OpenRaiser/Intern-Atlas huggingface dataset:
Tartarus: A Benchmarking Platform for Realistic And Practical Inverse Molecular Design
Venue: Conference NeurIPS 2023
Year: 2023

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.
Sample Complexity Bounds for Score-Matching: Causal Discovery and Generative Modeling
Venue: Conference NeurIPS 2023
Year: 2023

This paper provides statistical sample complexity bounds for score-matching and its applications in causal discovery. We demonstrate that accurate estimation of the score function is achievable by training a standard deep ReLU neural network using stochastic gradient descent. We establish bounds on the error rate of recovering causal relationships using the score-matching-based causal discovery method of Rolland et al. [2022], assuming a sufficiently good estimation of the score function. Finally, we analyze the upper bound of score-matching estimation within the score-based generative modeling, which has been applied for causal discovery but is also of independent interest within the domain of generative models.
Adversarial Robustness in Graph Neural Networks: A Hamiltonian Approach
Venue: Conference NeurIPS 2023
Year: 2023

Graph neural networks (GNNs) are vulnerable to adversarial perturbations, including those that affect both node features and graph topology. This paper investigates GNNs derived from diverse neural flows, concentrating on their connection to various stability notions such as BIBO stability, Lyapunov stability, structural stability, and conservative stability. We argue that Lyapunov stability, despite its common use, does not necessarily ensure adversarial robustness. Inspired by physics principles, we advocate for the use of conservative Hamiltonian neural flows to construct GNNs that are robust to adversarial attacks. The adversarial robustness of different neural flow GNNs is empirically compared on several benchmark datasets under a variety of adversarial attacks. Extensive numerical experiments demonstrate that GNNs leveraging conservative Hamiltonian flows with Lyapunov stability substantially improve robustness against adversarial perturbations. The implementation code of experiments is available at https://github.com/zknus/NeurIPS-2023-HANG-Robustness.
A Path to Simpler Models Starts With Noise
Venue: Conference NeurIPS 2023
Year: 2023

The Rashomon set is the set of models that perform approximately equally well on a given dataset, and the Rashomon ratio is the fraction of all models in a given hypothesis space that are in the Rashomon set. Rashomon ratios are often large for tabular datasets in criminal justice, healthcare, lending, education, and in other areas, which has practical implications about whether simpler models can attain the same level of accuracy as more complex models. An open question is why Rashomon ratios often tend to be large. In this work, we propose and study a mechanism of the data generation process, coupled with choices usually made by the analyst during the learning process, that determines the size of the Rashomon ratio. Specifically, we demonstrate that noisier datasets lead to larger Rashomon ratios through the way that practitioners train models. Additionally, we introduce a measure called pattern diversity, which captures the average difference in predictions between distinct classification patterns in the Rashomon set, and motivate why it tends to increase with label noise. Our results explain a key aspect of why simpler models often tend to perform as well as black box models on complex, noisier datasets.
Language Model Alignment with Elastic Reset
Venue: Conference NeurIPS 2023
Year: 2023

Finetuning language models with reinforcement learning (RL), e.g. from human feedback (HF), is a prominent method for alignment. But optimizing against a reward model can improve on reward while degrading performance in other areas, a phenomenon known as reward hacking, alignment tax, or language drift. First, we argue that commonly-used test metrics are insufficient and instead measure how different algorithms tradeoff between reward and drift. The standard method modified the reward with a Kullback-Lieber (KL) penalty between the online and initial model. We propose Elastic Reset, a new algorithm that achieves higher reward with less drift without explicitly modifying the training objective. We periodically reset the online model to an exponentially moving average (EMA) of itself, then reset the EMA model to the initial model. Through the use of an EMA, our model recovers quickly after resets and achieves higher reward with less drift in the same number of steps. We demonstrate that fine-tuning language models with Elastic Reset leads to state-of-the-art performance on a small scale pivot-translation benchmark, outperforms all baselines in a medium-scale RLHF-like IMDB mock sentiment task and leads to a more performant and more aligned technical QA chatbot with LLaMA-7B. Code available at github.com/mnoukhov/elastic-reset.
GlucoSynth: Generating Differentially-Private Synthetic Glucose Traces
Venue: Conference NeurIPS 2023
Year: 2023

