GenAI4ELab/papercli-papers huggingface dataset:
Exploiting Correlated Auxiliary Feedback in Parameterized Bandits
Authors: Arun Verma; Zhongxiang Dai; Yao Shu; Bryan Kian Hsiang Low
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: We study a novel variant of the parameterized bandits problem in which the learner can observe additional auxiliary feedback that is correlated with the observed reward. The auxiliary feedback is readily available in many real-life applications, e.g., an online platform that wants to recommend the best-rated services to its users can observe the user's rating of service (rewards) and collect additional information like service delivery time (auxiliary feedback). In this paper, we first develop a method that exploits auxiliary feedback to build a reward estimator with tight confidence bounds, leading to a smaller regret. We then characterize the regret reduction in terms of the correlation coefficient between reward and its auxiliary feedback. Experimental results in different settings also verify the performance gain achieved by our proposed method.
Characterizing Out-of-Distribution Error via Optimal Transport
Authors: Yuzhe Lu; Yilong Qin; Runtian Zhai; Andrew Shen; Ketong Chen; Zhenlin Wang; Soheil Kolouri; Simon Stepputtis; Joseph Campbell; Katia P. Sycara
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Out-of-distribution (OOD) data poses serious challenges in deployed machine learning models,
so methods of predicting a model's performance on OOD data without labels are important for machine learning safety.
While a number of methods have been proposed by prior work, they often underestimate the actual error, sometimes by a large margin, which greatly impacts their applicability to real tasks. In this work, we identify *pseudo-label shift*, or the difference between the predicted and true OOD label distributions, as a key indicator of this underestimation. Based on this observation, we introduce a novel method for estimating model performance by leveraging optimal transport theory, Confidence Optimal Transport (COT), and show that it provably provides more robust error estimates in the presence of pseudo-label shift. Additionally, we introduce an empirically-motivated variant of COT, Confidence Optimal Transport with Thresholding (COTT), which applies thresholding to the individual transport costs and further improves the accuracy of COT's error estimates. We evaluate COT and COTT on a variety of standard benchmarks that induce various types of distribution shift -- synthetic, novel subpopulation, and natural -- and show that our approaches significantly outperform existing state-of-the-art methods with up to 3x lower prediction errors.
Provable benefits of score matching
Authors: Chirag Pabbaraju; Dhruv Rohatgi; Anish Sevekari; Holden Lee; Ankur Moitra; Andrej Risteski
Venue: NeurIPS 2023 (NeurIPS 2023 spotlight)

Abstract: Score matching is an alternative to maximum likelihood (ML) for estimating a probability distribution parametrized up to a constant of proportionality. By fitting the ''score'' of the distribution, it sidesteps the need to compute this constant of proportionality (which is often intractable).
While score matching and variants thereof are popular in practice, precise theoretical understanding of the benefits and tradeoffs with maximum likelihood---both computational and statistical---are not well understood. In this work, we give the first example of a natural exponential family of distributions such that the score matching loss is computationally efficient to optimize, and has a comparable statistical efficiency to ML, while the ML loss is intractable to optimize using a gradient-based method. The family consists of exponentials of polynomials of fixed degree, and our result can be viewed as a continuous analogue of recent developments in the discrete setting. Precisely, we show: (1) Designing a zeroth-order or first-order oracle for optimizing the maximum likelihood loss is NP-hard. (2) Maximum likelihood has a statistical efficiency polynomial in the ambient dimension and the radius of the parameters of the family. (3) 
Minimizing the score matching loss is both computationally and statistically efficient, with complexity polynomial in the ambient dimension.
Generalized Semi-Supervised Learning via Self-Supervised Feature Adaptation
Authors: Jiachen Liang; RuiBing Hou; Hong Chang; Bingpeng Ma; Shiguang Shan; Xilin CHEN
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Traditional semi-supervised learning (SSL) assumes that the feature distributions of labeled and unlabeled data are consistent which rarely holds in realistic scenarios. 
In this paper, we propose a novel SSL setting, where unlabeled samples are drawn from a mixed distribution that deviates from the feature distribution of labeled samples.
Under this setting, previous SSL methods tend to predict wrong pseudo-labels with the model fitted on labeled data, resulting in noise accumulation. To tackle this issue, we propose \emph{Self-Supervised Feature Adaptation} (SSFA), a generic framework for improving SSL performance when labeled and unlabeled data come from different distributions. 
SSFA decouples the prediction of pseudo-labels from the current model to improve the quality of pseudo-labels. Particularly, SSFA incorporates a self-supervised task into the SSL framework and uses it to adapt the feature extractor of the model to the unlabeled data. In this way, the extracted features better fit the distribution of unlabeled data, thereby generating high-quality pseudo-labels. Extensive experiments show that our proposed SSFA is applicable to various pseudo-label-based SSL learners and significantly improves performance in labeled, unlabeled, and even unseen distributions.
