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Deep Learning · Attention Mechanisms

Yunzhe Hu, Difan Zou, Dong Xu

Deep neural networks have long been criticized for being black-box. To unveil the inner workings of modern neural architectures, a recent work proposed an information-theoretic objective function called Sparse Rate Reduction (SRR) and interpreted its unrolled optimization as a Transformer-like model called Coding Rate Reduction Transformer (CRATE). However, the focus of the study was primarily on the basic implementation, and whether this objective is optimized in practice and its causal relationship to generalization remain elusive. Going beyond this study, we derive different implementations by analyzing layer-wise behaviors of CRATE, both theoretically and empirically. To reveal the predictive power of SRR on generalization, we collect a set of model variants induced by varied implementations and hyperparameters and evaluate SRR as a complexity measure based on its correlation with generalization. Surprisingly, we find out that SRR has a positive correlation coefficient and outperforms other baseline measures, such as path-norm and sharpness-based ones. Furthermore, we show that generalization can be improved using SRR as regularization on benchmark image classification datasets. We hope this paper can shed light on leveraging SRR to design principled models and study their generalization ability.

Computer Vision

Kai Chen, Yiyao Ma, Xingyu Lin, Stephen James, Jianshu Zhou, Yun-Hui Liu, Pieter Abbeel, DOU QI

Object pose estimation plays a crucial role in robotic manipulation, however, its practical applicability still suffers from limited generalizability. This paper addresses the challenge of generalizable object pose estimation, particularly focusing on category-level object pose estimation for unseen object categories. Current methods either require impractical instance-level training or are confined to predefined categories, limiting their applicability. We propose VFM-6D, a novel framework that explores harnessing existing vision and language models, to elaborate object pose estimation into two stages: category-level object viewpoint estimation and object coordinate map estimation. Based on the two-stage framework, we introduce a 2D-to-3D feature lifting module and a shape-matching module, both of which leverage pre-trained vision foundation models to improve object representation and matching accuracy. VFM-6D is trained on cost-effective synthetic data and exhibits superior generalization capabilities. It can be applied to both instance-level unseen object pose estimation and category-level object pose estimation for novel categories. Evaluations on benchmark datasets demonstrate the effectiveness and versatility of VFM-6D in various real-world scenarios.

Peizhao Li, Junfeng He, Gang Li, Rachit Bhargava, Shaolei Shen, Nachiappan Valliappan, Youwei Liang, Hongxiang Gu, Venky Ramachandran, Golnaz farhadi 等

Progress in human behavior modeling involves understanding both implicit, early-stage perceptual behavior, such as human attention, and explicit, later-stage behavior, such as subjective preferences or likes. Yet most prior research has focused on modeling implicit and explicit human behavior in isolation; and often limited to a specific type of visual content. We propose UniAR -- a unified model of human attention and preference behavior across diverse visual content. UniAR leverages a multimodal transformer to predict subjective feedback, such as satisfaction or aesthetic quality, along with the underlying human attention or interaction heatmaps and viewing order. We train UniAR on diverse public datasets spanning natural images, webpages, and graphic designs, and achieve SOTA performance on multiple benchmarks across various image domains and behavior modeling tasks. Potential applications include providing instant feedback on the effectiveness of UIs/visual content, and enabling designers and content-creation models to optimize their creation for human-centric improvements.