We focus on the problem of generating high-quality, private synthetic glucose traces, a task generalizable to many other time series sources. Existing methods for time series data synthesis, such as those using Generative Adversarial Networks (GANs), are not able to capture the innate characteristics of glucose data and cannot provide any formal privacy guarantees without severely degrading the utility of the synthetic data. In this paper we present GlucoSynth, a novel privacy-preserving GAN framework to generate synthetic glucose traces. The core intuition behind our approach is to conserve relationships amongst motifs (glucose events) within the traces, in addition to temporal dynamics. Our framework incorporates differential privacy mechanisms to provide strong formal privacy guarantees. We provide a comprehensive evaluation on the real-world utility of the data using 1.2 million glucose traces; GlucoSynth outperforms all previous methods in its ability to generate high-quality synthetic glucose traces with strong privacy guarantees.
OBJECT 3DIT: Language-guided 3D-aware Image Editing
Venue: Conference NeurIPS 2023
Year: 2023

Existing image editing tools, while powerful, typically disregard the underlying 3D geometry from which the image is projected. As a result, edits made using these tools may become detached from the geometry and lighting conditions that are at the foundation of the image formation process. In this work, we formulate the newt ask of language-guided 3D-aware editing, where objects in an image should be edited according to a language instruction in context of the underlying 3D scene. To promote progress towards this goal, we release OBJECT: a dataset consisting of 400K editing examples created from procedurally generated 3D scenes. Each example consists of an input image, editing instruction in language, and the edited image. We also introduce 3DIT : single and multi-task models for four editing tasks. Our models show impressive abilities to understand the 3D composition of entire scenes, factoring in surrounding objects, surfaces, lighting conditions, shadows, and physically-plausible object configurations. Surprisingly, training on only synthetic scenes from OBJECT, editing capabilities of 3DIT generalize to real-world images.
Optimistic Natural Policy Gradient: a Simple Efficient Policy Optimization Framework  for Online RL
Venue: Conference NeurIPS 2023
Year: 2023

While policy optimization algorithms have played an important role in recent empirical success of Reinforcement Learning (RL), the existing theoretical understanding of policy optimization remains rather limited -- they are either restricted to tabular MDPs or suffer from highly suboptimal sample complexity, especial in online RL where exploration is necessary. This paper proposes a simple efficient policy optimization framework -- Optimistic NPG for online RL. Optimistic NPG can be viewed as a simple combination of the classic natural policy gradient (NPG) algorithm [Kakade, 2001] with optimistic policy evaluation subroutines to encourage exploration. For $d$-dimensional linear MDPs, Optimistic NPG is computationally efficient, and learns an $\varepsilon$-optimal policy within $\tilde{O}(d^2/\varepsilon^3)$ samples, which is the first computationally efficient algorithm whose sample complexity has the optimal dimension dependence $\tildeΘ(d^2)$. It also improves over state-of-the-art results of policy optimization algorithms [Zanette et al., 2021] by a factor of $d$. In the realm of general function approximation, which subsumes linear MDPs, Optimistic NPG, to our best knowledge, stands as the first policy optimization algorithm that achieves polynomial sample complexity for learning near-optimal policies.
A Computationally Efficient Sparsified Online Newton Method
Venue: Conference NeurIPS 2023
Year: 2023

Second-order methods hold significant promise for enhancing the convergence of deep neural network training; however, their large memory and computational demands have limited their practicality. Thus there is a need for scalable second-order methods that can efficiently train large models. In this paper, we introduce the Sparsified Online Newton (SONew) method, a memory-efficient second-order algorithm that yields a sparsified yet effective preconditioner. The algorithm emerges from a novel use of the LogDet matrix divergence measure; we combine it with sparsity constraints to minimize regret in the online convex optimization framework. Empirically, we test our method on large scale benchmarks of up to 1B parameters. We achieve up to 30% faster convergence, 3.4% relative improvement in validation performance, and 80% relative improvement in training loss, in comparison to memory efficient optimizers including first order methods. Powering the method is a surprising fact -- imposing structured sparsity patterns, like tridiagonal and banded structure, requires little to no overhead, making it as efficient and parallelizable as first-order methods. In wall-clock time, tridiagonal SONew is only about 3% slower per step than first-order methods but gives overall gains due to much faster convergence. In contrast, one of the state-of-the-art (SOTA) memory-intensive second-order methods, Shampoo, is unable to scale to large benchmarks. Additionally, while Shampoo necessitates significant engineering efforts to scale to large benchmarks, SONew offers a more straightforward implementation, increasing its practical appeal. SONew code is available at: https://github.com/devvrit/SONew
ConRad: Image Constrained Radiance Fields for 3D Generation from a Single Image
Venue: Conference NeurIPS 2023
Year: 2023