Weitzman's Rule for Pandora's Box with Correlations
Authors: Evangelia Gergatsouli; Christos Tzamos
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Pandora’s Box is a central problem in decision making under uncertainty that can model various real life scenarios. In this problem we are given n boxes, each with a fixed opening cost, and an unknown value drawn from a known distribution, only revealed if we pay the opening cost. Our goal is to find a strategy for opening boxes to minimize the sum of the value selected and the opening cost paid.
In this work we revisit Pandora’s Box when the value distributions are correlated, first studied in [CGT+20]. We show that the optimal algorithm for the independent case, given by Weitzman’s rule, directly works for the correlated case. In fact, our algorithm results in significantly improved approximation guarantees compared to the previous work, while also being substantially simpler. We also show how to implement the rule given only sample access to the correlated distribution of values. Specifically, we find that a number of samples that is polynomial in the number of boxes is sufficient for the algorithm to work.
Learning Mask-aware CLIP Representations for Zero-Shot Segmentation
Authors: Siyu Jiao; Yunchao Wei; Yaowei Wang; Yao Zhao; Humphrey Shi
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Recently, pre-trained vision-language models have been increasingly used to tackle the challenging zero-shot segmentation task. Typical solutions follow the paradigm of first generating mask proposals and then adopting CLIP to classify them. To maintain the CLIP's zero-shot transferability, previous practices favour to freeze CLIP during training. However, in the paper, we reveal that CLIP is insensitive to different mask proposals and tends to produce similar predictions for various mask proposals of the same image. This insensitivity results in numerous false positives when classifying mask proposals. This issue mainly relates to the fact that CLIP is trained with image-level supervision. To alleviate this issue, we propose a simple yet effective method, named Mask-aware Fine-tuning (MAFT). Specifically,  Image-Proposals CLIP Encoder (IP-CLIP Encoder) is proposed to handle arbitrary numbers of image and mask proposals simultaneously. Then, *mask-aware loss* and *self-distillation loss* are designed to fine-tune IP-CLIP Encoder, ensuring CLIP is responsive to different mask proposals while not sacrificing transferability. In this way, mask-aware representations can be easily learned to make the true positives stand out. Notably, our solution can seamlessly plug into most existing methods without introducing any new parameters during the fine-tuning process. We conduct extensive experiments on the popular zero-shot benchmarks. With MAFT, the performance of the state-of-the-art methods is promoted by a large margin: 50.4\% (+ 8.2\%) on COCO, 81.8\% (+ 3.2\%) on Pascal-VOC, and 8.7\% (+4.3\%) on ADE20K in terms of mIoU for unseen classes. Codes will be provided for reproducibility. Code is available at https://github.com/jiaosiyu1999/MAFT.git .
CoDrug: Conformal Drug Property Prediction with Density Estimation under Covariate Shift
Authors: Siddhartha Laghuvarapu; Zhen Lin; Jimeng Sun
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: In drug discovery, it is vital to confirm the predictions of pharmaceutical properties from computational models using costly wet-lab experiments. Hence, obtaining reliable uncertainty estimates is crucial for prioritizing drug molecules for subsequent experimental validation. Conformal Prediction (CP) is a promising tool for creating such prediction sets for molecular properties with a coverage guarantee. However, the exchangeability assumption of CP is often challenged with covariate shift in drug discovery tasks: Most datasets contain limited labeled data, which may not be representative of the vast chemical space from which molecules are drawn. To address this limitation, we propose a method called CoDrug that employs an energy-based model leveraging both training data and unlabelled data, and  Kernel Density Estimation (KDE) to assess the densities of a molecule set. The estimated densities are then used to weigh the molecule samples while building prediction sets and rectifying for distribution shift. In extensive experiments involving realistic distribution drifts in various small-molecule drug discovery tasks,  we demonstrate the ability of CoDrug to provide valid prediction sets and its utility in addressing the distribution shift arising from de novo drug design models. On average, using CoDrug can reduce the coverage gap by over 35% when compared to conformal prediction sets not adjusted for covariate shift.
