GenAI4ELab/papercli-papers huggingface dataset:
Mechanism design augmented with output advice
Authors: George Christodoulou; Alkmini Sgouritsa; Ioannis Vlachos
Venue: NeurIPS 2024 (NeurIPS 2024 spotlight)

Abstract: Our work revisits the design of mechanisms via the learning-augmented framework. In this model, the algorithm is enhanced with imperfect (machine-learned) information concerning the input, usually referred to as prediction. The goal is to design algorithms whose performance degrades gently as a function of the prediction error and, in particular, perform well if the prediction is accurate, but also provide a worst-case guarantee under any possible error. This framework has been successfully applied recently to various mechanism design settings, where in most cases the mechanism is provided with a prediction about the types of the players.

We adopt a perspective in which the mechanism is provided with an output recommendation. We make no assumptions about the quality of the suggested outcome, and the goal is to use the recommendation to design mechanisms with low approximation guarantees whenever the recommended outcome is reasonable, but at the same time to provide worst-case guarantees whenever the recommendation significantly deviates from the optimal one. We propose a generic, universal measure, which we call quality of recommendation, to evaluate mechanisms across various information settings. We demonstrate how this new metric can provide refined analysis in existing results.

This model introduces new challenges, as the mechanism receives limited information comparing to settings that use predictions about the types of the agents. We study, through this lens, several well-studied mechanism design paradigms, devising new mechanisms, but also providing refined analysis for existing ones, using as a metric the quality of recommendation. We complement our positive results, by exploring the limitations of known classes of strategyproof mechanisms that can be devised using output recommendation.
Accelerating Matroid Optimization through Fast Imprecise Oracles
Authors: Franziska Eberle; Felix Hommelsheim; Alexander Lindermayr; Zhenwei Liu; Nicole Megow; Jens Schlöter
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Querying complex models for precise information (e.g. traffic models, database systems, large ML models) often entails intense computations and results in long response times. Thus, weaker models which give imprecise results quickly can be advantageous, provided inaccuracies can be resolved using few queries to a stronger model. In the fundamental problem of computing a maximum-weight basis of a matroid, a well-known generalization of many combinatorial optimization problems, algorithms have access to a clean oracle to query matroid information. We additionally equip algorithms with a fast but dirty oracle. We design and analyze practical algorithms which only use few clean queries w.r.t. the quality of the dirty oracle, while maintaining robustness against arbitrarily poor dirty oracles, approaching the performance of classic algorithms for the given problem. Notably, we prove that our algorithms are, in many respects, best-possible. Further, we outline extensions to other matroid oracle types, non-free dirty oracles and other matroid problems.
Latent Neural Operator for Solving Forward and Inverse PDE Problems
Authors: Tian Wang; Chuang Wang
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Neural operators effectively solve PDE problems from data without knowing the explicit equations, which learn the map from the input sequences of observed samples to the predicted values. Most existing works build the model in the original geometric space, leading to high computational costs when the number of sample points is large. We present the Latent Neural Operator (LNO) solving PDEs in the latent space. In particular, we first propose Physics-Cross-Attention (PhCA) transforming representation from the geometric space to the latent space, then learn the operator in the latent space, and finally recover the real-world geometric space via the inverse PhCA map. Our model retains flexibility that can decode values in any position not limited to locations defined in the training set, and therefore can naturally perform interpolation and extrapolation tasks particularly useful for inverse problems. Moreover, the proposed LNO improves both prediction accuracy and computational efficiency. Experiments show that LNO reduces the GPU memory by 50%, speeds up training 1.8 times, and reaches state-of-the-art accuracy on four out of six benchmarks for forward problems and a benchmark for inverse problem. Code is available at https://github.com/L-I-M-I-T/LatentNeuralOperator.
