GenAI4ELab/papercli-papers huggingface dataset:
DeltaDock: A Unified Framework for Accurate, Efficient, and Physically Reliable Molecular Docking
Authors: Jiaxian Yan; ZAIXI ZHANG; Jintao Zhu; Kai Zhang; Jianfeng Pei; Qi Liu
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric deep learning (GDL), have demonstrated significant efficiency and accuracy advantages over traditional sampling methods. Despite these advancements, current methods are often tailored for specific docking settings, and limitations such as the neglect of protein side-chain structures, difficulties in handling large binding pockets, and challenges in predicting physically valid structures exist. To accommodate various docking settings and achieve accurate, efficient, and physically reliable docking, we propose a novel two-stage docking framework, DeltaDock, consisting of pocket prediction and site-specific docking. We innovatively reframe the pocket prediction task as a pocket-ligand alignment problem rather than direct prediction in the first stage. Then we follow a bi-level coarse-to-fine iterative refinement process to perform site-specific docking.  Comprehensive experiments demonstrate the superior performance of DeltaDock. Notably, in the blind docking setting, DeltaDock achieves a 31\% relative improvement over the docking success rate compared with the previous state-of-the-art GDL model 
DiffDock. With the consideration of physical validity, this improvement increases to about 300\%.
Partial Transportability for Domain Generalization
Authors: Kasra Jalaldoust; Alexis Bellot; Elias Bareinboim
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: A fundamental task in AI is providing performance guarantees for predictions made in unseen domains. In practice, there can be substantial uncertainty about the distribution of new data, and corresponding variability in the performance of existing predictors. Building on the theory of partial identification and transportability, this paper introduces new results for bounding the value of a functional of the target distribution, such as the generalization error of a classifiers, given data from source domains and assumptions about the data generating mechanisms, encoded in causal diagrams. Our contribution is to provide the first general estimation technique for transportability problems, adapting existing parameterization schemes such Neural Causal Models to encode the structural constraints necessary for cross-population inference. We demonstrate the expressiveness and consistency of this procedure and further propose a gradient-based optimization scheme for making scalable inferences in practice. Our results are corroborated with experiments.
Non-Stationary Learning of Neural Networks with Automatic Soft Parameter Reset
Authors: Alexandre Galashov; Michalis Titsias; András György; Clare Lyle; Razvan Pascanu; Yee Whye Teh; Maneesh Sahani
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Neural networks are most often trained under the assumption that data come from a stationary distribution. However, settings in which this assumption is violated are of increasing importance; examples include supervised learning with distributional shifts, reinforcement learning, continual learning and non-stationary contextual bandits. Here, we introduce a novel learning approach that automatically models and adapts to non-stationarity by linking parameters through an Ornstein-Uhlenbeck process with an adaptive drift parameter. The adaptive drift draws the parameters towards the distribution used at initialisation, so the approach can be understood as a form of soft parameter reset. We show empirically that our approach performs well in non-stationary supervised, and off-policy reinforcement learning settings.
Task-Agnostic Machine-Learning-Assisted Inference
Authors: Jiacheng Miao; Qiongshi Lu
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Machine learning (ML) is playing an increasingly important role in scientific research. In conjunction with classical statistical approaches, ML-assisted analytical strategies have shown great promise in accelerating research findings. This has also opened a whole field of methodological research focusing on integrative approaches that leverage both ML and statistics to tackle data science challenges. One type of study that has quickly gained popularity employs ML to predict unobserved outcomes in massive samples, and then uses predicted outcomes in downstream statistical inference. However, existing methods designed to ensure the validity of this type of post-prediction inference are limited to very basic tasks such as linear regression analysis. This is because any extension of these approaches to new, more sophisticated statistical tasks requires task-specific algebraic derivations and software implementations, which ignores the massive library of existing software tools already developed for the same scientific problem given observed data. This severely constrains the scope of application for post-prediction inference. To address this challenge, we introduce a novel statistical framework named PSPS for task-agnostic ML-assisted inference. It provides a post-prediction inference solution that can be easily plugged into almost any established data analysis routines. It delivers valid and efficient inference that is robust to arbitrary choice of ML model, allowing nearly all existing statistical frameworks to be incorporated into the analysis of ML-predicted data. Through extensive experiments, we showcase our method’s validity, versatility, and superiority compared to existing approaches. Our software is available at https://github.com/qlu-lab/psps.
Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning
Authors: Yuxuan Ren; Dihan Zheng; Chang Liu; Peiran Jin; Yu Shi; Lin Huang; Jiyan He; Shengjie Luo; Tao Qin; Tie-Yan Liu
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning models are trained in the multi-task learning paradigm. Nevertheless, data of different molecular properties are often not aligned: some quantities, e.g. equilibrium structure, demand more cost to compute than others, e.g. energy, so their data are often generated by cheaper computational methods at the cost of lower accuracy, which cannot be directly overcome through multi-task learning. Moreover, it is not straightforward to leverage abundant data of other tasks to benefit a particular task. To handle such data heterogeneity challenges, we exploit the specialty of molecular tasks that there are physical laws connecting them, and design consistency training approaches that allow different tasks to exchange information directly so as to improve one another. Particularly, we demonstrate that the more accurate energy data can improve the accuracy of structure prediction. We also find that consistency training can directly leverage force and off-equilibrium structure data to improve structure prediction, demonstrating a broad capability for integrating heterogeneous data.
Improved Particle Approximation Error for Mean Field Neural Networks
Authors: Atsushi Nitanda
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Mean-field Langevin dynamics (MFLD) minimizes an entropy-regularized nonlinear convex functional defined over the space of probability distributions. MFLD has gained attention due to its connection with noisy gradient descent for mean-field two-layer neural networks. Unlike standard Langevin dynamics, the nonlinearity of the objective functional induces particle interactions, necessitating multiple particles to approximate the dynamics in a finite-particle setting. Recent works (Chen et al., 2022; Suzuki et al., 2023b) have demonstrated the uniform-in-time propagation of chaos for MFLD, showing that the gap between the particle system and its mean-field limit uniformly shrinks over time as the number of particles increases. In this work, we improve the dependence on logarithmic Sobolev inequality (LSI) constants in their particle approximation errors, which can exponentially deteriorate with the regularization coefficient. Specifically, we establish an LSI-constant-free particle approximation error concerning the objective gap by leveraging the problem structure in risk minimization. As the application, we demonstrate improved convergence of MFLD, sampling guarantee for the mean-field stationary distribution, and uniform-in-time Wasserstein propagation of chaos in terms of particle complexity.
Scalable Kernel Inverse Optimization
Authors: Youyuan Long; Tolga Ok; Pedro Zattoni Scroccaro; Peyman Mohajerin Esfahani
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Inverse Optimization (IO) is a framework for learning the unknown objective function of an expert decision-maker from a past dataset.
In this paper, we extend the hypothesis class of IO objective functions to a reproducing kernel Hilbert space (RKHS), thereby enhancing feature representation to an infinite-dimensional space.
We demonstrate that a variant of the representer theorem holds for a specific training loss, allowing the reformulation of the problem as a finite-dimensional convex optimization program.
To address scalability issues commonly associated with kernel methods, we propose the Sequential Selection Optimization (SSO) algorithm to efficiently train the proposed Kernel Inverse Optimization (KIO) model.
Finally, we validate the generalization capabilities of the proposed KIO model and the effectiveness of the SSO algorithm through learning-from-demonstration tasks on the MuJoCo benchmark.
MAC Advice for facility location mechanism design
Authors: Zohar Barak; Anupam Gupta; Inbal Talgam-Cohen
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Algorithms with predictions are gaining traction across various domains, as a way to surpass traditional worst-case bounds through (machine-learned) advice. We study the canonical problem of $k$-facility location mechanism design,
where the $n$ agents are strategic and might misreport their locations. We receive a prediction for each agent's location, and these predictions are crucially allowed to be only "mostly" and "approximately" correct (MAC for short): a $\delta$-fraction of the predicted locations are allowed to be arbitrarily incorrect, and the remainder of the predictions are required to be correct up to an $\varepsilon$-error. Moreover, we make no assumption on the independence of the errors.
Can such "flawed" predictions allow us to beat the current best bounds for strategyproof
facility location?

We show how natural robustness of the $1$-median (also known as the geometric median) of a set of points leads to an algorithm for single-facility location with MAC predictions. We extend our results to a natural "balanced" variant of the $k$-facility case, and show that without balancedness, robustness completely breaks down even for $k=2$ facilities on a line. As our main result, for this "unbalanced" setting we devise a truthful random mechanism, which outperforms the best known mechanism (with no predictions) by Lu et al.~[2010]. En route, we introduce the problem of "second" facility location, in which the first facility location is already fixed. Our robustness findings may be of independent interest, as quantitative versions of classic breakdown-point results in robust statistics.
