the learning environment. With the abstract state representation, we design an effective reward function, which thoroughly measures the similarity between behavior data and expert data not only element-wise, but also from the trajectory level. We conduct extensive experiments to evaluate the proposed approach under various visual perturbations and in diverse visual control tasks. Our approach can achieve a near-expert performance in most environments, and significantly outperforms the state-of-the-art visual IL methods and robust IL methods.

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are unavailable. Predicted protein structures from AI tools (e.g., AlphaFold2) were utilized as alternatives. However, we observed that current practices, which simply employ accurately predicted structures during inference, suffer from notable degradation in prediction accuracy. While similar phenomena have been extensively studied in general fields (e.g., Computer Vision) as model robustness, their impact on protein property prediction remains unexplored. In this paper, we first investigate the reason behind the performance decrease when utilizing predicted structures, attributing it to the structure embedding bias from the perspective of structure representation learning. To study this problem, we identify a Protein 3D Graph Structure Learning Problem for Robust Protein Property Prediction (PGSL-RP3), collect benchmark datasets, and present a protein Structure embedding Alignment Optimization framework (SAO) to mitigate the problem of structure embedding bias between the predicted and experimental protein structures. Extensive experiments have shown that our framework is model-agnostic and effective in improving the property prediction of both predicted structures and experimental structures. The benchmark datasets and codes will be released to benefit the community.

Recently, various distributed strategies for large language model training have been proposed. However, these methods provided limited solutions for the trade-off between memory consumption and communication cost. In this paper, we rethink the impact of memory consumption and communication costs on the training speed of large language models, and propose a memory-communication balanced strategy set Partial Redundancy Optimizer (PaRO). PaRO provides comprehensive options which reduces the amount and frequency of inter-group communication with minor memory redundancy by fine-grained sharding strategy, thereby improving the training efficiency in various training scenarios. Additionally, we propose a Hierarchical Overlapping Ring (HO-Ring) communication topology to enhance communication efficiency between nodes or across switches in large language model training. Our experiments demonstrate that PaRO significantly improves training throughput by 1.19x-2.50x compared to the SOTA method and achieves a near-linear scalability. The HO-Ring algorithm improves communication efficiency by 36.5% compared to the traditional Ring algorithm.

Spatio-temporal predictive learning plays a crucial role in self-supervised learning, with wide-ranging applications across a diverse range of fields. Previous approaches for temporal modeling fall into two categories: recurrent-based and recurrent-free methods. The former, while meticulously processing frames one by one, neglect short-term spatio-temporal information redundancies, leading to inefficiencies. The latter naively stack frames sequentially, overlooking the inherent temporal dependencies. In this paper, we re-examine the two dominant temporal modeling approaches within the realm of spatio-temporal predictive learning, offering a unified perspective. Building upon this analysis, we introduce USTEP (Unified Spatio-TEmporal Predictive learning), an innovative framework that reconciles the recurrent-based and recurrent-free methods by integrating both micro-temporal and macro-temporal scales. Extensive experiments on a wide range of spatio-temporal predictive learning demonstrate that USTEP achieves significant improvements over existing temporal modeling approaches, thereby establishing it as a robust solution for a wide range of spatio-temporal applications., Comment: Under review

Semi-supervised learning (SSL) has witnessed great progress with various improvements in the self-training framework with pseudo labeling. The main challenge is how to distinguish high-quality pseudo labels against the confirmation bias. However, existing pseudo-label selection strategies are limited to pre-defined schemes or complex hand-crafted policies specially designed for classification, failing to achieve high-quality labels, fast convergence, and task versatility simultaneously. To these ends, we propose a Semi-supervised Reward framework (SemiReward) that predicts reward scores to evaluate and filter out high-quality pseudo labels, which is pluggable to mainstream SSL methods in wide task types and scenarios. To mitigate confirmation bias, SemiReward is trained online in two stages with a generator model and subsampling strategy. With classification and regression tasks on 13 standard SSL benchmarks across three modalities, extensive experiments verify that SemiReward achieves significant performance gains and faster convergence speeds upon Pseudo Label, FlexMatch, and Free/SoftMatch. Code and models are available at https://github.com/Westlake-AI/SemiReward., Comment: ICLR 2024 Camera Ready. Preprint V2 (25 pages) with the source code at https://github.com/Westlake-AI/SemiReward