Multimodal Models

Huanjin Yao, Wenhao Wu, Taojiannan Yang, YuXin Song, Mengxi Zhang, Haocheng Feng, Yifan Sun, Zhiheng Li, Wanli Ouyang, Jingdong Wang

*Do we fully leverage the potential of visual encoder in Multimodal Large Language Models (MLLMs)?* The recent outstanding performance of MLLMs in multimodal understanding has garnered broad attention from both academia and industry. In the current MLLM rat race, the focus seems to be predominantly on the linguistic side. We witness the rise of larger and higher-quality instruction datasets, as well as the involvement of larger-sized LLMs. Yet, scant attention has been directed towards the visual signals utilized by MLLMs, often assumed to be the final high-level features extracted by a frozen visual encoder. In this paper, we introduce the **Dense Connector** - a simple, effective, and plug-and-play vision-language connector that significantly enhances existing MLLMs by leveraging multi-layer visual features, with minimal additional computational overhead. Building on this, we also propose the Efficient Dense Connector, which achieves performance comparable to LLaVA-v1.5 with only 25% of the visual tokens. Furthermore, our model, trained solely on images, showcases remarkable zero-shot capabilities in video understanding as well. Experimental results across various vision encoders, image resolutions, training dataset scales, varying sizes of LLMs (2.7B→70B), and diverse architectures of MLLMs (e.g., LLaVA-v1.5, LLaVA-NeXT and Mini-Gemini) validate the versatility and scalability of our approach, achieving state-of-the-art performance across 19 image and video benchmarks. We hope that this work will provide valuable experience and serve as a basic module for future MLLM development. Code is available at https://github.com/HJYao00/DenseConnector.

Reinforcement Learning · Planning

Long Wei, Peiyan Hu, Ruiqi Feng, Haodong Feng, Yixuan Du, Tao Zhang, Rui Wang, Yue Wang, Zhi-Ming Ma, Tailin Wu

Controlling the evolution of complex physical systems is a fundamental task across science and engineering. Classical techniques suffer from limited applicability or huge computational costs. On the other hand, recent deep learning and reinforcement learning-based approaches often struggle to optimize long-term control sequences under the constraints of system dynamics. In this work, we introduce Diffusion Physical systems Control (DiffPhyCon), a new class of method to address the physical systems control problem. DiffPhyCon excels by simultaneously minimizing both the learned generative energy function and the predefined control objectives across the entire trajectory and control sequence. Thus, it can explore globally and plan near-optimal control sequences. Moreover, we enhance DiffPhyCon with prior reweighting, enabling the discovery of control sequences that significantly deviate from the training distribution. We test our method on three tasks: 1D Burgers' equation, 2D jellyfish movement control, and 2D high-dimensional smoke control, where our generated jellyfish dataset is released as a benchmark for complex physical system control research. Our method outperforms widely applied classical approaches and state-of-the-art deep learning and reinforcement learning methods. Notably, DiffPhyCon unveils an intriguing fast-close-slow-open pattern observed in the jellyfish, aligning with established findings in the field of fluid dynamics. The project website, jellyfish dataset, and code can be found at https://github.com/AI4Science-WestlakeU/diffphycon.

Computer Vision

Qinqian Lei, Bo Wang, Robby Tan

Detecting Human-Object Interactions (HOI) in zero-shot settings, where models must handle unseen classes, poses significant challenges. Existing methods that rely on aligning visual encoders with large Vision-Language Models (VLMs) to tap into the extensive knowledge of VLMs, require large, computationally expensive models and encounter training difficulties. Adapting VLMs with prompt learning offers an alternative to direct alignment. However, fine-tuning on task-specific datasets often leads to overfitting to seen classes and suboptimal performance on unseen classes, due to the absence of unseen class labels. To address these challenges, we introduce a novel prompt learning-based framework for Efficient Zero-Shot HOI detection (EZ-HOI). First, we introduce Large Language Model (LLM) and VLM guidance for learnable prompts, integrating detailed HOI descriptions and visual semantics to adapt VLMs to HOI tasks. However, because training datasets contain seen-class labels alone, fine-tuning VLMs on such datasets tends to optimize learnable prompts for seen classes instead of unseen ones. Therefore, we design prompt learning for unseen classes using information from related seen classes, with LLMs utilized to highlight the differences between unseen and related seen classes. Quantitative evaluations on benchmark datasets demonstrate that our EZ-HOI achieves state-of-the-art performance across various zero-shot settings with only 10.35\% to 33.95\% of the trainable parameters compared to existing methods. Code is available at https://github.com/ChelsieLei/EZ-HOI.

