NeurIPS 2024 论文列表

Conference on Neural Information Processing Systems

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4,562篇论文

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    721.6%
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    3828.4%
  • Poster
    4,06489.1%
  • 其他 / 未标注
    441.0%

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Hallo3D: Multi-Modal Hallucination Detection and Mitigation for Consistent 3D Content Generation

Hongbo Wang, Jie Cao, Jin Liu, Xiaoqiang Zhou, Huaibo Huang, Ran He

展开摘要

Recent advancements in 3D content generation have been significant, primarily due to the visual priors provided by pretrained diffusion models. However, large 2D visual models exhibit spatial perception hallucinations, leading to multi-view inconsistency in 3D content generated through Score Distillation Sampling (SDS). This phenomenon, characterized by overfitting to specific views, is referred to as the "Janus Problem". In this work, we investigate the hallucination issues of pretrained models and find that large multimodal models without geometric constraints possess the capability to infer geometric structures, which can be utilized to mitigate multi-view inconsistency. Building on this, we propose a novel tuning-free method. We represent the multimodal inconsistency query information to detect specific hallucinations in 3D content, using this as an enhanced prompt to re-consist the 2D renderings of 3D and jointly optimize the structure and appearance across different views. Our approach does not require 3D training data and can be implemented plug-and-play within existing frameworks. Extensive experiments demonstrate that our method significantly improves the consistency of 3D content generation and specifically mitigates hallucinations caused by pretrained large models, achieving state-of-the-art performance compared to other optimization methods.

Poster
Spectral Editing of Activations for Large Language Model Alignment

Yifu QIU, Zheng Zhao, Yftah Ziser, Anna Korhonen, Edoardo Ponti, Shay B Cohen

展开摘要

Large language models (LLMs) often exhibit undesirable behaviours, such as generating untruthful or biased content. Editing their internal representations has been shown to be effective in mitigating such behaviours on top of the existing alignment methods. We propose a novel inference-time editing method, namely spectral editing of activations (SEA), to project the input representations into directions with maximal covariance with the positive demonstrations (e.g., truthful) while minimising covariance with the negative demonstrations (e.g., hallucinated). We also extend our method to non-linear editing using feature functions. We run extensive experiments on benchmarks concerning truthfulness and bias with six open-source LLMs of different sizes and model families. The results demonstrate the superiority of SEA in effectiveness, generalisation to similar tasks, as well as computation and data efficiency. We also show that SEA editing only has a limited negative impact on other model capabilities.

Poster
SuperDeepFool: a new fast and accurate minimal adversarial attack

Alireza Abdolahpourrostam, Mahed Abroshan, Seyed-Mohsen Moosavi-Dezfooli

展开摘要

Deep neural networks have been known to be vulnerable to adversarial examples, which are inputs that are modified slightly to fool the network into making incorrect predictions. This has led to a significant amount of research on evaluating the robustness of these networks against such perturbations. One particularly important robustness metric is the robustness to minimal $\ell_{2}$ adversarial perturbations. However, existing methods for evaluating this robustness metric are either computationally expensive or not very accurate. In this paper, we introduce a new family of adversarial attacks that strike a balance between effectiveness and computational efficiency. Our proposed attacks are generalizations of the well-known DeepFool (DF) attack, while they remain simple to understand and implement. We demonstrate that our attacks outperform existing methods in terms of both effectiveness and computational efficiency. Our proposed attacks are also suitable for evaluating the robustness of large models and can be used to perform adversarial training (AT) to achieve state-of-the-art robustness to minimal $\ell_{2}$ adversarial perturbations.