We present a novel method for reconstructing 3D objects from a single RGB image. Our method leverages the latest image generation models to infer the hidden 3D structure while remaining faithful to the input image. While existing methods obtain impressive results in generating 3D models from text prompts, they do not provide an easy approach for conditioning on input RGB data. Naïve extensions of these methods often lead to improper alignment in appearance between the input image and the 3D reconstructions. We address these challenges by introducing Image Constrained Radiance Fields (ConRad), a novel variant of neural radiance fields. ConRad is an efficient 3D representation that explicitly captures the appearance of an input image in one viewpoint. We propose a training algorithm that leverages the single RGB image in conjunction with pretrained Diffusion Models to optimize the parameters of a ConRad representation. Extensive experiments show that ConRad representations can simplify preservation of image details while producing a realistic 3D reconstruction. Compared to existing state-of-the-art baselines, we show that our 3D reconstructions remain more faithful to the input and produce more consistent 3D models while demonstrating significantly improved quantitative performance on a ShapeNet object benchmark.
Fair Canonical Correlation Analysis
Venue: Conference NeurIPS 2023
Year: 2023

This paper investigates fairness and bias in Canonical Correlation Analysis (CCA), a widely used statistical technique for examining the relationship between two sets of variables. We present a framework that alleviates unfairness by minimizing the correlation disparity error associated with protected attributes. Our approach enables CCA to learn global projection matrices from all data points while ensuring that these matrices yield comparable correlation levels to group-specific projection matrices. Experimental evaluation on both synthetic and real-world datasets demonstrates the efficacy of our method in reducing correlation disparity error without compromising CCA accuracy.
DIFUSCO: Graph-based Diffusion Solvers for Combinatorial Optimization
Venue: Conference NeurIPS 2023
Year: 2023

Neural network-based Combinatorial Optimization (CO) methods have shown promising results in solving various NP-complete (NPC) problems without relying on hand-crafted domain knowledge. This paper broadens the current scope of neural solvers for NPC problems by introducing a new graph-based diffusion framework, namely DIFUSCO. Our framework casts NPC problems as discrete {0, 1}-vector optimization problems and leverages graph-based denoising diffusion models to generate high-quality solutions. We investigate two types of diffusion models with Gaussian and Bernoulli noise, respectively, and devise an effective inference schedule to enhance the solution quality. We evaluate our methods on two well-studied NPC combinatorial optimization problems: Traveling Salesman Problem (TSP) and Maximal Independent Set (MIS). Experimental results show that DIFUSCO strongly outperforms the previous state-of-the-art neural solvers, improving the performance gap between ground-truth and neural solvers from 1.76% to 0.46% on TSP-500, from 2.46% to 1.17% on TSP-1000, and from 3.19% to 2.58% on TSP10000. For the MIS problem, DIFUSCO outperforms the previous state-of-the-art neural solver on the challenging SATLIB benchmark.
Exposing flaws of generative model evaluation metrics and their unfair treatment of diffusion models
Venue: Conference NeurIPS 2023
Year: 2023

We systematically study a wide variety of generative models spanning semantically-diverse image datasets to understand and improve the feature extractors and metrics used to evaluate them. Using best practices in psychophysics, we measure human perception of image realism for generated samples by conducting the largest experiment evaluating generative models to date, and find that no existing metric strongly correlates with human evaluations. Comparing to 17 modern metrics for evaluating the overall performance, fidelity, diversity, rarity, and memorization of generative models, we find that the state-of-the-art perceptual realism of diffusion models as judged by humans is not reflected in commonly reported metrics such as FID. This discrepancy is not explained by diversity in generated samples, though one cause is over-reliance on Inception-V3. We address these flaws through a study of alternative self-supervised feature extractors, find that the semantic information encoded by individual networks strongly depends on their training procedure, and show that DINOv2-ViT-L/14 allows for much richer evaluation of generative models. Next, we investigate data memorization, and find that generative models do memorize training examples on simple, smaller datasets like CIFAR10, but not necessarily on more complex datasets like ImageNet. However, our experiments show that current metrics do not properly detect memorization: none in the literature is able to separate memorization from other phenomena such as underfitting or mode shrinkage. To facilitate further development of generative models and their evaluation we release all generated image datasets, human evaluation data, and a modular library to compute 17 common metrics for 9 different encoders at https://github.com/layer6ai-labs/dgm-eval.
Online Clustering of Bandits with Misspecified User Models
Venue: Conference NeurIPS 2023
Year: 2023

