GenAI4ELab/papercli-papers huggingface dataset:
ProtGO: Function-Guided Protein Modeling for Unified Representation Learning
Authors: Bozhen Hu; Cheng Tan; Yongjie Xu; Zhangyang Gao; Jun Xia; Lirong Wu; Stan Z. Li
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Protein representation learning is indispensable for various downstream applications of artificial intelligence for bio-medicine research, such as drug design and function prediction. However, achieving effective representation learning for proteins poses challenges due to the diversity of data modalities involved, including sequence, structure, and function annotations. Despite the impressive capabilities of large language models in biomedical text modelling, there remains a pressing need for a framework that seamlessly integrates these diverse modalities, particularly focusing on the three critical aspects of protein information: sequence, structure, and function. Moreover, addressing the inherent data scale differences among these modalities is essential. To tackle these challenges, we introduce ProtGO, a unified model that harnesses a teacher network equipped with a customized graph neural network (GNN) and a Gene Ontology (GO) encoder to learn hybrid embeddings. Notably, our approach eliminates the need for additional functions as input for the student network, which shares the same GNN module. Importantly, we utilize a domain adaptation method to facilitate distribution approximation for guiding the training of the teacher-student framework. This approach leverages distributions learned from latent representations to avoid the alignment of individual samples. Benchmark experiments highlight that ProtGO significantly outperforms state-of-the-art baselines, clearly demonstrating the advantages of the proposed unified framework.
Learning Complete Protein Representation by Dynamically Coupling of Sequence and Structure
Authors: Bozhen Hu; Cheng Tan; Jun Xia; Yue Liu; Lirong Wu; Jiangbin Zheng; Yongjie Xu; Yufei Huang; Stan Z. Li
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Learning effective representations is imperative for comprehending proteins and deciphering their biological functions. Recent strides in language models and graph neural networks have empowered protein models to harness primary or tertiary structure information for representation learning. Nevertheless, the absence of practical methodologies to appropriately model intricate inter-dependencies between protein sequences and structures has resulted in embeddings that exhibit low performance on tasks such as protein function prediction. In this study, we introduce CoupleNet, a novel framework designed to interlink protein sequences and structures to derive informative protein representations. CoupleNet integrates multiple levels and scales of features in proteins, encompassing residue identities and positions for sequences, as well as geometric representations for tertiary structures from both local and global perspectives. A two-type dynamic graph is constructed to capture adjacent and distant sequential features and structural geometries, achieving completeness at the amino acid and backbone levels. Additionally, convolutions are executed on nodes and edges simultaneously to generate comprehensive protein embeddings. Experimental results on benchmark datasets showcase that CoupleNet outperforms state-of-the-art methods, exhibiting particularly superior performance in low-sequence similarities scenarios,  adeptly identifying infrequently encountered functions and effectively capturing remote homology relationships in proteins.
DiGRAF: Diffeomorphic Graph-Adaptive Activation Function
Authors: Krishna Sri Ipsit Mantri; Xinzhi Wang; Carola-Bibiane Schönlieb; Bruno Ribeiro; Beatrice Bevilacqua; Moshe Eliasof
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: In this paper, we propose a novel activation function tailored specifically for graph data in Graph Neural Networks (GNNs). Motivated by the need for graph-adaptive and flexible activation functions, we introduce DiGRAF, leveraging Continuous Piecewise-Affine Based (CPAB) transformations, which we augment with an additional GNN to learn a graph-adaptive diffeomorphic activation function in an end-to-end manner. In addition to its graph-adaptivity and flexibility, DiGRAF also possesses properties that are widely recognized as desirable for activation functions, such as differentiability, boundness within the domain, and computational efficiency. 
We conduct an extensive set of experiments across diverse datasets and tasks, demonstrating a consistent and superior performance of DiGRAF compared to traditional and graph-specific activation functions, highlighting its effectiveness as an activation function for GNNs. Our code is available at https://github.com/ipsitmantri/DiGRAF.
Honor Among Bandits: No-Regret Learning for Online Fair Division
Authors: Ariel D. Procaccia; Benjamin Schiffer; Shirley Zhang
Venue: NeurIPS 2024 (NeurIPS 2024 spotlight)

Abstract: We consider the problem of online fair division of indivisible goods to players when there are a finite number of types of goods and player values are drawn from distributions with unknown means. Our goal is to maximize social welfare subject to allocating the goods fairly in expectation. When a player's value for an item is unknown at the time of allocation, we show that this problem reduces to a variant of (stochastic) multi-armed bandits, where there exists an arm for each player's value for each type of good. At each time step, we choose a distribution over arms which determines how the next item is allocated. We consider two sets of fairness constraints for this problem: envy-freeness in expectation and proportionality in expectation. Our main result is the design of an explore-then-commit algorithm that achieves $\tilde{O}(T^{2/3})$ regret while maintaining either fairness constraint. This result relies on unique properties fundamental to fair-division constraints that allow faster rates of learning, despite the restricted action space.