Poster
SnapKV: LLM Knows What You are Looking for Before Generation

Yuhong Li, Yingbing Huang, Bowen Yang, Bharat Venkitesh, Acyr Locatelli, Hanchen Ye, Tianle Cai, Patrick Lewis, Deming Chen

展开摘要

Large Language Models (LLMs) have made remarkable progress in processing extensive contexts, with the Key-Value (KV) cache playing a vital role in enhancing their performance. However, the growth of the KV cache in response to increasing input length poses challenges to memory and time efficiency. To address this problem, this paper introduces SnapKV, an innovative and fine-tuning-free approach that efficiently minimizes KV cache size while still delivering comparable performance in real-world applications. We discover that each attention head in the model consistently focuses on specific prompt attention features during generation. Meanwhile, this robust pattern can be obtained from an `observation' window located at the end of the prompts. Drawing on this insight, SnapKV automatically compresses KV caches by selecting clustered important KV positions for each attention head. Our approach significantly reduces the growing computational overhead and memory footprint when processing long input sequences. Specifically, SnapKV achieves a consistent decoding speed with a 3.6x increase in generation speed and an 8.2x enhancement in memory efficiency compared to baseline when processing inputs of 16K tokens. At the same time, it maintains comparable performance to baseline models across 16 long sequence datasets. Moreover, SnapKV can process up to 380K context tokens on a single A100-80GB GPU using HuggingFace implementation with minor changes, exhibiting only a negligible accuracy drop in the Needle-in-a-Haystack test. Further comprehensive studies suggest SnapKV's potential for practical applications.

Poster
CAT: Coordinating Anatomical-Textual Prompts for Multi-Organ and Tumor Segmentation

Zhongzhen Huang, Yankai Jiang, Rongzhao Zhang, Shaoting Zhang, Xiaofan Zhang

展开摘要

Existing promptable segmentation methods in the medical imaging field primarily consider either textual or visual prompts to segment relevant objects, yet they often fall short when addressing anomalies in medical images, like tumors, which may vary greatly in shape, size, and appearance. Recognizing the complexity of medical scenarios and the limitations of textual or visual prompts, we propose a novel dual-prompt schema that leverages the complementary strengths of visual and textual prompts for segmenting various organs and tumors. Specifically, we introduce $\textbf{\textit{CAT}}$, an innovative model that $\textbf{C}$oordinates $\textbf{A}$natomical prompts derived from 3D cropped images with $\textbf{T}$extual prompts enriched by medical domain knowledge. The model architecture adopts a general query-based design, where prompt queries facilitate segmentation queries for mask prediction. To synergize two types of prompts within a unified framework, we implement a ShareRefiner, which refines both segmentation and prompt queries while disentangling the two types of prompts. Trained on a consortium of 10 public CT datasets, $\textbf{\textit{CAT}}$ demonstrates superior performance in multiple segmentation tasks. Further validation on a specialized in-house dataset reveals the remarkable capacity of segmenting tumors across multiple cancer stages. This approach confirms that coordinating multimodal prompts is a promising avenue for addressing complex scenarios in the medical domain.

Poster
AllClear: A Comprehensive Dataset and Benchmark for Cloud Removal in Satellite Imagery

Hangyu Zhou, Chia Hsiang Kao, Cheng Perng Phoo, Utkarsh Mall, Bharath Hariharan, Kavita Bala

展开摘要

Clouds in satellite imagery pose a significant challenge for downstream applications. A major challenge in current cloud removal research is the absence of a comprehensive benchmark and a sufficiently large and diverse training dataset. To address this problem, we introduce the largest public dataset -- *AllClear* for cloud removal, featuring 23,742 globally distributed regions of interest (ROIs) with diverse land-use patterns, comprising 4 million images in total. Each ROI includes complete temporal captures from the year 2022, with (1) multi-spectral optical imagery from Sentinel-2 and Landsat 8/9, (2) synthetic aperture radar (SAR) imagery from Sentinel-1, and (3) auxiliary remote sensing products such as cloud masks and land cover maps. We validate the effectiveness of our dataset by benchmarking performance, demonstrating the scaling law - the PSNR rises from $28.47$ to $33.87$ with $30\times$ more data, and conducting ablation studies on the temporal length and the importance of individual modalities. This dataset aims to provide comprehensive coverage of the Earth's surface and promote better cloud removal results.