Time Series

Weiwei Ye, Songgaojun Deng, Qiaosha Zou, Ning Gui

Time series forecasting typically needs to address non-stationary data with evolving trend and seasonal patterns. To address the non-stationarity, reversible instance normalization has been recently proposed to alleviate impacts from the trend with certain statistical measures, e.g., mean and variance. Although they demonstrate improved predictive accuracy, they are limited to expressing basic trends and are incapable of handling seasonal patterns. To address this limitation, this paper proposes a new instance normalization solution, called frequency adaptive normalization (FAN), which extends instance normalization in handling both dynamic trend and seasonal patterns. Specifically, we employ the Fourier transform to identify instance-wise predominant frequent components that cover most non-stationary factors. Furthermore, the discrepancy of those frequency components between inputs and outputs is explicitly modeled as a prediction task with a simple MLP model. FAN is a model-agnostic method that can be applied to arbitrary predictive backbones. We instantiate FAN on four widely used forecasting models as the backbone and evaluate their prediction performance improvements on eight benchmark datasets. FAN demonstrates significant performance advancement, achieving 7.76\%$\sim$37.90\% average improvements in MSE. Our code is publicly available at http://github.com/icannotnamemyself/FAN.

Language · Knowledge

Haoran Luo, Haihong E, Yuhao Yang, Tianyu Yao, Yikai Guo, Zichen Tang, Wentai Zhang, Shiyao Peng, Kaiyang Wan, Meina Song 等

Beyond traditional binary relational facts, n-ary relational knowledge graphs (NKGs) are comprised of n-ary relational facts containing more than two entities, which are closer to real-world facts with broader applications. However, the construction of NKGs remains at a coarse-grained level, which is always in a single schema, ignoring the order and variable arity of entities. To address these restrictions, we propose Text2NKG, a novel fine-grained n-ary relation extraction framework for n-ary relational knowledge graph construction. We introduce a span-tuple classification approach with hetero-ordered merging and output merging to accomplish fine-grained n-ary relation extraction in different arity. Furthermore, Text2NKG supports four typical NKG schemas: hyper-relational schema, event-based schema, role-based schema, and hypergraph-based schema, with high flexibility and practicality. The experimental results demonstrate that Text2NKG achieves state-of-the-art performance in F1 scores on the fine-grained n-ary relation extraction benchmark. Our code and datasets are publicly available.

Peter Tong, Ellis Brown, Penghao Wu, Sanghyun Woo, Adithya Jairam Vedagiri IYER, Sai Charitha Akula, Shusheng Yang, Jihan Yang, Manoj Middepogu, Ziteng Wang 等

We introduce Cambrian-1, a family of multimodal LLMs (MLLMs) designed with a vision-centric approach. While stronger language models can enhance multimodal capabilities, the design choices for vision components are often insufficiently explored and disconnected from visual representation learning research. This gap hinders accurate sensory grounding in real-world scenarios. Our study uses LLMs and visual instruction tuning as an interface to evaluate various visual representations, offering new insights into different models and architectures—self-supervised, strongly supervised, or combinations thereof—based on experiments with over 15 vision models. We critically examine existing MLLM benchmarks, addressing the difficulties involved in consolidating and interpreting results from various tasks. To further improve visual grounding, we propose spatial vision aggregator (SVA), a dynamic and spatially-aware connector that integrates vision features with LLMs while reducing the number of tokens. Additionally, we discuss the curation of high-quality visual instruction-tuning data from publicly available sources, emphasizing the importance of distribution balancing. Collectively, Cambrian-1 not only achieves state-of-the-art performances but also serves as a comprehensive, open cookbook for instruction-tuned MLLMs. We provide model weights, code, supporting tools, datasets, and detailed instruction-tuning and evaluation recipes. We hope our release will inspire and accelerate advancements in multimodal systems and visual representation learning.