Information-theoretic Limits of Online Classification with Noisy Labels
Authors: Changlong Wu; Ananth Grama; Wojciech Szpankowski
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We study online classification with general hypothesis classes where the true labels are determined by some function within the class, but are corrupted by *unknown* stochastic noise, and the features are generated adversarially. Predictions are made using observed *noisy* labels and noiseless features, while the performance is  measured via minimax risk when comparing against *true* labels. The noisy mechanism is modeled via a general noisy kernel that specifies, for any individual data point, a set of distributions from which the actual noisy label distribution is chosen. We show that minimax risk is *tightly* characterized (up to a logarithmic factor of the hypothesis class size) by the *Hellinger gap* of the noisy label distributions induced by the kernel, *independent* of other properties such as the means and variances of the noise. Our main technique is based on a novel reduction to an online comparison scheme of two hypotheses, along with a new *conditional* version of Le Cam-Birgé testing suitable for online settings. Our work provides the first comprehensive characterization of noisy online classification with guarantees that apply to the *ground truth* while addressing *general* noisy observations.
The Power of Extrapolation in Federated Learning
Authors: Hanmin Li; Kirill Acharya; Peter Richtárik
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We propose and study several server-extrapolation strategies for enhancing the theoretical and empirical convergence properties of the popular federated learning optimizer FedProx [Li et al., 2020]. While it has long been known that some form of extrapolation can help in the practice of FL, only a handful of works provide any theoretical guarantees. The phenomenon seems elusive, and our current theoretical understanding remains severely incomplete. In our work, we focus on smooth convex or strongly convex problems in the interpolation regime. In particular, we propose Extrapolated FedProx (FedExProx), and study three extrapolation strategies: a constant strategy (depending on various smoothness parameters and the number of participating devices), and two smoothness-adaptive strategies; one based on the notion of gradient diversity (FedExProx-GraDS), and the other one based on the stochastic Polyak stepsize (FedExProx-StoPS). Our theory is corroborated with carefully constructed numerical experiments.
First-Order Minimax Bilevel Optimization
Authors: Yifan Yang; Zhaofeng Si; Siwei Lyu; Kaiyi Ji
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Multi-block minimax bilevel optimization has been studied recently due to its great potential in multi-task learning, robust machine learning, and few-shot learning. However, due to the complex three-level optimization structure, existing algorithms often suffer from issues such as high computing costs due to the second-order model derivatives or high memory consumption in storing all blocks' parameters. In this paper, we tackle these challenges by proposing two novel fully first-order algorithms named FOSL and MemCS. FOSL features a fully single-loop structure by updating all three variables simultaneously, and MemCS is a memory-efficient double-loop algorithm with cold-start initialization. We provide a comprehensive convergence analysis for both algorithms under full and partial block participation, and show that their sample complexities match or outperform those of the same type of methods in standard bilevel optimization. We evaluate our methods in two applications: the recently proposed multi-task deep AUC maximization and a novel rank-based robust meta-learning. Our methods consistently improve over existing methods with better performance over various datasets.
A Functional Extension of Semi-Structured Networks
Authors: David Rügamer; Bernard X.W. Liew; Zainab Altai; Almond Stöcker
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Semi-structured networks (SSNs) merge the structures familiar from additive models with deep neural networks, allowing the modeling of interpretable partial feature effects while capturing higher-order non-linearities at the same time. A significant challenge in this integration is maintaining the interpretability of the additive model component. Inspired by large-scale biomechanics datasets, this paper explores extending SSNs to functional data. Existing methods in functional data analysis are promising but often not expressive enough to account for all interactions and non-linearities and do not scale well to large datasets. Although the SSN approach presents a compelling potential solution, its adaptation to functional data remains complex. In this work, we propose a functional SSN method that retains the advantageous properties of classical functional regression approaches while also improving scalability. Our numerical experiments demonstrate that this approach accurately recovers underlying signals, enhances predictive performance, and performs favorably compared to competing methods.