Poster
Towards Heterogeneous Long-tailed Learning: Benchmarking, Metrics, and Toolbox

Haohui Wang, Weijie Guan, Jianpeng Chen, Zi Wang, Dawei Zhou

展开摘要

Long-tailed data distributions pose challenges for a variety of domains like e-commerce, finance, biomedical science, and cyber security, where the performance of machine learning models is often dominated by head categories while tail categories are inadequately learned. This work aims to provide a systematic view of long-tailed learning with regard to three pivotal angles: (A1) the characterization of data long-tailedness, (A2) the data complexity of various domains, and (A3) the heterogeneity of emerging tasks. We develop HeroLT, a comprehensive long-tailed learning benchmark integrating 18 state-of-the-art algorithms, 10 evaluation metrics, and 17 real-world datasets across 6 tasks and 4 data modalities. HeroLT with novel angles and extensive experiments (315 in total) enables effective and fair evaluation of newly proposed methods compared with existing baselines on varying dataset types. Finally, we conclude by highlighting the significant applications of long-tailed learning and identifying several promising future directions. For accessibility and reproducibility, we open-source our benchmark HeroLT and corresponding results at https://github.com/SSSKJ/HeroLT.

Poster
Algorithmic Capabilities of Random Transformers

Ziqian Zhong, Jacob Andreas

展开摘要

Trained transformer models have been found to implement interpretable procedures for tasks like arithmetic and associative recall, but little is understood about how the circuits that implement these procedures originate during training. To what extent do they depend on the supervisory signal provided to models, and to what extent are they attributable to behavior already present in models at the beginning of training? To investigate these questions, we investigate what functions can be learned by randomly initialized transformers in which only the embedding layers are optimized, so that the only input--output mappings learnable from data are those already implemented (up to a choice of encoding scheme) by the randomly initialized model. We find that these random transformers can perform a wide range of meaningful algorithmic tasks, including modular arithmetic, in-weights and in-context associative recall, decimal addition, parenthesis balancing, and even some aspects of natural language text generation. Our results indicate that some algorithmic capabilities are present in transformers (and accessible via appropriately structured inputs) even before these models are trained.

Poster
Cost-efficient Knowledge-based Question Answering with Large Language Models

Junnan Dong, Qinggang Zhang, Chuang Zhou, Hao Chen, Daochen Zha, Xiao Huang

展开摘要

Knowledge-based question answering (KBQA) is widely used in many scenarios that necessitate domain knowledge. Large language models (LLMs) bring opportunities to KBQA, while their costs are significantly higher and absence of domain-specific knowledge during pre-training. We are motivated to combine LLMs and prior small models on knowledge graphs (KGMs) for both inferential accuracy and cost saving. However, it remains challenging since accuracy and cost are not readily combined in the optimization as two distinct metrics. It is also laborious for model selection since different models excel in diverse knowledge. To this end, we propose Coke, a novel cost-efficient strategy for KBQA with LLMs, modeled as a tailored multi-armed bandit problem to minimize calls to LLMs within limited budgets. We first formulate the accuracy expectation with a cluster-level Thompson Sampling for either KGMs or LLMs. A context-aware policy is optimized to further distinguish the expert model subject to the question semantics. The overall decision is bounded by the cost regret according to historical expenditure on failures. Extensive experiments showcase the superior performance of Coke, which moves the Pareto frontier with up to 20.89% saving of GPT-4 fees while achieving a 2.74% higher accuracy on the benchmark datasets.