Market making (MM) has attracted significant attention in financial trading owing to its essential function in ensuring market liquidity. With strong capabilities in sequential decision-making, Reinforcement Learning (RL) technology has achieved remarkable success in quantitative trading. Nonetheless, most existing RL-based MM methods focus on optimizing single-price level strategies which fail at frequent order cancellations and loss of queue priority. Strategies involving multiple price levels align better with actual trading scenarios. However, given the complexity that multi-price level strategies involves a comprehensive trading action space, the challenge of effectively training profitable RL agents for MM persists. Inspired by the efficient workflow of professional human market makers, we propose Imitative Market Maker (IMM), a novel RL framework leveraging both knowledge from suboptimal signal-based experts and direct policy interactions to develop multi-price level MM strategies efficiently. The framework start with introducing effective state and action representations adept at encoding information about multi-price level orders. Furthermore, IMM integrates a representation learning unit capable of capturing both short- and long-term market trends to mitigate adverse selection risk. Subsequently, IMM formulates an expert strategy based on signals and trains the agent through the integration of RL and imitation learning techniques, leading to efficient learning. Extensive experimental results on four real-world market datasets demonstrate that IMM outperforms current RL-based market making strategies in terms of several financial criteria. The findings of the ablation study substantiate the effectiveness of the model components.

Humans have the ability to reuse previously learned policies to solve new tasks quickly, and reinforcement learning (RL) agents can do the same by transferring knowledge from source policies to a related target task. Transfer RL methods can reshape the policy optimization objective (optimization transfer) or influence the behavior policy (behavior transfer) using source policies. However, selecting the appropriate source policy with limited samples to guide target policy learning has been a challenge. Previous methods introduce additional components, such as hierarchical policies or estimations of source policies' value functions, which can lead to non-stationary policy optimization or heavy sampling costs, diminishing transfer effectiveness. To address this challenge, we propose a novel transfer RL method that selects the source policy without training extra components. Our method utilizes the Q function in the actor-critic framework to guide policy selection, choosing the source policy with the largest one-step improvement over the current target policy. We integrate optimization transfer and behavior transfer (IOB) by regularizing the learned policy to mimic the guidance policy and combining them as the behavior policy. This integration significantly enhances transfer effectiveness, surpasses state-of-the-art transfer RL baselines in benchmark tasks, and improves final performance and knowledge transferability in continual learning scenarios. Additionally, we show that our optimization transfer technique is guaranteed to improve target policy learning., Comment: 26 pages, 9 figures

Accurately reconstructing a three-dimensional ocean sound speed field (3D SSF) is essential for various ocean acoustic applications, but the sparsity and uncertainty of sound speed samples across a vast ocean region make it a challenging task. To tackle this challenge, a large body of reconstruction methods has been developed, including spline interpolation, matrix/tensor-based completion, and deep neural networks-based reconstruction. However, a principled analysis of their effectiveness in 3D SSF reconstruction is still lacking. This paper performs a thorough analysis of the reconstruction error and highlights the need for a balanced representation model that integrates both expressiveness and conciseness. To meet this requirement, a 3D SSF-tailored tensor deep neural network is proposed, which utilizes tensor computations and deep neural network architectures to achieve remarkable 3D SSF reconstruction. The proposed model not only includes the previous tensor-based SSF representation model as a special case, but also has a natural ability to reject noise. The numerical results using the South China Sea 3D SSF data demonstrate that the proposed method outperforms state-of-the-art methods. The code is available at https://github.com/OceanSTARLab/Tensor-Neural-Network.