Adam with model exponential moving average is effective for nonconvex optimization
Authors: Kwangjun Ahn; Ashok Cutkosky
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: In this work, we offer a theoretical analysis of two modern optimization techniques for training large and complex models: (i) adaptive optimization algorithms, such as Adam, and (ii) the model exponential moving average (EMA). Specifically, we demonstrate that a clipped version of Adam with model EMA achieves the optimal convergence rates in various nonconvex optimization settings, both smooth and nonsmooth. Moreover, when the scale varies significantly across different coordinates, we demonstrate that the coordinate-wise adaptivity of Adam is provably advantageous. Notably, unlike previous analyses of Adam, our analysis crucially relies on its core elements---momentum and discounting factors---as well as model EMA, motivating their wide applications in practice.
Uni-Med: A Unified Medical Generalist Foundation Model For Multi-Task Learning Via Connector-MoE
Authors: Xun Zhu; Ying Hu; Fanbin Mo; Miao Li; Ji Wu
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Multi-modal large language models (MLLMs) have shown impressive capabilities as a general-purpose interface for various visual and linguistic tasks. However, building a unified MLLM for multi-task learning in the medical field remains a thorny challenge. To mitigate the tug-of-war problem of multi-modal multi-task optimization in MLLMs, recent advances primarily focus on improving the LLM components, while neglecting the connector that bridges the gap between modalities. In this paper, we introduce Uni-Med, a novel medical generalist foundation model which consists of a universal visual feature extraction module, a connector mixture-of-experts (CMoE) module, and an LLM. Benefiting from the proposed CMoE that leverages a well-designed router with a mixture of projection experts at the connector, Uni-Med achieves efficient solution to the tug-of-war problem and can perform six different medical tasks including question answering, visual question answering, report generation, referring expression comprehension, referring expression generation and image classification. To the best of our knowledge, Uni-Med is the first effort to tackle multi-task interference at the connector in MLLMs. Extensive ablation experiments validate the effectiveness of introducing CMoE under any configuration, with up to an average 8% performance gains. We further provide interpretation analysis of the tug-of-war problem from the perspective of gradient optimization and parameter statistics. Compared to previous state-of-the-art medical MLLMs, Uni-Med achieves competitive or superior evaluation metrics on diverse tasks. Code and resources are available at https://github.com/MSIIP/Uni-Med.
Mixture of Adversarial LoRAs: Boosting Robust Generalization in Meta-Tuning
Authors: Xu Yang; Chen Liu; Ying Wei
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: This paper introduces AMT, an \textbf{A}dversarial \textbf{M}eta-\textbf{T}uning methodology, to boost the robust generalization of pre-trained models in the out-of-domain (OOD) few-shot learning. To address the challenge of transferring knowledge from source domains to unseen target domains, we construct the robust LoRAPool by meta-tuning LoRAs with dual perturbations applied to not only the inputs but also singular values and vectors of the weight matrices at various robustness levels. On top of that, we introduce a simple yet effective test-time merging mechanism to dynamically merge discriminative LoRAs for test-time task customization. Extensive evaluations demonstrate that AMT yields significant improvements, up to 12.92\% in clean generalization and up to 49.72\% in adversarial generalization, over previous state-of-the-art methods across a diverse range of OOD few-shot image classification tasks on three benchmarks, confirming the effectiveness of our approach to boost the robust generalization of pre-trained models. Our code is available at \href{https://github.com/xyang583/AMT}{https://github.com/xyang583/AMT}.
Tight Bounds for Learning RUMs from Small Slates
Authors: Flavio Chierichetti; Mirko Giacchini; Ravi Kumar; Alessandro Panconesi; Andrew Tomkins
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: A Random Utility Model (RUM) is a classical model of user behavior defined by a distribution over $\mathbb{R}^n$. A user, presented with a subset of $\\{1,\ldots,n\\}$, will select the item of the subset with the highest utility, according to a utility vector drawn from the specified distribution. In practical settings, the subset is often of small size, as in the ``ten blue links'' of web search. 