Poster
HumanVLA: Towards Vision-Language Directed Object Rearrangement by Physical Humanoid

Xinyu Xu, Yizheng Zhang, Yong-Lu Li, Lei Han, Cewu Lu

展开摘要

Physical Human-Scene Interaction (HSI) plays a crucial role in numerous applications. However, existing HSI techniques are limited to specific object dynamics and privileged information, which prevents the development of more comprehensive applications. To address this limitation, we introduce HumanVLA for general object rearrangement directed by practical vision and language. A teacher-student framework is utilized to develop HumanVLA. A state-based teacher policy is trained first using goal-conditioned reinforcement learning and adversarial motion prior. Then, it is distilled into a vision-language-action model via behavior cloning. We propose several key insights to facilitate the large-scale learning process. To support general object rearrangement by physical humanoid, we introduce a novel Human-in-the-Room dataset encompassing various rearrangement tasks. Through extensive experiments and analysis, we demonstrate the effectiveness of our approach.

Poster
Wasserstein Distributionally Robust Optimization through the Lens of Structural Causal Models and Individual Fairness

Ahmad Reza Ehyaei, Golnoosh Farnadi, Samira Samadi

展开摘要

In recent years, Wasserstein Distributionally Robust Optimization (DRO) has garnered substantial interest for its efficacy in data-driven decision-making under distributional uncertainty. However, limited research has explored the application of DRO to address individual fairness concerns, particularly when considering causal structures and discrete sensitive attributes in learning problems. To address this gap, we first formulate the DRO problem from the perspectives of causality and individual fairness. We then present the DRO dual formulation as an efficient tool to convert the main problem into a more tractable and computationally efficient form. Next, we characterize the closed form of the approximate worst-case loss quantity as a regularizer, eliminating the max-step in the Min-Max DRO problem. We further estimate the regularizer in more general cases and explore the relationship between DRO and classical robust optimization. Finally, by removing the assumption of a known structural causal model, we provide finite sample error bounds when designing DRO with empirical distributions and estimated causal structures to ensure efficiency and robust learning.

Poster
Near-Optimal Distributed Minimax Optimization under the Second-Order Similarity

Qihao Zhou, Haishan Ye, Luo Luo

展开摘要

This paper considers the distributed convex-concave minimax optimization under the second-order similarity. We propose stochastic variance-reduced optimistic gradient sliding (SVOGS) method, which takes the advantage of the finite-sum structure in the objective by involving the mini-batch client sampling and variance reduction. We prove SVOGS can achieve the $\varepsilon$-duality gap within communication rounds of ${\mathcal O}(\delta D^2/\varepsilon)$, communication complexity of ${\mathcal O}(n+\sqrt{n}\delta D^2/\varepsilon)$, and local gradient calls of $\tilde{\mathcal O}(n+(\sqrt{n}\delta+L)D^2/\varepsilon\log(1/\varepsilon))$, where $n$ is the number of nodes, $\delta$ is the degree of the second-order similarity, $L$ is the smoothness parameter and $D$ is the diameter of the constraint set. We can verify that all of above complexity (nearly) matches the corresponding lower bounds. For the specific $\mu$-strongly-convex-$\mu$-strongly-convex case, our algorithm has the upper bounds on communication rounds, communication complexity, and local gradient calls of $\mathcal O(\delta/\mu\log(1/\varepsilon))$, ${\mathcal O}((n+\sqrt{n}\delta/\mu)\log(1/\varepsilon))$, and $\tilde{\mathcal O}(n+(\sqrt{n}\delta+L)/\mu)\log(1/\varepsilon))$ respectively, which are also nearly tight. Furthermore, we conduct the numerical experiments to show the empirical advantages of proposed method.

