NeurIPS 2024 Papers

Conference on Neural Information Processing Systems

Decision breakdown

4,562papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Oral
    721.6%
  • Spotlight
    3828.4%
  • Poster
    4,06489.1%
  • Other / unlabeled
    441.0%

Browse all papers

Key-Grid: Unsupervised 3D Keypoints Detection using Grid Heatmap Features

Chengkai Hou, Zhengrong Xue, Bingyang Zhou, Jinghan Ke, Lin Shao, Huazhe Xu

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Detecting 3D keypoints with semantic consistency is widely used in many scenarios such as pose estimation, shape registration and robotics. Currently, most unsupervised 3D keypoint detection methods focus on the rigid-body objects. However, when faced with deformable objects, the keypoints they identify do not preserve semantic consistency well. In this paper, we introduce an innovative unsupervised keypoint detector Key-Grid for both the rigid-body and deformable objects, which is an autoencoder framework. The encoder predicts keypoints and the decoder utilizes the generated keypoints to reconstruct the objects. Unlike previous work, we leverage the identified keypoint in formation to form a 3D grid feature heatmap called grid heatmap, which is used in the decoder section. Grid heatmap is a novel concept that represents the latent variables for grid points sampled uniformly in the 3D cubic space, where these variables are the shortest distance between the grid points and the “skeleton” connected by keypoint pairs. Meanwhile, we incorporate the information from each layer of the encoder into the decoder section. We conduct an extensive evaluation of Key-Grid on a list of benchmark datasets. Key-Grid achieves the state-of-the-art performance on the semantic consistency and position accuracy of keypoints. Moreover, we demonstrate the robustness of Key-Grid to noise and downsampling. In addition, we achieve SE-(3) invariance of keypoints though generalizing Key-Grid to a SE(3)-invariant backbone.

Poster
ArkVale: Efficient Generative LLM Inference with Recallable Key-Value Eviction

Renze Chen, Zhuofeng Wang, Beiquan Cao, Tong Wu, Size Zheng, Xiuhong Li, Xuechao Wei, Shengen Yan, Meng Li, Yun Liang

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Large Language Models (LLMs) are widely used in today's tasks of natural language processing. To support applications like multi-turn chats, document understanding, and content generation, models with long context lengths are growing in importance. However, managing long contexts brings substantial challenges due to the expansion of key-value cache (KV cache). Longer KV cache requires larger memory, limiting the batch-size thus decreasing throughput. Also, computing attention over long KV cache incurs more memory access, hurting the end-to-end latency. Prior works find that it is sufficient to use only the recent and high-impact tokens for attention computation, allowing the eviction of less vital tokens to shrink cache size. Nonetheless, we observe a dynamic shift in token importance across different decoding steps. Tokens initially evicted might regain importance after certain decoding steps. To address this, we propose ArkVale, a page-based KV cache manager that can recognize and recall currently important tokens evicted before. We asynchronously copy the filled page into external memory (e.g., CPU memory) as backup and summarize it into a much smaller digest by constructing the bounding-volume of its keys. Before attention computation, we measure all pages' importance based on their digests, recall the important ones, evict the unimportant ones, and select the top-ranked pages for attention computation. Experiment results show that ArkVale performs well on various long context tasks with negligible accuracy loss under 2k$\sim$4k cache budget and can improve decoding latency to $2.2\times$ and batching throughput to $4.6\times$ because it applies attention on only a small subset of pages and reduce per-sample memory usage of KV cache.

Poster
Rethinking Weight Decay for Robust Fine-Tuning of Foundation Models

Junjiao Tian, Chengyue Huang, Zsolt Kira

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Modern optimizers such as AdamW, equipped with momentum and adaptive learning rate, are designed to escape local minima and explore the vast parameter space. This exploration is beneficial for finding good loss basins when training from scratch. It is not necessarily ideal when resuming from a powerful foundation model because it can lead to large deviations from the pre-trained initialization and, consequently, worse robustness and generalization. At the same time, strong regularization on all parameters can lead to under-fitting. We hypothesize that selectively regularizing the parameter space is the key to fitting and retraining the pre-trained knowledge. This paper proposes a new weight decay technique, Selective Projection Decay (SPD), that selectively imposes a strong penalty on certain layers while allowing others to change freely. Intuitively, SPD expands and contracts the parameter search space for layers with consistent and inconsistent loss reduction, respectively. Experimentally, when equipped with SPD, Adam consistently provides better in-distribution generalization and out-of-distribution robustness performance on multiple popular vision and language benchmarks.