Improving Linear System Solvers for Hyperparameter Optimisation in Iterative Gaussian Processes
Authors: Jihao Andreas Lin; Shreyas Padhy; Bruno Kacper Mlodozeniec; Javier Antoran; José Miguel Hernández-Lobato
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Scaling hyperparameter optimisation to very large datasets remains an open problem in the Gaussian process community. This paper focuses on iterative methods, which use linear system solvers, like conjugate gradients, alternating projections or stochastic gradient descent, to construct an estimate of the marginal likelihood gradient. We discuss three key improvements which are applicable across solvers: (i) a pathwise gradient estimator, which reduces the required number of solver iterations and amortises the computational cost of making predictions, (ii) warm starting linear system solvers with the solution from the previous step, which leads to faster solver convergence at the cost of negligible bias, (iii) early stopping linear system solvers after a limited computational budget, which synergises with warm starting, allowing solver progress to accumulate over multiple marginal likelihood steps. These techniques provide speed-ups of up to $72\times$ when solving to tolerance, and decrease the average residual norm by up to $7\times$ when stopping early.
BendVLM: Test-Time Debiasing of Vision-Language Embeddings
Authors: Walter Gerych; Haoran Zhang; Kimia Hamidieh; Eileen Pan; Maanas Sharma; Thomas Hartvigsen; Marzyeh Ghassemi
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Vision-language (VL) embedding models have been shown to encode biases present in their training data, such as societal biases that prescribe negative characteristics to members of various racial and gender identities. Due to their wide-spread adoption for various tasks ranging from few-shot classification to text-guided image generation, debiasing VL models is crucial. Debiasing approaches that fine-tune the VL model often suffer from catastrophic forgetting. On the other hand, fine-tuning-free methods typically utilize a ``one-size-fits-all" approach that assumes that correlation with the spurious attribute can be explained using a single linear direction across all possible inputs. In this work, we propose a nonlinear, fine-tuning-free approach for VL embedding model debiasing that tailors the debiasing operation to each unique input. This allows for a more flexible debiasing approach. Additionally, we do not require knowledge of the set of inputs a priori to inference time, making our method more appropriate for online tasks such as retrieval and text guided image generation.
Boosting Alignment for Post-Unlearning Text-to-Image Generative Models
Authors: Myeongseob Ko; Henry Li; Zhun Wang; Jonathan Patsenker; Jiachen T. Wang; Qinbin Li; Ming Jin; Dawn Song; Ruoxi Jia
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Large-scale generative models have shown impressive image-generation capabilities, propelled by massive data. However, this often inadvertently leads to the generation of harmful or inappropriate content and raises copyright concerns. Driven by these concerns, machine unlearning has become crucial to effectively purge undesirable knowledge from models. While existing literature has studied various unlearning techniques, these often suffer from either poor unlearning quality or degradation in text-image alignment after unlearning, due to the competitive nature of these objectives. To address these challenges, we propose a framework that seeks an optimal model update at each unlearning iteration, ensuring monotonic improvement on both objectives. We further derive the characterization of such an update.
  In addition, we design procedures to strategically diversify the unlearning and remaining datasets to boost performance improvement. Our evaluation demonstrates that our method effectively removes target classes from recent diffusion-based generative models and concepts from stable diffusion models while maintaining close alignment with the models' original trained states, thus outperforming state-of-the-art baselines.
Bileve: Securing Text Provenance in Large Language Models Against Spoofing with Bi-level Signature
Authors: Tong Zhou; Xuandong Zhao; Xiaolin Xu; Shaolei Ren
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Text watermarks for large language models (LLMs) have been commonly used to identify the origins of machine-generated content, which is promising for assessing liability when combating deepfake or harmful content. While existing watermarking techniques typically prioritize robustness against removal attacks, unfortunately, they are vulnerable to spoofing attacks: malicious actors can subtly alter the meanings of LLM-generated responses or even forge harmful content, potentially misattributing blame to the LLM developer. To overcome this, we introduce a bi-level signature scheme, Bileve, which embeds fine-grained signature bits for integrity checks (mitigating spoofing attacks) as well as a coarse-grained signal to trace text sources when the signature is invalid (enhancing detectability) via a novel rank-based sampling strategy. Compared to conventional watermark detectors that only output binary results, Bileve can differentiate 5 scenarios during detection, reliably tracing text provenance and regulating LLMs. The experiments conducted on OPT-1.3B and LLaMA-7B demonstrate the effectiveness of Bileve in defeating spoofing attacks with enhanced detectability.