Poster
AdaptiveISP: Learning an Adaptive Image Signal Processor for Object Detection

Yujin Wang, Xu Tian yi, Zhang Fan, Tianfan Xue, Jinwei Gu

展开摘要

Image Signal Processors (ISPs) convert raw sensor signals into digital images, which significantly influence the image quality and the performance of downstream computer vision tasks. Designing ISP pipeline and tuning ISP parameters are two key steps for building an imaging and vision system. To find optimal ISP configurations, recent works use deep neural networks as a proxy to search for ISP parameters or ISP pipelines. However, these methods are primarily designed to maximize the image quality, which are sub-optimal in the performance of high-level computer vision tasks such as detection, recognition, and tracking. Moreover, after training, the learned ISP pipelines are mostly fixed at the inference time, whose performance degrades in dynamic scenes. To jointly optimize ISP structures and parameters, we propose AdaptiveISP, a task-driven and scene-adaptive ISP. One key observation is that for the majority of input images, only a few processing modules are needed to improve the performance of downstream recognition tasks, and only a few inputs require more processing. Based on this, AdaptiveISP utilizes deep reinforcement learning to automatically generate an optimal ISP pipeline and the associated ISP parameters to maximize the detection performance. Experimental results show that AdaptiveISP not only surpasses the prior state-of-the-art methods for object detection but also dynamically manages the trade-off between detection performance and computational cost, especially suitable for scenes with large dynamic range variations. Project website: https://openimaginglab.github.io/AdaptiveISP/.

Poster
On Causal Discovery in the Presence of Deterministic Relations

Loka Li, Haoyue Dai, Hanin Al Ghothani, Biwei Huang, Jiji Zhang, Shahar Harel, Isaac Bentwich, Guangyi Chen, Kun Zhang

展开摘要

Many causal discovery methods typically rely on the assumption of independent noise, yet real-life situations often involve deterministic relationships. In these cases, observed variables are represented as deterministic functions of their parental variables without noise. When determinism is present, constraint-based methods encounter challenges due to the violation of the faithfulness assumption. In this paper, we find, supported by both theoretical analysis and empirical evidence, that score-based methods with exact search can naturally address the issues of deterministic relations under rather mild assumptions. Nonetheless, exact score-based methods can be computationally expensive. To enhance the efficiency and scalability, we develop a novel framework for causal discovery that can detect and handle deterministic relations, called Determinism-aware Greedy Equivalent Search (DGES). DGES comprises three phases: (1) identify minimal deterministic clusters (i.e., a minimal set of variables with deterministic relationships), (2) run modified Greedy Equivalent Search (GES) to obtain an initial graph, and (3) perform exact search exclusively on the deterministic cluster and its neighbors. The proposed DGES accommodates both linear and nonlinear causal relationships, as well as both continuous and discrete data types. Furthermore, we investigate the identifiability conditions of DGES. We conducted extensive experiments on both simulated and real-world datasets to show the efficacy of our proposed method.

Poster
Scaling Laws for Reward Model Overoptimization in Direct Alignment Algorithms

Rafael Rafailov, Yaswanth Chittepu, Ryan Park, Harshit Sikchi, Joey Hejna, W. Bradley Knox, Chelsea Finn, Scott Niekum

展开摘要

Reinforcement Learning from Human Feedback (RLHF)has been crucial to the recent success of Large Language Models (LLMs), however it is often a complex and brittle process. In the classical RLHF framework, a reward model is first trained to represent human preferences, which is in turn used by an online reinforcement learning (RL) algorithm to optimized the LLM. A prominent issue with such methods is reward over-optimization or reward hacking, where the performance as measured by the learned proxy reward model increases, but the true model quality plateaus or even deteriorates. Direct Alignment Algorithms (DDAs), such as Direct Preference Optimization (DPO) have emerged as alternatives to the classical RLHF pipeline. However, despite not training a separate proxy reward model or using RL, they still commonly deteriorate from over-optimization. While the so-called reward hacking phenomenon is not well-defined for DAAs, we still uncover similar trends: at higher KL-budgets, DAA algorithms exhibit similar degradation patters to their classic RLHF counterparts. In particular, we find that DAA methods deteriorate not only across a wide range of KL-budgets, but also often before even a single epoch of the dataset is completed. Through extensive empirical experimentation this work formulates the reward over-optimization or hacking problem for DAAs and explores its consequences across objectives, training regimes, and model scales.