Poster
Magnet: We Never Know How Text-to-Image Diffusion Models Work, Until We Learn How Vision-Language Models Function

Chenyi Zhuang, Ying Hu, Pan Gao

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Text-to-image diffusion models particularly Stable Diffusion, have revolutionized the field of computer vision. However, the synthesis quality often deteriorates when asked to generate images that faithfully represent complex prompts involving multiple attributes and objects. While previous studies suggest that blended text embeddings lead to improper attribute binding, few have explored this in depth. In this work, we critically examine the limitations of the CLIP text encoder in understanding attributes and investigate how this affects diffusion models. We discern a phenomenon of attribute bias in the text space and highlight a contextual issue in padding embeddings that entangle different concepts. We propose Magnet, a novel training-free approach to tackle the attribute binding problem. We introduce positive and negative binding vectors to enhance disentanglement, further with a neighbor strategy to increase accuracy. Extensive experiments show that Magnet significantly improves synthesis quality and binding accuracy with negligible computational cost, enabling the generation of unconventional and unnatural concepts.

Poster
Is Cross-validation the Gold Standard to Estimate Out-of-sample Model Performance?

Garud Iyengar, Henry Lam, Tianyu Wang

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Cross-Validation (CV) is the default choice for estimate the out-of-sample performance of machine learning models. Despite its wide usage, their statistical benefits have remained half-understood, especially in challenging nonparametric regimes. In this paper we fill in this gap and show that, in terms of estimating the out-of-sample performances, for a wide spectrum of models, CV does not statistically outperform the simple ``plug-in'' approach where one reuses training data for testing evaluation. Specifically, in terms of both the asymptotic bias and coverage accuracy of the associated interval for out-of-sample evaluation, $K$-fold CV provably cannot outperform plug-in regardless of the rate at which the parametric or nonparametric models converge. Leave-one-out CV can have a smaller bias as compared to plug-in; however, this bias improvement is negligible compared to the variability of the evaluation, and in some important cases leave-one-out again does not outperform plug-in once this variability is taken into account. We obtain our theoretical comparisons via a novel higher-order Taylor analysis that dissects the limit theorems of testing evaluations, which applies to model classes that are not amenable to previously known sufficient conditions. Our numerical results demonstrate that plug-in performs indeed no worse than CV in estimating model performance across a wide range of examples.

Poster
Goal Conditioned Reinforcement Learning for Photo Finishing Tuning

Jiarui Wu, Yujin Wang, Lingen Li, Zhang Fan, Tianfan Xue

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Photo finishing tuning aims to automate the manual tuning process of the photo finishing pipeline, like Adobe Lightroom or Darktable. Previous works either use zeroth-order optimization, which is slow when the set of parameters increases, or rely on a differentiable proxy of the target finishing pipeline, which is hard to train. To overcome these challenges, we propose a novel goal-conditioned reinforcement learning framework for efficiently tuning parameters using a goal image as a condition. Unlike previous approaches, our tuning framework does not rely on any proxy and treats the photo finishing pipeline as a black box. Utilizing a trained reinforcement learning policy, it can efficiently find the desired set of parameters within just 10 queries, while optimization based approaches normally take 200 queries. Furthermore, our architecture utilizes a goal image to guide the iterative tuning of pipeline parameters, allowing for flexible conditioning on pixel-aligned target images, style images, or any other visually representable goals. We conduct detailed experiments on photo finishing tuning and photo stylization tuning tasks, demonstrating the advantages of our method.

Poster
Improving Robustness of 3D Point Cloud Recognition from a Fourier Perspective

Yibo Miao, Yinpeng Dong, Jinlai Zhang, Lijia Yu, Xiao Yang, Xiao-Shan Gao

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Although 3D point cloud recognition has achieved substantial progress on standard benchmarks, the typical models are vulnerable to point cloud corruptions, leading to security threats in real-world applications. To improve the corruption robustness, various data augmentation methods have been studied, but they are mainly limited to the spatial domain. As the point cloud has low information density and significant spatial redundancy, it is challenging to analyze the effects of corruptions. In this paper, we focus on the frequency domain to observe the underlying structure of point clouds and their corruptions. Through graph Fourier transform (GFT), we observe a correlation between the corruption robustness of point cloud recognition models and their sensitivity to different frequency bands, which is measured by the GFT spectrum of the model’s Jacobian matrix. To reduce the sensitivity and improve the corruption robustness, we propose Frequency Adversarial Training (FAT) that adopts frequency-domain adversarial examples as data augmentation to train robust point cloud recognition models against corruptions. Theoretically, we provide a guarantee of FAT on its out-of-distribution generalization performance. Empirically, we conduct extensive experiments with various network architectures to validate the effectiveness of FAT, which achieves the new state-of-the-art results.