Pitfall of Optimism: Distributional Reinforcement Learning by Randomizing Risk Criterion
Authors: Taehyun Cho; Seungyub Han; Heesoo Lee; Kyungjae Lee; Jungwoo Lee
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Distributional reinforcement learning algorithms have attempted to utilize estimated uncertainty for exploration, such as optimism in the face of uncertainty. However, using the estimated variance for optimistic exploration may cause biased data collection and hinder convergence or performance. In this paper, we present a novel distributional reinforcement learning that selects actions by randomizing risk criterion without losing the risk-neutral objective. We provide a perturbed distributional Bellman optimality operator by distorting the risk measure. Also,we prove the convergence and optimality of the proposed method with the weaker contraction property. Our theoretical results support that the proposed method does not fall into biased exploration and is guaranteed to converge to an optimal return. Finally, we empirically show that our method outperforms other existing distribution-based algorithms in various environments including Atari 55 games.
Learning Rule-Induced Subgraph Representations for Inductive Relation Prediction
Authors: Tianyu Liu; Qitan Lv; Jie Wang; Shuling Yang; Hanzhu Chen
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Inductive relation prediction (IRP)---where entities can be different during training and inference---has shown great power for completing evolving knowledge graphs. Existing works mainly focus on using graph neural networks (GNNs) to learn the representation of the subgraph induced from the target link, which can be seen as an implicit rule-mining process to measure the plausibility of the target link. However, these methods are not able to differentiate the target link and other links during message passing, hence the final subgraph representation will contain irrelevant rule information to the target link, which reduces the reasoning performance and severely hinders the applications for real-world scenarios. To tackle this problem, we propose a novel $\textit{single-source edge-wise}$ GNN model to learn the $\textbf{R}$ule-induc$\textbf{E}$d $\textbf{S}$ubgraph represen$\textbf{T}$ations $(\textbf{REST}$), which encodes relevant rules and eliminates irrelevant rules within the subgraph. Specifically, we propose a $\textit{single-source}$ initialization approach to initialize edge features only for the target link, which guarantees the relevance of mined rules and target link. Then we propose several RNN-based functions for $\textit{edge-wise}$ message passing to model the sequential property of mined rules. REST is a simple and effective approach with theoretical support to learn the $\textit{rule-induced subgraph representation}$. Moreover, REST does not need node labeling, which significantly accelerates the subgraph preprocessing time by up to $\textbf{11.66}\times$. Experiments on inductive relation prediction benchmarks demonstrate the effectiveness of our REST.
An Iterative Self-Learning Framework for Medical Domain Generalization
Authors: Zhenbang Wu; Huaxiu Yao; David Liebovitz; Jimeng Sun
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Deep learning models have been widely used to assist doctors with clinical decision-making. However, these models often encounter a significant performance drop when applied to data that differs from the distribution they were trained on. This challenge is known as the domain shift problem. Existing domain generalization algorithms attempt to address this problem by assuming the availability of domain IDs and training a single model to handle all domains. However, in healthcare settings, patients can be classified into numerous latent domains, where the actual domain categorizations are unknown. Furthermore, each patient domain exhibits distinct clinical characteristics, making it sub-optimal to train a single model for all domains. To overcome these limitations, we propose SLGD, a self-learning framework that iteratively discovers decoupled domains and trains personalized classifiers for each decoupled domain. We evaluate the generalizability of SLGD across spatial and temporal data distribution shifts on two real-world public EHR datasets: eICU and MIMIC-IV. Our results show that SLGD achieves up to 11% improvement in the AUPRC score over the best baseline.
HQA-Attack: Toward High Quality Black-Box Hard-Label Adversarial Attack on Text
Authors: Han Liu; Zhi Xu; Xiaotong Zhang; Feng Zhang; Fenglong Ma; Hongyang Chen; Hong Yu; Xianchao Zhang
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Black-box hard-label adversarial attack on text is a practical and challenging task, as the text data space is inherently discrete and non-differentiable, and only the predicted label is accessible. Research on this problem is still in the embryonic stage and only a few methods are available. Nevertheless, existing methods rely on the complex heuristic algorithm or unreliable gradient estimation strategy, which probably fall into the local optimum and inevitably consume numerous queries, thus are difficult to craft satisfactory adversarial examples with high semantic similarity and low perturbation rate in a limited query budget. To alleviate above issues, we propose a simple yet effective framework to generate high quality textual adversarial examples under the black-box hard-label attack scenarios, named HQA-Attack. Specifically, after initializing an adversarial example randomly, HQA-attack first constantly substitutes original words back as many as possible, thus shrinking the perturbation rate. Then it leverages the synonym set of the remaining changed words to further optimize the adversarial example with the direction which can improve the semantic similarity and satisfy the adversarial condition simultaneously. In addition, during the optimizing procedure, it searches a transition synonym word for each changed word, thus avoiding traversing the whole synonym set and reducing the query number to some extent. Extensive experimental results on five text classification datasets, three natural language inference datasets and two real-world APIs have shown that the proposed HQA-Attack method outperforms other strong baselines significantly.