Multimodal Models

Peter Tong, Ellis Brown, Penghao Wu, Sanghyun Woo, Adithya Jairam Vedagiri IYER, Sai Charitha Akula, Shusheng Yang, Jihan Yang, Manoj Middepogu, Ziteng Wang 等

We introduce Cambrian-1, a family of multimodal LLMs (MLLMs) designed with a vision-centric approach. While stronger language models can enhance multimodal capabilities, the design choices for vision components are often insufficiently explored and disconnected from visual representation learning research. This gap hinders accurate sensory grounding in real-world scenarios. Our study uses LLMs and visual instruction tuning as an interface to evaluate various visual representations, offering new insights into different models and architectures—self-supervised, strongly supervised, or combinations thereof—based on experiments with over 15 vision models. We critically examine existing MLLM benchmarks, addressing the difficulties involved in consolidating and interpreting results from various tasks. To further improve visual grounding, we propose spatial vision aggregator (SVA), a dynamic and spatially-aware connector that integrates vision features with LLMs while reducing the number of tokens. Additionally, we discuss the curation of high-quality visual instruction-tuning data from publicly available sources, emphasizing the importance of distribution balancing. Collectively, Cambrian-1 not only achieves state-of-the-art performances but also serves as a comprehensive, open cookbook for instruction-tuned MLLMs. We provide model weights, code, supporting tools, datasets, and detailed instruction-tuning and evaluation recipes. We hope our release will inspire and accelerate advancements in multimodal systems and visual representation learning.

Generative Models · Diffusion models

Jie Zhu, Yixiong Chen, Mingyu Ding, Ping Luo, Leye Wang, Jingdong Wang

Text-to-image diffusion has attracted vast attention due to its impressive image-generation capabilities. However, when it comes to human-centric text-to-image generation, particularly in the context of faces and hands, the results often fall short of naturalness due to insufficient training priors. We alleviate the issue in this work from two perspectives. 1) From the data aspect, we carefully collect a human-centric dataset comprising over one million high-quality human-in-the-scene images and two specific sets of close-up images of faces and hands. These datasets collectively provide a rich prior knowledge base to enhance the human-centric image generation capabilities of the diffusion model. 2) On the methodological front, we propose a simple yet effective method called Mixture of Low-rank Experts (MoLE) by considering low-rank modules trained on close-up hand and face images respectively as experts. This concept draws inspiration from our observation of low-rank refinement, where a low-rank module trained by a customized close-up dataset has the potential to enhance the corresponding image part when applied at an appropriate scale. To validate the superiority of MoLE in the context of human-centric image generation compared to state-of-the-art, we construct two benchmarks and perform evaluations with diverse metrics and human studies. Datasets, model, and code are released at https://sites.google.com/view/mole4diffuser/.

Mingze Wang, Jinbo Wang, Haotian He, Zilin Wang, Guanhua Huang, Feiyu Xiong, Zhiyu li, Weinan E, Lei Wu

In this work, we propose an Implicit Regularization Enhancement (IRE) framework to accelerate the discovery of flat solutions in deep learning, thereby improving generalization and convergence. Specifically, IRE decouples the dynamics of flat and sharp directions, which boosts the sharpness reduction along flat directions while maintaining the training stability in sharp directions. We show that IRE can be practically incorporated with *generic base optimizers* without introducing significant computational overload. Experiments show that IRE consistently improves the generalization performance for image classification tasks across a variety of benchmark datasets (CIFAR-10/100, ImageNet) and models (ResNets and ViTs). Surprisingly, IRE also achieves a $2\times$ *speed-up* compared to AdamW in the pre-training of Llama models (of sizes ranging from 60M to 229M) on datasets including Wikitext-103, Minipile, and Openwebtext. Moreover, we provide theoretical guarantees, showing that IRE can substantially accelerate the convergence towards flat minima in Sharpness-aware Minimization (SAM).