Poster
MetaUAS: Universal Anomaly Segmentation with One-Prompt Meta-Learning

Bin-Bin Gao

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Zero- and few-shot visual anomaly segmentation relies on powerful vision-language models that detect unseen anomalies using manually designed textual prompts. However, visual representations are inherently independent of language. In this paper, we explore the potential of a pure visual foundation model as an alternative to widely used vision-language models for universal visual anomaly segmentation. We present a novel paradigm that unifies anomaly segmentation into change segmentation. This paradigm enables us to leverage large-scale synthetic image pairs, featuring object-level and local region changes, derived from existing image datasets, which are independent of target anomaly datasets. We propose a one-prompt Meta-learning framework for Universal Anomaly Segmentation (MetaUAS) that is trained on this synthetic dataset and then generalizes well to segment any novel or unseen visual anomalies in the real world. To handle geometrical variations between prompt and query images, we propose a soft feature alignment module that bridges paired-image change perception and single-image semantic segmentation. This is the first work to achieve universal anomaly segmentation using a pure vision model without relying on special anomaly detection datasets and pre-trained visual-language models. Our method effectively and efficiently segments any anomalies with only one normal image prompt and enjoys training-free without guidance from language. Our MetaUAS significantly outperforms previous zero-shot, few-shot, and even full-shot anomaly segmentation methods. Code and Models: https://github.com/gaobb/MetaUAS.

Poster
ZOPP: A Framework of Zero-shot Offboard Panoptic Perception for Autonomous Driving

Tao MA, Hongbin Zhou, Qiusheng Huang, Xuemeng Yang, Jianfei Guo, Bo Zhang, Min Dou, Yu Qiao, Botian Shi, Hongsheng Li

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Offboard perception aims to automatically generate high-quality 3D labels for autonomous driving (AD) scenes. Existing offboard methods focus on 3D object detection with closed-set taxonomy and fail to match human-level recognition capability on the rapidly evolving perception tasks. Due to heavy reliance on human labels and the prevalence of data imbalance and sparsity, a unified framework for offboard auto-labeling various elements in AD scenes that meets the distinct needs of perception tasks is not being fully explored. In this paper, we propose a novel multi-modal Zero-shot Offboard Panoptic Perception (ZOPP) framework for autonomous driving scenes. ZOPP integrates the powerful zero-shot recognition capabilities of vision foundation models and 3D representations derived from point clouds. To the best of our knowledge, ZOPP represents a pioneering effort in the domain of multi-modal panoptic perception and auto labeling for autonomous driving scenes. We conduct comprehensive empirical studies and evaluations on Waymo open dataset to validate the proposed ZOPP on various perception tasks. To further explore the usability and extensibility of our proposed ZOPP, we also conduct experiments in downstream applications. The results further demonstrate the great potential of our ZOPP for real-world scenarios. The source code will be released at \url{https://github.com/PJLab-ADG/ZOPP}.

Poster
DETAIL: Task DEmonsTration Attribution for Interpretable In-context Learning

Zijian Zhou, Xiaoqiang Lin, Xinyi Xu, Alok Prakash, Daniela Rus, Bryan Kian Hsiang Low

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In-context learning (ICL) allows transformer-based language models that are pre-trained on general text to quickly learn a specific task with a few "task demonstrations" without updating their parameters, significantly boosting their flexibility and generality. ICL possesses many distinct characteristics from conventional machine learning, thereby requiring new approaches to interpret this learning paradigm. Taking the viewpoint of recent works showing that transformers learn in context by formulating an internal optimizer, we propose an influence function-based attribution technique, DETAIL, that addresses the specific characteristics of ICL. We empirically verify the effectiveness of our approach for demonstration attribution while being computationally efficient. Leveraging the results, we then show how DETAIL can help improve model performance in real-world scenarios through demonstration reordering and curation. Finally, we experimentally prove the wide applicability of DETAIL by showing our attribution scores obtained on white-box models are transferable to black-box models in improving model performance.