The contextual linear bandit is an important online learning problem where given arm features, a learning agent selects an arm at each round to maximize the cumulative rewards in the long run. A line of works, called the clustering of bandits (CB), utilize the collaborative effect over user preferences and have shown significant improvements over classic linear bandit algorithms. However, existing CB algorithms require well-specified linear user models and can fail when this critical assumption does not hold. Whether robust CB algorithms can be designed for more practical scenarios with misspecified user models remains an open problem. In this paper, we are the first to present the important problem of clustering of bandits with misspecified user models (CBMUM), where the expected rewards in user models can be perturbed away from perfect linear models. We devise two robust CB algorithms, RCLUMB and RSCLUMB (representing the learned clustering structure with dynamic graph and sets, respectively), that can accommodate the inaccurate user preference estimations and erroneous clustering caused by model misspecifications. We prove regret upper bounds of $O(ε_*T\sqrt{md\log T} + d\sqrt{mT}\log T)$ for our algorithms under milder assumptions than previous CB works (notably, we move past a restrictive technical assumption on the distribution of the arms), which match the lower bound asymptotically in $T$ up to logarithmic factors, and also match the state-of-the-art results in several degenerate cases. The techniques in proving the regret caused by misclustering users are quite general and may be of independent interest. Experiments on both synthetic and real-world data show our outperformance over previous algorithms.
Double Auctions with Two-sided Bandit Feedback
Venue: Conference NeurIPS 2023
Year: 2023

Double Auction enables decentralized transfer of goods between multiple buyers and sellers, thus underpinning functioning of many online marketplaces. Buyers and sellers compete in these markets through bidding, but do not often know their own valuation a-priori. As the allocation and pricing happens through bids, the profitability of participants, hence sustainability of such markets, depends crucially on learning respective valuations through repeated interactions. We initiate the study of Double Auction markets under bandit feedback on both buyers' and sellers' side. We show with confidence bound based bidding, and `Average Pricing' there is an efficient price discovery among the participants. In particular, the regret on combined valuation of the buyers and the sellers -- a.k.a. the social regret -- is $O(\log(T)/Δ)$ in $T$ rounds, where $Δ$ is the minimum price gap. Moreover, the buyers and sellers exchanging goods attain $O(\sqrt{T})$ regret, individually. The buyers and sellers who do not benefit from exchange in turn only experience $O(\log{T}/ Δ)$ regret individually in $T$ rounds. We augment our upper bound by showing that $ω(\sqrt{T})$ individual regret, and $ω(\log{T})$ social regret is unattainable in certain Double Auction markets. Our paper is the first to provide decentralized learning algorithms in a two-sided market where \emph{both sides have uncertain preference} that need to be learned.
Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking
Venue: Conference NeurIPS 2023
Year: 2023

Link prediction attempts to predict whether an unseen edge exists based on only a portion of edges of a graph. A flurry of methods have been introduced in recent years that attempt to make use of graph neural networks (GNNs) for this task. Furthermore, new and diverse datasets have also been created to better evaluate the effectiveness of these new models. However, multiple pitfalls currently exist that hinder our ability to properly evaluate these new methods. These pitfalls mainly include: (1) Lower than actual performance on multiple baselines, (2) A lack of a unified data split and evaluation metric on some datasets, and (3) An unrealistic evaluation setting that uses easy negative samples. To overcome these challenges, we first conduct a fair comparison across prominent methods and datasets, utilizing the same dataset and hyperparameter search settings. We then create a more practical evaluation setting based on a Heuristic Related Sampling Technique (HeaRT), which samples hard negative samples via multiple heuristics. The new evaluation setting helps promote new challenges and opportunities in link prediction by aligning the evaluation with real-world situations. Our implementation and data are available at https://github.com/Juanhui28/HeaRT
EHRXQA: A Multi-Modal Question Answering Dataset for Electronic Health Records with Chest X-ray Images
Venue: Conference NeurIPS 2023
Year: 2023

Electronic Health Records (EHRs), which contain patients' medical histories in various multi-modal formats, often overlook the potential for joint reasoning across imaging and table modalities underexplored in current EHR Question Answering (QA) systems. In this paper, we introduce EHRXQA, a novel multi-modal question answering dataset combining structured EHRs and chest X-ray images. To develop our dataset, we first construct two uni-modal resources: 1) The MIMIC-CXR-VQA dataset, our newly created medical visual question answering (VQA) benchmark, specifically designed to augment the imaging modality in EHR QA, and 2) EHRSQL (MIMIC-IV), a refashioned version of a previously established table-based EHR QA dataset. By integrating these two uni-modal resources, we successfully construct a multi-modal EHR QA dataset that necessitates both uni-modal and cross-modal reasoning. To address the unique challenges of multi-modal questions within EHRs, we propose a NeuralSQL-based strategy equipped with an external VQA API. This pioneering endeavor enhances engagement with multi-modal EHR sources and we believe that our dataset can catalyze advances in real-world medical scenarios such as clinical decision-making and research. EHRXQA is available at https://github.com/baeseongsu/ehrxqa.