In this paper, we consider a learning setting with complete information on user choices from subsets of size at most $k$. We show that $k=\Theta(\sqrt{n})$ is both necessary and sufficient to predict the distribution of all user choices with an arbitrarily small, constant error.


Based on the upper bound, we obtain new algorithms for approximate RUM learning and variations thereof. Furthermore, we employ our lower bound for approximate RUM learning to derive lower bounds to fractional extensions of the well-studied $k$-deck and trace reconstruction problems.
Web-Scale Visual Entity Recognition: An LLM-Driven Data Approach
Authors: Mathilde Caron; Alireza Fathi; Cordelia Schmid; Ahmet Iscen
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Web-scale visual entity recognition, the task of associating images with their corresponding entities within vast knowledge bases like Wikipedia, presents significant challenges due to the lack of clean, large-scale training data. In this paper, we propose a novel methodology to curate such a dataset, leveraging a multimodal large language model (LLM) for label verification, metadata generation, and rationale explanation. Instead of relying on the multimodal LLM to directly annotate data, which we found to be suboptimal, we prompt it to reason about potential candidate entity labels by accessing additional contextually relevant information (such as Wikipedia), resulting in more accurate annotations. We further use the multimodal LLM to enrich the dataset by generating question-answer pairs and a grounded fine-grained textual description (referred to as "rationale") that explains the connection between images and their assigned entities. Experiments demonstrate that models trained on this automatically curated data achieve state-of-the-art performance on web-scale visual entity recognition tasks (e.g. +6.9% improvement in OVEN entity task), underscoring the importance of high-quality training data in this domain.
You Don’t Need Domain-Specific Data Augmentations When Scaling Self-Supervised Learning
Authors: Théo Moutakanni; Maxime Oquab; Marc Szafraniec; Maria Vakalopoulou; Piotr Bojanowski
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Self-Supervised learning (SSL) with Joint-Embedding Architectures (JEA) has led to outstanding performances. All instantiations of this paradigm were trained using strong and well-established hand-crafted data augmentations, leading to the general belief that they are required for the proper training and performance of such models. On the other hand, generative reconstruction-based models such as BEIT and MAE or Joint-Embedding Predictive Architectures such as I-JEPA have shown strong performance without using data augmentations except masking. In this work, we challenge the importance of invariance and data-augmentation in JEAs at scale. By running a case-study on a recent SSL foundation model -- DINOv2 -- we show that strong image representations can be obtained with JEAs and only cropping without resizing provided the training data is large enough, reaching state-of-the-art results and using the least amount of augmentation in the literature. Through this study, we also discuss the impact of compute constraints on the outcomes of experimental deep learning research, showing that they can lead to very different conclusions.
Differentially Private Equivalence Testing for Continuous Distributions and Applications
Authors: Or Sheffet; Daniel Omer
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We present the first algorithm for testing equivalence  between two continuous distributions using differential privacy (DP). Our algorithm is a private version of the algorithm of Diakonikolas et al. 
The algorithm of Diakonikolas et al uses the data itself to repeatedly discretize the real line so that --- when the two distributions are far apart in ${\cal A}_k$-norm --- one of the discretized distributions exhibits large $L_2$-norm difference; and upon repeated sampling such large gap would be detected. Designing its private analogue poses two difficulties. First, our DP algorithm can not resample new datapoints as a change to a single datapoint may lead to a very large change in the descretization of the real line. In contrast, the (sorted) index of the discretization point changes only by $1$ between neighboring instances, and so we use a novel algorithm that set the discretization points using random Bernoulli noise, resulting in only a few buckets being affected under the right coupling. Second, our algorithm, which doesn't resample data, requires we also revisit the utility analysis of the original algorithm and prove its correctness w.r.t. the original sorted data; a problem we tackle using sampling a subset of Poisson-drawn size from each discretized bin. Lastly, since any distribution can be reduced to a continuous distribution, our algorithm is successfully carried to multiple other families of distributions and thus has numerous applications.