Poster
BECAUSE: Bilinear Causal Representation for Generalizable Offline Model-based Reinforcement Learning

Haohong Lin, Wenhao Ding, Jian Chen, Laixi Shi, Jiacheng Zhu, Bo Li, Ding Zhao

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Offline model-based reinforcement learning (MBRL) enhances data efficiency by utilizing pre-collected datasets to learn models and policies, especially in scenarios where exploration is costly or infeasible. Nevertheless, its performance often suffers from the objective mismatch between model and policy learning, resulting in inferior performance despite accurate model predictions. This paper first identifies the primary source of this mismatch comes from the underlying confounders present in offline data for MBRL. Subsequently, we introduce **B**ilin**E**ar **CAUS**al r**E**presentation (BECAUSE), an algorithm to capture causal representation for both states and actions to reduce the influence of the distribution shift, thus mitigating the objective mismatch problem. Comprehensive evaluations on 18 tasks that vary in data quality and environment context demonstrate the superior performance of BECAUSE over existing offline RL algorithms. We show the generalizability and robustness of BECAUSE under fewer samples or larger numbers of confounders. Additionally, we offer theoretical analysis of BECAUSE to prove its error bound and sample efficiency when integrating causal representation into offline MBRL. See more details in our project page: [https://sites.google.com/view/be-cause](https://sites.google.com/view/be-cause).

Poster
Unveiling Induction Heads: Provable Training Dynamics and Feature Learning in Transformers

Siyu Chen, Heejune Sheen, Tianhao Wang, Zhuoran Yang

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In-context learning (ICL) is a cornerstone of large language model (LLM) functionality, yet its theoretical foundations remain elusive due to the complexity of transformer architectures. In particular, most existing work only theoretically explains how the attention mechanism facilitates ICL under certain data models. It remains unclear how the other building blocks of the transformer contribute to ICL. To address this question, we study how a two-attention-layer transformer is trained to perform ICL on $n$-gram Markov chain data, where each token in the Markov chain statistically depends on the previous n tokens. We analyze a sophisticated transformer model featuring relative positional embedding, multi-head softmax attention, and a feed-forward layer with normalization. We prove that the gradient flow with respect to a cross-entropy ICL loss converges to a limiting model that performs a generalized version of the "induction head" mechanism with a learned feature, resulting from the congruous contribution of all the building blocks. Specifically, the first attention layer acts as a copier, copying past tokens within a given window to each position, and the feed-forward network with normalization acts as a selector that generates a feature vector by only looking at informationally relevant parents from the window. Finally, the second attention layer is a classifier that compares these features with the feature at the output position, and uses the resulting similarity scores to generate the desired output. Our theory is further validated by simulation experiments.

Poster
RepLiQA: A Question-Answering Dataset for Benchmarking LLMs on Unseen Reference Content

Joao Monteiro, Pierre-Andre Noel, Étienne Marcotte, Sai Rajeswar, Valentina Zantedeschi, David Vazquez, Nicolas Chapados, Christopher Pal, Perouz Taslakian

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Large Language Models (LLMs) are trained on vast amounts of data, most of which is automatically scraped from the internet. This data includes encyclopedic documents that harbor a vast amount of general knowledge (*e.g.*, Wikipedia) but also potentially overlap with benchmark datasets used for evaluating LLMs. Consequently, evaluating models on test splits that might have leaked into the training set is prone to misleading conclusions. To foster sound evaluation of language models, we introduce a new test dataset named RepLiQA, suited for question-answering and topic retrieval tasks. RepLiQA is a collection of five splits of test sets, four of which have not been released to the internet or exposed to LLM APIs prior to this publication. Each sample in RepLiQA comprises (1) a reference document crafted by a human annotator and depicting an imaginary scenario (*e.g.*, a news article) absent from the internet; (2) a question about the document’s topic; (3) a ground-truth answer derived directly from the information in the document; and (4) the paragraph extracted from the reference document containing the answer. As such, accurate answers can only be generated if a model can find relevant content within the provided document. We run a large-scale benchmark comprising several state-of-the-art LLMs to uncover differences in performance across models of various types and sizes in a context-conditional language modeling setting. Released splits of RepLiQA can be found here: https://huggingface.co/datasets/ServiceNow/repliqa.