Causality

Kai Helli, David Schnurr, Noah Hollmann, Samuel Müller, Frank Hutter

While most ML models expect independent and identically distributed data, this assumption is often violated in real-world scenarios due to distribution shifts, resulting in the degradation of machine learning model performance. Until now, no tabular method has consistently outperformed classical supervised learning, which ignores these shifts. To address temporal distribution shifts, we present Drift-Resilient TabPFN, a fresh approach based on In-Context Learning with a Prior-Data Fitted Network that learns the learning algorithm itself: it accepts the entire training dataset as input and makes predictions on the test set in a single forward pass. Specifically, it learns to approximate Bayesian inference on synthetic datasets drawn from a prior that specifies the model's inductive bias. This prior is based on structural causal models (SCM), which gradually shift over time. To model shifts of these causal models, we use a secondary SCM, that specifies changes in the primary model parameters. The resulting Drift-Resilient TabPFN can be applied to unseen data, runs in seconds on small to moderately sized datasets and needs no hyperparameter tuning. Comprehensive evaluations across 18 synthetic and real-world datasets demonstrate large performance improvements over a wide range of baselines, such as XGB, CatBoost, TabPFN, and applicable methods featured in the Wild-Time benchmark. Compared to the strongest baselines, it improves accuracy from 0.688 to 0.744 and ROC AUC from 0.786 to 0.832 while maintaining stronger calibration. This approach could serve as significant groundwork for further research on out-of-distribution prediction.

Computer Vision · Image Generation

Tianwei Yin, Michaël Gharbi, Taesung Park, Richard Zhang, Eli Shechtman, Fredo Durand, Bill Freeman

Recent approaches have shown promises distilling expensive diffusion models into efficient one-step generators.Amongst them, Distribution Matching Distillation (DMD) produces one-step generators that match their teacher in distribution, i.e., the distillation process does not enforce a one-to-one correspondence with the sampling trajectories of their teachers.However, to ensure stable training in practice, DMD requires an additional regression loss computed using a large set of noise--image pairs, generated by the teacher with many steps of a deterministic sampler.This is not only computationally expensive for large-scale text-to-image synthesis, but it also limits the student's quality, tying it too closely to the teacher's original sampling paths.We introduce DMD2, a set of techniques that lift this limitation and improve DMD training.First, we eliminate the regression loss and the need for expensive dataset construction.We show that the resulting instability is due to the "fake" critic not estimating the distribution of generated samples with sufficient accuracy and propose a two time-scale update rule as a remedy.Second, we integrate a GAN loss into the distillation procedure, discriminating between generated samples and real images.This lets us train the student model on real data, thus mitigating the imperfect "real" score estimation from the teacher model, and thereby enhancing quality.Third, we introduce a new training procedure that enables multi-step sampling in the student, andaddresses the training--inference input mismatch of previous work, by simulating inference-time generator samples during training. Taken together, our improvements set new benchmarks in one-step image generation, with FID scores of 1.28 on ImageNet-64×64 and 8.35 on zero-shot COCO 2014, surpassing the original teacher despite a 500X reduction in inference cost.Further, we show our approach can generate megapixel images by distilling SDXL, demonstrating exceptional visual quality among few-step methods, and surpassing the teacher. We release our code and pretrained models.