Small steps no more: Global convergence of stochastic gradient bandits for arbitrary learning rates
Authors: Jincheng Mei; Bo Dai; Alekh Agarwal; Sharan Vaswani; Anant Raj; Csaba Szepesvari; Dale Schuurmans
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We provide a new understanding of the stochastic gradient bandit algorithm by showing that it converges to a globally optimal policy almost surely using \emph{any} constant learning rate. This result demonstrates that the stochastic gradient algorithm continues to balance exploration and exploitation appropriately even in scenarios where standard smoothness and noise control assumptions break down. The proofs are based on novel findings about action sampling rates and the relationship between cumulative progress and noise, and extend the current understanding of how simple stochastic gradient methods behave in bandit settings.
Prospective Learning: Learning for a Dynamic Future
Authors: Ashwin De Silva; Rahul Ramesh; Rubing Yang; Siyu Yu; Joshua T Vogelstein; Pratik Chaudhari
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: In real-world applications, the distribution of the data, and our goals, evolve over time. The prevailing theoretical framework for studying machine learning, namely probably approximately correct (PAC) learning, largely ignores time. As a consequence, existing strategies to address the dynamic nature of data and goals exhibit poor real-world performance. This paper develops a theoretical framework called
"Prospective Learning" that is tailored for situations when the optimal hypothesis changes over time. In PAC learning, empirical risk minimization (ERM) is known to be consistent. We develop a learner called Prospective ERM, which returns a sequence of predictors that  make predictions on future data.  We prove that the risk of prospective ERM converges to the Bayes risk under certain assumptions on the stochastic process  generating the data. Prospective ERM, roughly speaking, incorporates time as an input in addition to the data. We show that standard ERM as done in PAC learning, without incorporating time, can result in failure to learn when distributions are dynamic. Numerical experiments illustrate that prospective ERM can learn synthetic and visual recognition problems constructed from MNIST and CIFAR-10. Code at https://github.com/neurodata/prolearn.
Boosting Generalization in Parametric PDE Neural Solvers through Adaptive Conditioning
Authors: Armand Kassaï Koupaï; Jorge Mifsut Benet; Yuan Yin; Jean-Noël Vittaut; Patrick Gallinari
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Solving parametric partial differential equations (PDEs) presents significant challenges for data-driven methods due to the sensitivity of spatio-temporal dynamics to variations in PDE parameters. Machine learning approaches often struggle to capture this variability. To address this, data-driven approaches learn parametric PDEs by sampling a very large variety of trajectories with varying PDE parameters. We first show that incorporating conditioning mechanisms for learning parametric PDEs is essential and that among them, \textit{adaptive conditioning}, allows stronger generalization. As existing adaptive conditioning methods do not scale well with respect to the number of parameters to adapt in the neural solver, we propose GEPS, a simple adaptation mechanism to boost GEneralization in Pde Solvers via a first-order optimization and low-rank rapid adaptation of a small set of context parameters. We demonstrate the versatility of our approach for both fully data-driven and for physics-aware neural solvers. Validation performed on a whole range of spatio-temporal forecasting problems demonstrates excellent performance for generalizing to unseen conditions including initial conditions, PDE coefficients, forcing terms and solution domain. *Project page*: https://geps-project.github.io
Constrained Adaptive Attack: Effective Adversarial Attack Against Deep Neural Networks for Tabular Data
Authors: Thibault Simonetto; Salah GHAMIZI; Maxime Cordy
Venue: NeurIPS 2024 (NeurIPS 2024 spotlight)

Abstract: State-of-the-art deep learning models for tabular data have recently achieved acceptable performance to be deployed in industrial settings. However, the robustness of these models remains scarcely explored. Contrary to computer vision, there are no effective attacks to properly evaluate the adversarial robustness of deep tabular models due to intrinsic properties of tabular data, such as categorical features, immutability, and feature relationship constraints. To fill this gap, we first propose CAPGD, a gradient attack that overcomes the failures of existing gradient attacks with adaptive mechanisms. This new attack does not require parameter tuning and further degrades the accuracy, up to 81\% points compared to the previous gradient attacks. Second, we design CAA, an efficient evasion attack that combines our CAPGD attack and MOEVA, the best search-based attack.  We demonstrate the effectiveness of our attacks on five architectures and four critical use cases. Our empirical study demonstrates that CAA outperforms all existing attacks in 17 over the 20 settings, and leads to a drop in the accuracy by up to 96.1\% points and 21.9\% points compared to CAPGD and MOEVA respectively while being up to five times faster than MOEVA. Given the effectiveness and efficiency of our new attacks, we argue that they should become the minimal test for any new defense or robust architectures in tabular machine learning.