Discriminative Feature Attributions: Bridging Post Hoc Explainability and Inherent Interpretability
Authors: Usha Bhalla; Suraj Srinivas; Himabindu Lakkaraju
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: With the increased deployment of machine learning models in various real-world applications, researchers and practitioners alike have emphasized the need for explanations of model behaviour. To this end, two broad strategies have been outlined in prior literature to explain models. Post hoc explanation methods explain the behaviour of complex black-box models by identifying features critical to model predictions; however, prior work has shown that these explanations may not be faithful, in that they incorrectly attribute high importance to features that are unimportant or non-discriminative for the underlying task. Inherently interpretable models, on the other hand, circumvent these issues by explicitly encoding explanations into model architecture, meaning their explanations are naturally faithful, but they often exhibit poor predictive performance due to their limited expressive power. In this work, we identify a key reason for the lack of faithfulness of feature attributions: the lack of robustness of the underlying black-box models, especially the erasure of unimportant distractor features in the input. To address this issue, we propose Distractor Erasure Tuning (DiET), a method that adapts black-box models to be robust to distractor erasure, thus providing discriminative and faithful attributions. This strategy naturally combines the ease-of-use of post hoc explanations with the faithfulness of inherently interpretable models. We perform extensive experiments on semi-synthetic and real-world datasets, and show that DiET produces models that (1) closely approximate the original black-box models they are intended to explain, and (2) yield explanations that match approximate ground truths available by construction.
EMMA-X: An EM-like Multilingual Pre-training Algorithm for Cross-lingual Representation Learning
Authors: Ping Guo; Xiangpeng Wei; Yue Hu; Baosong Yang; Dayiheng Liu; Fei Huang; Jun Xie
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Expressing universal semantics common to all languages is helpful to understand the meanings of complex and culture-specific sentences. The research theme underlying this scenario focuses on learning universal representations across languages with the usage of massive parallel corpora. However, due to the sparsity and scarcity of parallel data, there is still a big challenge in learning authentic ``universals'' for any two languages. In this paper, we propose Emma-X: an EM-like Multilingual pre-training Algorithm, to learn Cross-lingual universals with the aid of excessive multilingual non-parallel data. Emma-X unifies the cross-lingual representation learning task and an extra semantic relation prediction task within an EM framework. Both the extra semantic classifier and the cross-lingual sentence encoder approximate the semantic relation of two sentences, and supervise each other until convergence. To evaluate Emma-X, we conduct experiments on xrete, a newly introduced benchmark containing 12 widely studied cross-lingual tasks that fully depend on sentence-level representations. Results reveal that Emma-X achieves state-of-the-art performance. Further geometric analysis of the built representation space with three requirements demonstrates the superiority of Emma-X over advanced models.
Large Language Models Are Semi-Parametric Reinforcement Learning Agents
Authors: Danyang Zhang; Lu Chen; Situo Zhang; Hongshen Xu; Zihan Zhao; Kai Yu
Venue: NeurIPS 2023 (NeurIPS 2023 poster)

Abstract: Inspired by the insights in cognitive science with respect to human memory and reasoning mechanism, a novel evolvable LLM-based (Large Language Model) agent framework is proposed as Rememberer. By equipping the LLM with a long-term experience memory, Rememberer is capable of exploiting the experiences from the past episodes even for different task goals, which excels an LLM-based agent with fixed exemplars or equipped with a transient working memory. We further introduce **R**einforcement **L**earning with **E**xperience **M**emory (**RLEM**) to update the memory. Thus, the whole system can learn from the experiences of both success and failure, and evolve its capability without fine-tuning the parameters of the LLM. In this way, the proposed Rememberer constitutes a semi-parametric RL agent. Extensive experiments are conducted on two RL task sets to evaluate the proposed framework. The average results with different initialization and training sets exceed the prior SOTA by 4% and 2% for the success rate on two task sets and demonstrate the superiority and robustness of Rememberer.
HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution
Authors: Eric Nguyen; Michael Poli; Marjan Faizi; Armin W Thomas; Michael Wornow; Callum Birch-Sykes; Stefano Massaroli; Aman Patel; Clayton M. Rabideau; Yoshua Bengio; Stefano Ermon; Christopher Re; Stephen Baccus
Venue: NeurIPS 2023 (NeurIPS 2023 spotlight)

Abstract: Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers or fixed k-mers to aggregate meaningful DNA units, losing single nucleotide resolution (i.e. DNA "characters") where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyena’s new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level – an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 18 datasets using a model with orders of magnitude less parameters and pretraining data.1 On the GenomicBenchmarks, HyenaDNA surpasses SotA on 7 of 8 datasets on average by +10 accuracy points. Code at https://github.com/HazyResearch/hyena-dna.