Computer Vision · Image Generation

Tianwei Yin, Michaël Gharbi, Taesung Park, Richard Zhang, Eli Shechtman, Fredo Durand, Bill Freeman

Recent approaches have shown promises distilling expensive diffusion models into efficient one-step generators.Amongst them, Distribution Matching Distillation (DMD) produces one-step generators that match their teacher in distribution, i.e., the distillation process does not enforce a one-to-one correspondence with the sampling trajectories of their teachers.However, to ensure stable training in practice, DMD requires an additional regression loss computed using a large set of noise--image pairs, generated by the teacher with many steps of a deterministic sampler.This is not only computationally expensive for large-scale text-to-image synthesis, but it also limits the student's quality, tying it too closely to the teacher's original sampling paths.We introduce DMD2, a set of techniques that lift this limitation and improve DMD training.First, we eliminate the regression loss and the need for expensive dataset construction.We show that the resulting instability is due to the "fake" critic not estimating the distribution of generated samples with sufficient accuracy and propose a two time-scale update rule as a remedy.Second, we integrate a GAN loss into the distillation procedure, discriminating between generated samples and real images.This lets us train the student model on real data, thus mitigating the imperfect "real" score estimation from the teacher model, and thereby enhancing quality.Third, we introduce a new training procedure that enables multi-step sampling in the student, andaddresses the training--inference input mismatch of previous work, by simulating inference-time generator samples during training. Taken together, our improvements set new benchmarks in one-step image generation, with FID scores of 1.28 on ImageNet-64×64 and 8.35 on zero-shot COCO 2014, surpassing the original teacher despite a 500X reduction in inference cost.Further, we show our approach can generate megapixel images by distilling SDXL, demonstrating exceptional visual quality among few-step methods, and surpassing the teacher. We release our code and pretrained models.

Huy Hoang, Tien Mai, Pradeep Varakantham

We focus on offline imitation learning (IL), which aims to mimic an expert's behavior using demonstrations without any interaction with the environment. One of the main challenges in offline IL is the limited support of expert demonstrations, which typically cover only a small fraction of the state-action space. While it may not be feasible to obtain numerous expert demonstrations, it is often possible to gather a larger set of sub-optimal demonstrations. For example, in treatment optimization problems, there are varying levels of doctor treatments available for different chronic conditions. These range from treatment specialists and experienced general practitioners to less experienced general practitioners. Similarly, when robots are trained to imitate humans in routine tasks, they might learn from individuals with different levels of expertise and efficiency. In this paper, we propose an offline IL approach that leverages the larger set of sub-optimal demonstrations while effectively mimicking expert trajectories. Existing offline IL methods based on behavior cloning or distribution matching often face issues such as overfitting to the limited set of expert demonstrations or inadvertently imitating sub-optimal trajectories from the larger dataset. Our approach, which is based on inverse soft-Q learning, learns from both expert and sub-optimal demonstrations. It assigns higher importance (through learned weights) to aligning with expert demonstrations and lower importance to aligning with sub-optimal ones. A key contribution of our approach, called SPRINQL, is transforming the offline IL problem into a convex optimization over the space of Q functions. Through comprehensive experimental evaluations, we demonstrate that the SPRINQL algorithm achieves state-of-the-art (SOTA) performance on offline IL benchmarks. Code is available at https://github.com/hmhuy0/SPRINQL .

Multimodal Models

Mengxi Zhang, Wenhao Wu, Yu Lu, YuXin Song, KANG RONG, Huanjin Yao, Jianbo Zhao, Fanglong Liu, Haocheng Feng, Jingdong Wang 等

Current multimodal Large Language Models (MLLMs) suffer from ''hallucination'', occasionally generating responses that are not grounded in the input images. To tackle this challenge, one promising path is to utilize reinforcement learning from human feedback (RLHF), which steers MLLMs towards learning superior responses while avoiding inferior ones. We rethink the common practice of using binary preferences (*i.e.*, superior, inferior), and find that adopting multi-level preferences (*e.g.*, superior, medium, inferior) is better for two benefits: 1) It narrows the gap between adjacent levels, thereby encouraging MLLMs to discern subtle differences. 2) It further integrates cross-level comparisons (beyond adjacent-level comparisons), thus providing a broader range of comparisons with hallucination examples. To verify our viewpoint, we present the Automated Multi-level Preference (**AMP**) framework for MLLMs. To facilitate this framework, we first develop an automated dataset generation pipeline that provides high-quality multi-level preference datasets without any human annotators. Furthermore, we design the Multi-level Direct Preference Optimization (MDPO) algorithm to robustly conduct complex multi-level preference learning. Additionally, we propose a new hallucination benchmark, MRHal-Bench. Extensive experiments across public hallucination and general benchmarks, as well as our MRHal-Bench, demonstrate the effectiveness of our proposed method. Code is available at https://github.com/takomc/amp.