Multimodal reasoning is a critical component in the pursuit of artificial intelligence systems that exhibit human-like intelligence, especially when tackling complex tasks. While the chain-of-thought (CoT) technique has gained considerable attention, the existing ScienceQA dataset, which focuses on multimodal scientific questions and explanations from elementary and high school textbooks, lacks a comprehensive evaluation of diverse approaches. To address this gap, we present COCO Multi-Modal Reasoning(COCO-MMR) dataset, a novel dataset that encompasses an extensive collection of open-ended questions, rationales, and answers derived from the large object dataset COCO. Unlike previous datasets that rely on multiple-choice questions, our dataset pioneers the use of open-ended questions in the context of multimodal CoT, introducing a more challenging problem that effectively assesses the reasoning capability of CoT models. Through comprehensive evaluations and detailed analyses, we provide valuable insights and propose innovative techniques, including multi-hop cross-modal attention and sentence-level contrastive learning, to enhance the image and text encoders. Extensive experiments demonstrate the efficacy of the proposed dataset and techniques, offering novel perspectives for advancing multimodal reasoning. The data and code are available at \href{https://github.com/weijingxuan/COCO-MMR}{https://github.com/weijingxuan/COCO-MMR}.

Object localization in general environments is a fundamental part of vision systems. While dominating on the COCO benchmark, recent Transformer-based detection methods are not competitive in diverse domains. Moreover, these methods still struggle to very accurately estimate the object bounding boxes in complex environments. We introduce Cascade-DETR for high-quality universal object detection. We jointly tackle the generalization to diverse domains and localization accuracy by proposing the Cascade Attention layer, which explicitly integrates object-centric information into the detection decoder by limiting the attention to the previous box prediction. To further enhance accuracy, we also revisit the scoring of queries. Instead of relying on classification scores, we predict the expected IoU of the query, leading to substantially more well-calibrated confidences. Lastly, we introduce a universal object detection benchmark, UDB10, that contains 10 datasets from diverse domains. While also advancing the state-of-the-art on COCO, Cascade-DETR substantially improves DETR-based detectors on all datasets in UDB10, even by over 10 mAP in some cases. The improvements under stringent quality requirements are even more pronounced. Our code and models will be released at https://github.com/SysCV/cascade-detr., Comment: Accepted in ICCV 2023. Our code and models will be released at https://github.com/SysCV/cascade-detr

Demonstrations are widely used in Deep Reinforcement Learning (DRL) for facilitating solving tasks with sparse rewards. However, the tasks in real-world scenarios can often have varied initial conditions from the demonstration, which would require additional prior behaviours. For example, consider we are given the demonstration for the task of \emph{picking up an object from an open drawer}, but the drawer is closed in the training. Without acquiring the prior behaviours of opening the drawer, the robot is unlikely to solve the task. To address this, in this paper we propose an Intrinsic Rewards Driven Example-based Control \textbf{(IRDEC)}. Our method can endow agents with the ability to explore and acquire the required prior behaviours and then connect to the task-specific behaviours in the demonstration to solve sparse-reward tasks without requiring additional demonstration of the prior behaviours. The performance of our method outperforms other baselines on three navigation tasks and one robotic manipulation task with sparse rewards. Codes are available at https://github.com/Ricky-Zhu/IRDEC.

Spatio-temporal predictive learning is a learning paradigm that enables models to learn spatial and temporal patterns by predicting future frames from given past frames in an unsupervised manner. Despite remarkable progress in recent years, a lack of systematic understanding persists due to the diverse settings, complex implementation, and difficult reproducibility. Without standardization, comparisons can be unfair and insights inconclusive. To address this dilemma, we propose OpenSTL, a comprehensive benchmark for spatio-temporal predictive learning that categorizes prevalent approaches into recurrent-based and recurrent-free models. OpenSTL provides a modular and extensible framework implementing various state-of-the-art methods. We conduct standard evaluations on datasets across various domains, including synthetic moving object trajectory, human motion, driving scenes, traffic flow and weather forecasting. Based on our observations, we provide a detailed analysis of how model architecture and dataset properties affect spatio-temporal predictive learning performance. Surprisingly, we find that recurrent-free models achieve a good balance between efficiency and performance than recurrent models. Thus, we further extend the common MetaFormers to boost recurrent-free spatial-temporal predictive learning. We open-source the code and models at https://github.com/chengtan9907/OpenSTL., Comment: Accepted by NeurIPS 2023. 33 pages, 17 figures, 19 tables. Under review. For more details, please refer to https://github.com/chengtan9907/OpenSTL