Gradient-based Discrete Sampling with Automatic Cyclical Scheduling
Authors: Patrick Pynadath; Riddhiman Bhattacharya; ARUN NARAYANAN HARIHARAN; Ruqi Zhang
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Discrete distributions, particularly in high-dimensional deep models, are often highly multimodal due to inherent discontinuities. While gradient-based discrete sampling has proven effective, it is susceptible to becoming trapped in local modes due to the gradient information. To tackle this challenge, we propose an automatic cyclical scheduling, designed for efficient and accurate sampling in multimodal discrete distributions. Our method contains three key components: (1) a cyclical step size schedule where large steps discover new modes and small steps exploit each mode; (2) a cyclical balancing schedule, ensuring "balanced" proposals for given step sizes and high efficiency of the Markov chain; and (3) an automatic tuning scheme for adjusting the hyperparameters in the cyclical schedules, allowing adaptability across diverse datasets with minimal tuning.  We prove the non-asymptotic convergence and inference guarantee for our method in general discrete distributions. Extensive experiments demonstrate the superiority of our method in sampling complex multimodal discrete distributions.
Soft Superpixel Neighborhood Attention
Authors: Kent Gauen; Stanley H. Chan
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Images contain objects with deformable boundaries, such as the contours of a human face, yet attention operators act on square windows. This mixes features from perceptually unrelated regions, which can degrade the quality of a denoiser. One can exclude pixels using an estimate of perceptual groupings, such as superpixels, but the naive use of superpixels can be theoretically and empirically worse than standard attention. Using superpixel probabilities rather than superpixel assignments, this paper proposes soft superpixel neighborhood attention (SNA), which interpolates between the existing neighborhood attention and the naive superpixel neighborhood attention. This paper presents theoretical results showing SNA is the optimal denoiser under a latent superpixel model. SNA outperforms alternative local attention modules on image denoising, and we compare the superpixels learned from denoising with those learned with supervision.
Minimax Optimal and Computationally Efficient Algorithms for Distributionally Robust Offline Reinforcement Learning
Authors: Zhishuai Liu; Pan Xu
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Distributionally robust offline reinforcement learning (RL), which seeks robust policy training against environment perturbation by modeling dynamics uncertainty, calls for function approximations when facing large state-action spaces. However, the consideration of dynamics uncertainty introduces essential nonlinearity and computational burden, posing unique challenges for analyzing and practically employing function approximation. Focusing on a basic setting where the nominal model and perturbed models are linearly parameterized, we propose minimax optimal and computationally efficient algorithms realizing function approximation and initiate the study on instance-dependent suboptimality analysis in the context of robust offline RL. Our results uncover that function approximation in robust offline RL is essentially distinct from and probably harder than that in standard offline RL. Our algorithms and theoretical results crucially depend on a novel function approximation mechanism incorporating variance information, a new procedure of suboptimality and estimation uncertainty decomposition, a quantification of the robust value function shrinkage, and a meticulously designed family of hard instances, which might be of independent interest.
Prior-itizing Privacy: A Bayesian Approach to Setting the Privacy Budget in Differential Privacy
Authors: Zeki Kazan; Jerome Reiter
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: When releasing outputs from confidential data, agencies need to balance the analytical usefulness of the released data with the obligation to protect data subjects' confidentiality. For releases satisfying differential privacy, this balance is reflected by the privacy budget, $\varepsilon$. We provide a framework for setting $\varepsilon$ based on its relationship with Bayesian posterior probabilities of disclosure. The agency responsible for the data release decides how much posterior risk it is willing to accept at various levels of prior risk, which implies a unique $\varepsilon$. Agencies can evaluate different risk profiles to determine one that leads to an acceptable trade-off in risk and utility.
Coherence-free Entrywise Estimation of Eigenvectors in Low-rank Signal-plus-noise Matrix Models
Authors: Hao Yan; Keith Levin
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Spectral methods are widely used to estimate eigenvectors of a low-rank signal matrix subject to noise. These methods use the leading eigenspace of an observed matrix to estimate this low-rank signal. Typically, the entrywise estimation error of these methods depends on the coherence of the low-rank signal matrix with respect to the standard basis. In this work, we present a novel method for eigenvector estimation that avoids this dependence on coherence. Assuming a rank-one signal matrix, under mild technical conditions, the entrywise estimation error of our method provably has no dependence on the coherence under Gaussian noise (i.e., in the spiked Wigner model), and achieves the optimal estimation rate up to logarithmic factors. Simulations demonstrate that our method performs well under non-Gaussian noise and that an extension of our method to the case of a rank-$r$ signal matrix has little to no dependence on the coherence. In addition, we derive new metric entropy bounds for rank-$r$ singular subspaces under $\ell_{2,\infty}$ distance, which may be of independent interest. We use these new bounds to improve the best known lower bound for rank-$r$ eigenspace estimation under $\ell_{2,\infty}$ distance.