Trustworthy Machine Learning

Weilin Lin, Li Liu, Shaokui Wei, Jianze Li, Hui Xiong

The security threat of backdoor attacks is a central concern for deep neural networks (DNNs). Recently, without poisoned data, unlearning models with clean data and then learning a pruning mask have contributed to backdoor defense. Additionally, vanilla fine-tuning with those clean data can help recover the lost clean accuracy. However, the behavior of clean unlearning is still under-explored, and vanilla fine-tuning unintentionally induces back the backdoor effect. In this work, we first investigate model unlearning from the perspective of weight changes and gradient norms, and find two interesting observations in the backdoored model: 1) the weight changes between poison and clean unlearning are positively correlated, making it possible for us to identify the backdoored-related neurons without using poisoned data; 2) the neurons of the backdoored model are more active (*i.e.*, larger gradient norm) than those in the clean model, suggesting the need to suppress the gradient norm during fine-tuning. Then, we propose an effective two-stage defense method. In the first stage, an efficient *Neuron Weight Change (NWC)-based Backdoor Reinitialization* is proposed based on observation 1). In the second stage, based on observation 2), we design an *Activeness-Aware Fine-Tuning* to replace the vanilla fine-tuning. Extensive experiments, involving eight backdoor attacks on three benchmark datasets, demonstrate the superior performance of our proposed method compared to recent state-of-the-art backdoor defense approaches. The code is available at https://github.com/linweiii/TSBD.git.

Deep Learning · Representation Learning

Tao Yang, Cuiling Lan, Yan Lu, Nanning Zheng

Disentangled representation learning strives to extract the intrinsic factors within the observed data. Factoring these representations in an unsupervised manner is notably challenging and usually requires tailored loss functions or specific structural designs. In this paper, we introduce a new perspective and framework, demonstrating that diffusion models with cross-attention itself can serve as a powerful inductive bias to facilitate the learning of disentangled representations. We propose to encode an image into a set of concept tokens and treat them as the condition of the latent diffusion model for image reconstruction, where cross attention over the concept tokens is used to bridge the encoder and the U-Net of the diffusion model. We analyze that the diffusion process inherently possesses the time-varying information bottlenecks. Such information bottlenecks and cross attention act as strong inductive biases for promoting disentanglement. Without any regularization term in the loss function, this framework achieves superior disentanglement performance on the benchmark datasets, surpassing all previous methods with intricate designs. We have conducted comprehensive ablation studies and visualization analyses, shedding a light on the functioning of this model. We anticipate that our findings will inspire more investigation on exploring diffusion model for disentangled representation learning towards more sophisticated data analysis and understanding.

Computational Biology

LE ZHANG, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun

Deep learning models like AlphaFold2 have revolutionized protein structure prediction, achieving unprecedented accuracy. However, the dependence on robust multiple sequence alignments (MSAs) continues to pose a challenge, especially for proteins that lack a wealth of homologous sequences. To overcome this limitation, we introduce MSA-Generator, a self-supervised generative protein language model. Trained on a sequence-to-sequence task using an automatically constructed dataset, MSA-Generator employs protein-specific attention mechanisms to harness large-scale protein databases, generating virtual MSAs that enrich existing ones and boost prediction accuracy. Our experiments on CASP14 and CASP15 benchmarks reveal significant improvements in LDDT scores, particularly for complex and challenging sequences, enhancing the performance of both AlphaFold2 and RoseTTAFold. The code is released at \url{https://github.com/lezhang7/MSAGen}.