MMSite: A Multi-modal Framework for the Identification of Active Sites in Proteins
Authors: Song Ouyang; Huiyu Cai; Yong Luo; Kehua Su; Lefei Zhang; Bo Du
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: The accurate identification of active sites in proteins is essential for the advancement of life sciences and pharmaceutical development, as these sites are of critical importance for enzyme activity and drug design. Recent advancements in protein language models (PLMs), trained on extensive datasets of amino acid sequences, have significantly improved our understanding of proteins. However, compared to the abundant protein sequence data, functional annotations, especially precise per-residue annotations, are scarce, which limits the performance of PLMs. On the other hand, textual descriptions of proteins, which could be annotated by human experts or a pretrained protein sequence-to-text model, provide meaningful context that could assist in the functional annotations, such as the localization of active sites. This motivates us to construct a $\textbf{ProT}$ein-$\textbf{A}$ttribute text $\textbf{D}$ataset ($\textbf{ProTAD}$), comprising over 570,000 pairs of protein sequences and multi-attribute textual descriptions. Based on this dataset, we propose $\textbf{MMSite}$, a multi-modal framework that improves the performance of PLMs to identify active sites by leveraging biomedical language models (BLMs). In particular, we incorporate manual prompting and design a MACross module to deal with the multi-attribute characteristics of textual descriptions. MMSite is a two-stage ("First Align, Then Fuse") framework: first aligns the textual modality with the sequential modality through soft-label alignment, and then identifies active sites via multi-modal fusion. Experimental results demonstrate that MMSite achieves state-of-the-art performance compared to existing protein representation learning methods. The dataset and code implementation are available at https://github.com/Gift-OYS/MMSite.
Identifying Selections for Unsupervised Subtask Discovery
Authors: Yiwen Qiu; Yujia Zheng; Kun Zhang
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: When solving long-horizon tasks, it is intriguing to decompose the high-level task into subtasks. Decomposing experiences into reusable subtasks can improve data efficiency, accelerate policy generalization, and in general provide promising solutions to multi-task reinforcement learning and imitation learning problems. However, the concept of subtasks is not sufficiently understood and modeled yet, and existing works often overlook the true structure of the data generation process: subtasks are the results of a *selection* mechanism on actions, rather than possible underlying confounders or intermediates. Specifically, we provide a theory to identify, and experiments to verify the existence of selection variables in such data. These selections serve as subgoals that indicate subtasks and guide policy. In light of this idea, we develop a sequential non-negative matrix factorization (seq- NMF) method to learn these subgoals and extract meaningful behavior patterns as subtasks. Our empirical results on a challenging Kitchen environment demonstrate that the learned subtasks effectively enhance the generalization to new tasks in multi-task imitation learning scenarios. The codes are provided at this [*link*](https://anonymous.4open.science/r/Identifying\_Selections\_for\_Unsupervised\_Subtask\_Discovery/README.md).
The Dormant Neuron Phenomenon in Multi-Agent Reinforcement Learning Value Factorization
Authors: Haoyuan Qin; Chennan Ma; Mian Deng; Zhengzhu Liu; Songzhu Mei; Xinwang Liu; Cheng Wang; Siqi Shen
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: In this work, we study the dormant neuron phenomenon in multi-agent reinforcement learning value factorization, where the mixing network suffers from reduced network expressivity caused by an increasing number of inactive neurons. We demonstrate the presence of the dormant neuron phenomenon across multiple environments and algorithms, and show that this phenomenon negatively affects the learning process. We show that dormant neurons correlates with the existence of over-active neurons, which have large activation scores. To address the dormant neuron issue, we propose ReBorn, a simple but effective method that transfers the weights from over-active neurons to dormant neurons. We theoretically show that this method can ensure the learned action preferences are not forgotten after the weight-transferring procedure, which increases learning effectiveness. Our extensive experiments reveal that ReBorn achieves promising results across various environments and improves the performance of multiple popular value factorization approaches. The source code of ReBorn is available in \url{https://github.com/xmu-rl-3dv/ReBorn}.