Video Token Merging for Long Video Understanding
Authors: Seon-Ho Lee; Jue Wang; Zhikang Zhang; David Fan; Xinyu Li
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: As the scale of data and models for video understanding rapidly expand, handling long-form video input in transformer-based models presents a practical challenge. Rather than resorting to input sampling or token dropping, which may result in information loss, token merging shows promising results when used in collaboration with transformers. However, the application of token merging for long-form video processing is not trivial. We begin with the premise that token merging should not rely solely on the similarity of video tokens; the saliency of tokens should also be considered. To address this, we explore various video token merging strategies for long-form video classification, starting with a simple extension of image token merging, moving to region-concentrated merging, and finally proposing a learnable video token merging (VTM) algorithm that dynamically merges tokens based on their saliency. Extensive experimental results show that we achieve better or comparable performances on the LVU, COIN, and Breakfast datasets. Moreover, our approach significantly reduces memory costs by 84% and boosts throughput by approximately 6.89 times compared to baseline algorithms.
Optimal Algorithms for Online Convex Optimization with Adversarial Constraints
Authors: Abhishek Sinha; Rahul Vaze
Venue: NeurIPS 2024 (NeurIPS 2024 spotlight)

Abstract: A well-studied generalization of the standard online convex optimization (OCO) framework is constrained online convex optimization (COCO). In COCO, on every round, a convex cost function and a convex constraint function are revealed to the learner after it chooses the action for that round. The objective is to design an online learning policy that simultaneously achieves a small regret while ensuring a small cumulative constraint violation (CCV) against an adaptive adversary interacting over a horizon of length $T$. A long-standing open question in COCO is whether an online policy can simultaneously achieve $O(\sqrt{T})$ regret and $\tilde{O}(\sqrt{T})$ CCV without any restrictive assumptions. For the first time, we answer this in the affirmative and show that a simple first-order policy can simultaneously achieve these bounds. Furthermore, in the case of strongly convex cost and convex constraint functions, the regret guarantee can be improved to $O(\log T)$ while keeping the CCV bound the same as above. We establish these results by effectively combining adaptive OCO policies as a blackbox with Lyapunov optimization - a classic tool from control theory. Surprisingly, the analysis is short and elegant.
DistillNeRF: Perceiving 3D Scenes from Single-Glance Images by Distilling Neural Fields and Foundation Model Features
Authors: Letian Wang; Seung Wook Kim; Jiawei Yang; Cunjun Yu; Boris Ivanovic; Steven L. Waslander; Yue Wang; Sanja Fidler; Marco Pavone; Peter Karkus
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We propose DistillNeRF, a self-supervised learning framework addressing the challenge of understanding 3D environments from limited 2D observations in outdoor autonomous driving scenes. Our method is a generalizable feedforward model that predicts a rich neural scene representation from sparse, single-frame multi-view camera inputs with limited view overlap, and is trained self-supervised with differentiable rendering to reconstruct RGB, depth, or feature images. Our first insight is to exploit per-scene optimized Neural Radiance Fields (NeRFs) by generating dense depth and virtual camera targets from them, which helps our model to learn enhanced 3D geometry from sparse non-overlapping image inputs. Second, to learn a semantically rich 3D representation, we propose distilling features from pre-trained 2D foundation models, such as CLIP or DINOv2, thereby enabling various downstream tasks without the need for costly 3D human annotations. To leverage these two insights, we introduce a novel model architecture with a two-stage lift-splat-shoot encoder and a parameterized sparse hierarchical voxel representation. Experimental results on the NuScenes and Waymo NOTR datasets demonstrate that DistillNeRF significantly outperforms existing comparable state-of-the-art self-supervised methods for scene reconstruction, novel view synthesis, and depth estimation; and it allows for competitive zero-shot 3D semantic occupancy prediction, as well as open-world scene understanding through distilled foundation model features. Demos and code will be available at https://distillnerf.github.io/.
Navigating Chemical Space with Latent Flows
Authors: Guanghao Wei; Yining Huang; Chenru Duan; Yue Song; Yuanqi Du
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and a comprehensive understanding of the vast chemical space are of great importance to molecular science and applications in drug design and materials discovery.
In this paper, we propose a new framework, ChemFlow, to traverse chemical space through navigating the latent space learned by molecule generative models through flows. We introduce a dynamical system perspective that formulates the problem as learning a vector field that transports the mass of the molecular distribution to the region with desired molecular properties or structure diversity. 
Under this framework, we unify previous approaches on molecule latent space traversal and optimization and propose alternative competing methods incorporating different physical priors. 
We validate the efficacy of ChemFlow on molecule manipulation and single- and multi-objective molecule optimization tasks under both supervised and unsupervised molecular discovery settings.
Codes and demos are publicly available on GitHub at 
[https://github.com/garywei944/ChemFlow](https://github.com/garywei944/ChemFlow).