Poster
Sharing Key Semantics in Transformer Makes Efficient Image Restoration

Bin Ren, Yawei Li, Jingyun Liang, Rakesh Ranjan, Mengyuan Liu, Rita Cucchiara, Luc Van Gool, Ming-Hsuan Yang, Nicu Sebe

展开摘要

Image Restoration (IR), a classic low-level vision task, has witnessed significant advancements through deep models that effectively model global information. Notably, the emergence of Vision Transformers (ViTs) has further propelled these advancements. When computing, the self-attention mechanism, a cornerstone of ViTs, tends to encompass all global cues, even those from semantically unrelated objects or regions. This inclusivity introduces computational inefficiencies, particularly noticeable with high input resolution, as it requires processing irrelevant information, thereby impeding efficiency. Additionally, for IR, it is commonly noted that small segments of a degraded image, particularly those closely aligned semantically, provide particularly relevant information to aid in the restoration process, as they contribute essential contextual cues crucial for accurate reconstruction. To address these challenges, we propose boosting IR's performance by sharing the key semantics via Transformer for IR (i.e., SemanIR) in this paper. Specifically, SemanIR initially constructs a sparse yet comprehensive key-semantic dictionary within each transformer stage by establishing essential semantic connections for every degraded patch. Subsequently, this dictionary is shared across all subsequent transformer blocks within the same stage. This strategy optimizes attention calculation within each block by focusing exclusively on semantically related components stored in the key-semantic dictionary. As a result, attention calculation achieves linear computational complexity within each window. Extensive experiments across 6 IR tasks confirm the proposed SemanIR's state-of-the-art performance, quantitatively and qualitatively showcasing advancements. The visual results, code, and trained models are available at: https://github.com/Amazingren/SemanIR.

Poster
LoTLIP: Improving Language-Image Pre-training for Long Text Understanding

Wei Wu, Kecheng Zheng, Shuailei Ma, Fan Lu, Yuxin Guo, Yifei Zhang, Wei Chen, Qingpei Guo, Yujun Shen, Zheng-Jun Zha

展开摘要

In this work, we empirically confirm that the key reason causing such an issue is that the training images are usually paired with short captions, leaving certain tokens easily overshadowed by salient tokens. Towards this problem, our initial attempt is to relabel the data with long captions, however, directly learning with which may lead to performance degradation in understanding short text (e.g., in the image classification task). Then, after incorporating corner tokens to aggregate diverse textual information, we manage to help the model catch up to its original level of short text understanding yet greatly enhance its capability of long text understanding. We further look into whether the model can continuously benefit from longer captions and notice a clear trade-off between the performance and the efficiency. Finally, we validate the effectiveness of our approach using a self-constructed large-scale dataset, which consists of 100M long caption oriented text-image pairs. Our method achieves superior performance in long-text-image retrieval tasks. The project page is available at https://wuw2019.github.io/lot-lip.

Poster
RealMAN: A Real-Recorded and Annotated Microphone Array Dataset for Dynamic Speech Enhancement and Localization

Bing Yang, Changsheng Quan, Yabo Wang, Pengyu Wang, Yujie Yang, Ying Fang, Nian Shao, Hui Bu, Xin Xu, Xiaofei Li