Poster
ActSort: An active-learning accelerated cell sorting algorithm for large-scale calcium imaging datasets

yiqi jiang, Hakki Orhun Akengin, Ji Zhou, Mehmet Anil Aslihak, Yang Li, Radoslaw Chrapkiewicz, Oscar Hernandez, Sadegh Ebrahimi, Omar Jaidar, Yanping Zhang, Hakan Inan, Christopher Miranda, Fatih Dinc, Marta Blanco-Pozo, Mark Schnitzer

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Recent advances in calcium imaging enable simultaneous recordings of up to a million neurons in behaving animals, producing datasets of unprecedented scales. Although individual neurons and their activity traces can be extracted from these videos with automated algorithms, the results often require human curation to remove false positives, a laborious process called \emph{cell sorting}. To address this challenge, we introduce ActSort, an active-learning algorithm for sorting large-scale datasets that integrates features engineered by domain experts together with data formats with minimal memory requirements. By strategically bringing outlier cell candidates near the decision boundary up for annotation, ActSort reduces human labor to about 1–3\% of cell candidates and improves curation accuracy by mitigating annotator bias. To facilitate the algorithm's widespread adoption among experimental neuroscientists, we created a user-friendly software and conducted a first-of-its-kind benchmarking study involving about 160,000 annotations. Our tests validated ActSort's performance across different experimental conditions and datasets from multiple animals. Overall, ActSort addresses a crucial bottleneck in processing large-scale calcium videos of neural activity and thereby facilitates systems neuroscience experiments at previously inaccessible scales. (\url{https://github.com/schnitzer-lab/ActSort-public})

Poster
What is my quantum computer good for? Quantum capability learning with physics-aware neural networks

Daniel Hothem, Ashe Miller, Timothy Proctor

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Quantum computers have the potential to revolutionize diverse fields, including quantum chemistry, materials science, and machine learning. However, contemporary quantum computers experience errors that often cause quantum programs run on them to fail. Until quantum computers can reliably execute large quantum programs, stakeholders will need fast and reliable methods for assessing a quantum computer’s capability—i.e., the programs it can run and how well it can run them. Previously, off-the-shelf neural network architectures have been used to model quantum computers' capabilities, but with limited success, because these networks fail to learn the complex quantum physics that determines real quantum computers' errors. We address this shortcoming with a new quantum-physics-aware neural network architecture for learning capability models. Our scalable architecture combines aspects of graph neural networks with efficient approximations to the physics of errors in quantum programs. This approach achieves up to $\sim50\%$ reductions in mean absolute error on both experimental and simulated data, over state-of-the-art models based on convolutional neural networks, and scales to devices with 100+ qubits.

Poster
On Learning Multi-Modal Forgery Representation for Diffusion Generated Video Detection

Xiufeng Song, Xiao Guo, Jiache Zhang, Qirui Li, Lei Bai, Xiaoming Liu, Guangtao Zhai, Xiaohong Liu

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Large numbers of synthesized videos from diffusion models pose threats to information security and authenticity, leading to an increasing demand for generated content detection. However, existing video-level detection algorithms primarily focus on detecting facial forgeries and often fail to identify diffusion-generated content with a diverse range of semantics. To advance the field of video forensics, we propose an innovative algorithm named Multi-Modal Detection(MM-Det) for detecting diffusion-generated videos. MM-Det utilizes the profound perceptual and comprehensive abilities of Large Multi-modal Models (LMMs) by generating a Multi-Modal Forgery Representation (MMFR) from LMM's multi-modal space, enhancing its ability to detect unseen forgery content. Besides, MM-Det leverages an In-and-Across Frame Attention (IAFA) mechanism for feature augmentation in the spatio-temporal domain. A dynamic fusion strategy helps refine forgery representations for the fusion. Moreover, we construct a comprehensive diffusion video dataset, called Diffusion Video Forensics (DVF), across a wide range of forgery videos. MM-Det achieves state-of-the-art performance in DVF, demonstrating the effectiveness of our algorithm. Both source code and DVF are available at https://github.com/SparkleXFantasy/MM-Det.