Using Time-Aware Graph Neural Networks to Predict Temporal Centralities in Dynamic Graphs
Authors: Franziska Heeg; Ingo Scholtes
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Node centralities play a pivotal role in network science, social network analysis, and recommender systems.
In temporal data, static path-based centralities like closeness or betweenness can give misleading results about the true importance of nodes in a temporal graph. To address this issue, temporal generalizations of betweenness and closeness have been defined that are based on the shortest time-respecting paths between pairs of nodes. However, a major issue of those generalizations is that the calculation of such paths is computationally expensive.
Addressing this issue, we study the application of De Bruijn Graph Neural Networks (DBGNN), a time-aware graph neural network architecture, to predict temporal path-based centralities in time series data. We experimentally evaluate our approach in 13 temporal graphs from biological and social systems and show that it considerably improves the prediction of betweenness and closeness centrality compared to (i) a static Graph Convolutional Neural Network, (ii) an efficient sampling-based approximation technique for temporal betweenness, and (iii) two state-of-the-art time-aware graph learning techniques for dynamic graphs.
Multi-Scale Representation Learning for Protein Fitness Prediction
Authors: Zuobai Zhang; Pascal Notin; Yining Huang; Aurelie Lozano; Vijil Chenthamarakshan; Debora Susan Marks; Payel Das; Jian Tang
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experiments, previous methods have primarily relied on self-supervised models trained on vast, unlabeled protein sequence or structure datasets. While initial protein representation learning studies solely focused on either sequence or structural features, recent hybrid architectures have sought to merge these modalities to harness their respective strengths. However, these sequence-structure models have so far achieved only incremental improvements when compared to the leading sequence-only approaches, highlighting unresolved challenges effectively leveraging these modalities together. Moreover, the function of certain proteins is highly dependent on the granular aspects of their surface topology, which have been overlooked by prior models.
To address these limitations, we introduce the Sequence-Structure-Surface Fitness (**S3F**) model — a novel multimodal representation learning framework that integrates protein features across several scales. Our approach combines sequence representations from a protein language model with Geometric Vector Perceptron networks encoding protein backbone and detailed surface topology. The proposed method achieves state-of-the-art fitness prediction on the ProteinGym benchmark encompassing 217 substitution deep mutational scanning assays, and provides insights into the determinants of protein function.
Our code is at https://github.com/DeepGraphLearning/S3F.
Discrete Modeling via Boundary Conditional Diffusion Processes
Authors: Yuxuan Gu; Xiaocheng Feng; Lei Huang; Yingsheng Wu; Zekun Zhou; Weihong Zhong; kun Zhu; Bing Qin
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We present an novel framework for efficiently and effectively extending the powerful continuous diffusion processes to discrete modeling.
Previous approaches have suffered from the discrepancy between discrete data and continuous modeling.
Our study reveals that the absence of guidance from discrete boundaries in learning probability contours is one of the main reasons.
To address this issue, we propose a two-step forward process that first estimates the boundary as a prior distribution and then rescales the forward trajectory to construct a boundary conditional diffusion model.
The reverse process is proportionally adjusted to guarantee that the learned contours yield more precise discrete data.
Experimental results indicate that our approach achieves strong performance in both language modeling and discrete image generation tasks.
In language modeling, our approach surpasses previous state-of-the-art continuous diffusion language models in three translation tasks and a summarization task, while also demonstrating competitive performance compared to auto-regressive transformers. Moreover, our method achieves comparable results to continuous diffusion models when using discrete ordinal pixels and establishes a new state-of-the-art for categorical image generation on the Cifar-10 dataset.