GenAI4ELab/papercli-papers huggingface dataset:
On the Scalability of GNNs for Molecular Graphs
Authors: Maciej Sypetkowski; Frederik Wenkel; Farimah Poursafaei; Nia Dickson; Karush Suri; Philip Fradkin; Dominique Beaini
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have observed a strong relationship between model size, dataset size, and performance. However, structure-based architectures such as Graph Neural Networks (GNNs) are yet to show the benefits of scale mainly due to lower efficiency of sparse operations, large data requirements, and lack of clarity about the effectiveness of various architectures. We address this drawback of GNNs by studying their scaling behavior. Specifically, we analyze message-passing networks, graph Transformers, and hybrid architectures on the largest public collection of 2D molecular graphs for supervised pretraining. For the first time, we observe that GNNs benefit tremendously from the increasing scale of depth, width, number of molecules and associated labels. A major factor is the diversity of the pretraining data that comprises thousands of labels per molecule derived from bio-assays, quantum simulations, transcriptomics and phenomic imaging. We further demonstrate strong finetuning scaling behavior on 38 highly competitive downstream tasks, outclassing previous large models. This gives rise to MolGPS, a new graph foundation model that allows to navigate the chemical space, outperforming the previous state-of-the-arts on 26 out the 38 downstream tasks. We hope that our work paves the way for an era where foundational GNNs drive pharmaceutical drug discovery.
DiffPO: A causal diffusion model for learning distributions of potential outcomes
Authors: Yuchen Ma; Valentyn Melnychuk; Jonas Schweisthal; Stefan Feuerriegel
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Predicting potential outcomes of interventions from observational data is crucial for decision-making in medicine, but the task is challenging due to the fundamental problem of causal inference. Existing methods are largely limited to point estimates of potential outcomes with no uncertain quantification; thus, the full information about the distributions of potential outcomes is typically ignored. In this paper, we propose a novel causal diffusion model called DiffPO, which is carefully designed for reliable inferences in medicine by learning the distribution of potential outcomes. In our DiffPO, we leverage a tailored conditional denoising diffusion model to learn complex distributions, where we address the selection bias through a novel orthogonal diffusion loss. Another strength of our DiffPO method is that it is highly flexible (e.g., it can also be used to estimate different causal quantities such as CATE). Across a wide range of experiments, we show that our method achieves state-of-the-art performance.
CAT3D: Create Anything in 3D with Multi-View Diffusion Models
Authors: Ruiqi Gao; Aleksander Holynski; Philipp Henzler; Arthur Brussee; Ricardo Martin Brualla; Pratul P. Srinivasan; Jonathan T. Barron; Ben Poole
Venue: NeurIPS 2024 (NeurIPS 2024 oral)

Abstract: Advances in 3D reconstruction have enabled high-quality 3D capture, but require a user to collect hundreds to thousands of images to create a 3D scene. We present CAT3D, a method for creating anything in 3D by simulating this real-world capture process with a multi-view diffusion model. Given any number of input images and a set of target novel viewpoints, our model generates highly consistent novel views of a scene. These generated views can be used as input to robust 3D reconstruction techniques to produce 3D representations that can be rendered from any viewpoint in real-time. CAT3D can create entire 3D scenes in as little as one minute, and outperforms existing methods for single image and few-view 3D scene creation.
Online Learning with Sublinear Best-Action Queries
Authors: Matteo Russo; Andrea Celli; Riccardo Colini Baldeschi; Federico Fusco; Daniel Haimovich; Dima Karamshuk; Stefano Leonardi; Niek Tax
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: In online learning, a decision maker repeatedly selects one of a set of actions, with the goal of minimizing the overall loss incurred. Following the recent line of research on algorithms endowed with additional predictive features, we revisit this problem by allowing the decision maker to acquire additional information on the actions to be selected. In particular, we study the power of \emph{best-action queries}, which reveal beforehand the identity of the best action at a given time step. In practice, predictive features may be expensive, so we allow the decision maker to issue at most $k$ such queries.

We establish tight bounds on the performance any algorithm can achieve when given access to $k$ best-action queries for different types of feedback models. In particular, we prove that in the full feedback model,  $k$ queries are enough to achieve an optimal regret of $\Theta(\min\{\sqrt T, \frac{T}{k}\})$. This finding highlights the significant multiplicative advantage in the regret rate achievable with even a modest (sublinear) number $k \in \Omega(\sqrt{T})$ of queries.
    