Poster
AttnDreamBooth: Towards Text-Aligned Personalized Text-to-Image Generation

Lianyu Pang, Jian Yin, Baoquan Zhao, Feize Wu, Fu Lee Wang, Qing Li, Xudong Mao

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Recent advances in text-to-image models have enabled high-quality personalized image synthesis based on user-provided concepts with flexible textual control. In this work, we analyze the limitations of two primary techniques in text-to-image personalization: Textual Inversion and DreamBooth. When integrating the learned concept into new prompts, Textual Inversion tends to overfit the concept, while DreamBooth often overlooks it. We attribute these issues to the incorrect learning of the embedding alignment for the concept. To address this, we introduce AttnDreamBooth, a novel approach that separately learns the embedding alignment, the attention map, and the subject identity across different training stages. We also introduce a cross-attention map regularization term to enhance the learning of the attention map. Our method demonstrates significant improvements in identity preservation and text alignment compared to the baseline methods.

Poster
Chain-of-Thought Reasoning Without Prompting

Xuezhi Wang, Denny Zhou

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In enhancing the reasoning capabilities of large language models (LLMs), prior research primarily focuses on specific prompting techniques such as few-shot or zero-shot chain-of-thought (CoT) prompting. These methods, while effective, often involve manually intensive prompt engineering. Our study takes a novel approach by asking: Can LLMs reason effectively without any prompting? Our findings reveal that, intriguingly, CoT reasoning paths can be elicited from pre-trained LLMs by simply altering the \textit{decoding} process. Rather than conventional greedy decoding, we investigate the top-$k$ alternative tokens, uncovering that CoT paths are frequently inherent in these sequences. This approach not only bypasses the confounders of prompting but also allows us to assess the LLMs' \textit{intrinsic} reasoning abilities. Moreover, we observe that the presence of a CoT in the decoding path correlates with a higher confidence in the model's decoded answer. This confidence metric effectively differentiates between CoT and non-CoT paths. Extensive empirical studies on various reasoning benchmarks show that the proposed CoT-decoding effectively elicits reasoning capabilities from language models, which were previously obscured by standard greedy decoding.

Poster
Active, anytime-valid risk controlling prediction sets

Ziyu Xu, Nikos Karampatziakis, Paul Mineiro

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Rigorously establishing the safety of black-box machine learning models with respect to critical risk measures is important for providing guarantees about the behavior of the model. Recently, a notion of a risk controlling prediction set (RCPS) has been introduced by Bates et. al. (JACM '24) for producing prediction sets that are statistically guaranteed to have low risk from machine learning models. Our method extends this notion to the sequential setting, where we provide guarantees even when the data is collected adaptively, and ensures the risk guarantee is anytime-valid, i.e., simultaneously holds at all time steps. Further, we propose a framework for constructing RCPSes for active labeling, i.e., allowing one to use a labeling policy that chooses whether to query the true label for each received data point, and ensures the expected proportion data points whose labels are queried are below a predetermined label budget. We also describe how to use predictors (e.g., the machine learning model we are providing risk control guarantees for) to further improve the utility of our RCPSes by estimating the expected risk conditioned on the covariates. We characterize the optimal choices of label policy under a fixed label budget, and predictor, and show a regret result that relates the estimation error of the optimal labeling policy and predictor to the wealth process that underlies our RCPSes. Lastly, we present practical ways of formulating label policies and we empirically show that our label policies use fewer labels to reach higher utility than naive baseline labeling strategies on both simulations and real data.

Poster
ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention

Mingchen Li, Yang Tan, Xinzhu Ma, Bozitao Zhong, Huiqun Yu, Ziyi Zhou, Wanli Ouyang, Bingxin Zhou, Pan Tan, Liang Hong

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Protein language models (PLMs) have shown remarkable capabilities in various protein function prediction tasks. However, while protein function is intricately tied to structure, most existing PLMs do not incorporate protein structure information. To address this issue, we introduce ProSST, a Transformer-based protein language model that seamlessly integrates both protein sequences and structures. ProSST incorporates a structure quantization module and a Transformer architecture with disentangled attention. The structure quantization module translates a 3D protein structure into a sequence of discrete tokens by first serializing the protein structure into residue-level local structures and then embeds them into dense vector space. These vectors are then quantized into discrete structure tokens by a pre-trained clustering model. These tokens serve as an effective protein structure representation. Furthermore, ProSST explicitly learns the relationship between protein residue token sequences and structure token sequences through the sequence-structure disentangled attention. We pre-train ProSST on millions of protein structures using a masked language model objective, enabling it to learn comprehensive contextual representations of proteins. To evaluate the proposed ProSST, we conduct extensive experiments on the zero-shot mutation effect prediction and several supervised downstream tasks, where ProSST achieves the state-of-the-art performance among all baselines. Our code and pre-trained models are publicly available.

Poster