展开摘要

The training of deep learning-based multichannel speech enhancement and source localization systems relies heavily on the simulation of room impulse response and multichannel diffuse noise, due to the lack of large-scale real-recorded datasets. However, the acoustic mismatch between simulated and real-world data could degrade the model performance when applying in real-world scenarios. To bridge this simulation-to-real gap, this paper presents a new relatively large-scale Real-recorded and annotated Microphone Array speech&Noise (RealMAN) dataset. The proposed dataset is valuable in two aspects: 1) benchmarking speech enhancement and localization algorithms in real scenarios; 2) offering a substantial amount of real-world training data for potentially improving the performance of real-world applications. Specifically, a 32-channel array with high-fidelity microphones is used for recording. A loudspeaker is used for playing source speech signals (about 35 hours of Mandarin speech). A total of 83.7 hours of speech signals (about 48.3 hours for static speaker and 35.4 hours for moving speaker) are recorded in 32 different scenes, and 144.5 hours of background noise are recorded in 31 different scenes. Both speech and noise recording scenes cover various common indoor, outdoor, semi-outdoor and transportation environments, which enables the training of general-purpose speech enhancement and source localization networks. To obtain the task-specific annotations, speaker location is annotated with an omni-directional fisheye camera by automatically detecting the loudspeaker. The direct-path signal is set as the target clean speech for speech enhancement, which is obtained by filtering the source speech signal with an estimated direct-path propagation filter. Baseline experiments demonstrate that i) compared to using simulated data, the proposed dataset is indeed able to train better speech enhancement and source localization networks; ii) using various sub-arrays of the proposed 32-channel microphone array can successfully train variable-array networks that can be directly used to unseen arrays.

Poster
End-to-End Video Semantic Segmentation in Adverse Weather using Fusion Blocks and Temporal-Spatial Teacher-Student Learning

Xin Yang, YAN WENDING, Michael Bi Mi, Yuan Yuan, Robby T. Tan

展开摘要

Adverse weather conditions can significantly degrade the video frames, causing existing video semantic segmentation methods to produce erroneous predictions. In this work, we target adverse weather conditions and introduce an end-to-end domain adaptation strategy that leverages a fusion block, temporal-spatial teacher-student learning, and a temporal weather degradation augmentation approach. The fusion block integrates temporal information from adjacent frames at the feature level, trained end-to-end, eliminating the need for pretrained optical flow, distinguishing our method from existing approaches. Our teacher-student approach involves two teachers: one focuses on exploring temporal information from adjacent frames, and the other harnesses spatial information from the current frame. Finally, we apply temporal weather degradation augmentation to consecutive frames to more accurately represent adverse weather degradations. Our method achieves a performance of 25.4 and 33.0 mIoU on the adaptation from VIPER and Synthia to MVSS, respectively, representing an improvement of 4.3 and 5.8 mIoU over the existing state-of-the-art method.

Poster
Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Generation

Guillaume Huguet, James Vuckovic, Kilian FATRAS, Eric Thibodeau-Laufer, Pablo Lemos, Riashat Islam, Cheng-Hao Liu, Jarrid Rector-Brooks, Tara Akhound-Sadegh, Michael M. Bronstein, Alexander Tong, Joey Bose

展开摘要

Proteins are essential for almost all biological processes and derive their diverse functions from complex $3 \rm D$ structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive bias of amino acid sequences and introduce FoldFlow++, a novel sequence-conditioned $\text{SE}(3)$-equivariant flow matching model for protein structure generation. FoldFlow++ presents substantial new architectural features over the previous FoldFlow family of models including a protein large language model to encode sequence, a new multi-modal fusion trunk that combines structure and sequence representations, and a geometric transformer based decoder. To increase diversity and novelty of generated samples -- crucial for de-novo drug design -- we train FoldFlow++ at scale on a new dataset that is an order of magnitude larger than PDB datasets of prior works, containing both known proteins in PDB and high-quality synthetic structures achieved through filtering. We further demonstrate the ability to align FoldFlow++ to arbitrary rewards, e.g. increasing secondary structures diversity, by introducing a Reinforced Finetuning (ReFT) objective. We empirically observe that FoldFlow++ outperforms previous state-of-the-art protein structure-based generative models, improving over RFDiffusion in terms of unconditional generation across all metrics including designability, diversity, and novelty across all protein lengths, as well as exhibiting generalization on the task of equilibrium conformation sampling. Finally, we demonstrate that a fine-tuned FoldFlow++ makes progress on challenging conditional design tasks such as designing scaffolds for the VHH nanobody.

Poster