Additionally, we study the challenging setting in which the only available feedback is  obtained during the time steps corresponding to the $k$ best-action queries. There, we provide a tight regret rate of $\Theta(\min\{\frac{T}{\sqrt k},\frac{T^2}{k^2}\})$, which improves over the standard $\Theta(\frac{T}{\sqrt k})$ regret rate for label efficient prediction for $k \in \Omega(T^{2/3})$.
Parallelizing Linear Transformers with the Delta Rule over Sequence Length
Authors: Songlin Yang; Bailin Wang; Yu Zhang; Yikang Shen; Yoon Kim
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Transformers with linear attention (i.e., linear transformers) and state-space models have recently been suggested as a viable linear-time alternative to transformers with softmax attention. However, these models still underperform transformers especially on tasks that require in-context retrieval. While more expressive variants of linear transformers which replace the additive update in linear transformers with the delta rule (DeltaNet) have been found to be more effective at associative recall, existing algorithms for training such models do not parallelize over sequence length and are thus inefficient to train on modern hardware. This work describes a hardware-efficient algorithm for training linear transformers with the delta rule, which exploits a memory-efficient representation for computing products of Householder matrices. This algorithm allows us to scale up DeltaNet to standard language modeling settings. We train a 1.3B model for 100B tokens and find that it outperforms recent linear-time baselines such as Mamba and GLA in terms of perplexity and zero-shot performance on downstream tasks. We also experiment with two hybrid models which combine DeltaNet layers with (1) sliding-window attention layers every other layer or (2) two global attention layers, and find that these hybrids outperform strong transformer baselines.
Preference Alignment with Flow Matching
Authors: Minu Kim; Yongsik Lee; Sehyeok Kang; Jihwan Oh; Song Chong; Se-Young Yun
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We present Preference Flow Matching (PFM), a new framework for preference alignment that streamlines the integration of preferences into an arbitrary class of pre-trained models. Existing alignment methods require fine-tuning pre-trained models, which presents challenges such as scalability, inefficiency, and the need for model modifications, especially with black-box APIs like GPT-4. In contrast, PFM utilizes flow matching techniques to directly learn from preference data, thereby reducing the dependency on extensive fine-tuning of pre-trained models. By leveraging flow-based models, PFM transforms less preferred data into preferred outcomes, and effectively aligns model outputs with human preferences without relying on explicit or implicit reward function estimation, thus avoiding common issues like overfitting in reward models. We provide theoretical insights that support our method’s alignment with standard preference alignment objectives. Experimental results indicate the practical effectiveness of our method, offering a new direction in aligning a pre-trained model to preference. Our code is available at https://github.com/jadehaus/preference-flow-matching.
Dynamic Service Fee Pricing under Strategic Behavior: Actions as Instruments and Phase Transition
Authors: Rui Ai; David Simchi-Levi; Feng Zhu
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We study a dynamic pricing problem for third-party platform service fees under strategic, far-sighted customers. In each time period, the platform sets a service fee based on historical data, observes the resulting transaction quantities, and collects revenue. The platform also monitors equilibrium prices influenced by both demand and supply. The objective is to maximize total revenue over a time horizon $T$. Our problem incorporates three practical challenges: (a) initially, the platform lacks knowledge of the demand side beforehand, necessitating a balance between exploring (learning the demand curve) and exploiting (maximizing revenue) simultaneously; (b) since only equilibrium prices and quantities are observable, traditional Ordinary Least Squares (OLS) estimators would be biased and inconsistent; (c) buyers are rational and strategic, seeking to maximize their consumer surplus and potentially misrepresenting their preferences. To address these challenges, we propose novel algorithmic solutions. Our approach involves: (i) a carefully designed active randomness injection to balance exploration and exploitation effectively; (ii) using non-i.i.d. actions as instrumental variables (IV) to consistently estimate demand; (iii) a low-switching cost design that promotes nearly truthful buyer behavior. We show an expected regret bound of $\tilde{\mathcal{O}} (\sqrt{T}\wedge\sigma_S^{-2})$ and demonstrate its optimality, up to logarithmic factors, with respect to both the time horizon $T$ and the randomness in supply $\sigma_S$. Despite its simplicity, our model offers valuable insights into the use of actions as estimation instruments, the benefits of low-switching pricing policies in mitigating strategic buyer behavior, and the role of supply randomness in facilitating exploration which leads to a phase transition of policy performance.
Boosted Conformal Prediction Intervals
Authors: Ran Xie; Rina Foygel Barber; Emmanuel Candes
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: This paper introduces a boosted conformal procedure designed to tailor conformalized prediction intervals toward specific desired properties, such as enhanced conditional coverage or reduced interval length. We employ machine learning techniques, notably gradient boosting, to systematically improve upon a predefined conformity score function. This process is guided by carefully constructed loss functions that measure the deviation of prediction intervals from the targeted properties. The procedure operates post-training, relying solely on model predictions and without modifying the trained model (e.g., the deep network).  Systematic experiments demonstrate that starting from conventional conformal methods, our boosted procedure achieves substantial improvements in reducing interval length and decreasing deviation from target conditional coverage.
The tree autoencoder model, with application to hierarchical data visualization
Authors: Miguel Á. Carreira-Perpiñán; Kuat Gazizov
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: We propose a new model for dimensionality reduction, the PCA tree, which works like a regular autoencoder, having explicit projection and reconstruction mappings. The projection is effected by a sparse oblique tree, having hard, hyperplane splits using few features and linear leaves. The reconstruction mapping is a set of local linear mappings. Thus, rather than producing a global map as in t-SNE and other methods, which often leads to distortions, it produces a hierarchical set of local PCAs. The use of a sparse oblique tree and PCA makes the overall model interpretable and very fast to project or reconstruct new points. Joint optimization of all the parameters in the tree is a nonconvex nondifferentiable problem. We propose an algorithm that is guaranteed to decrease the error monotonically and which scales to large datasets without any approximation. In experiments, we show PCA trees are able to identify a wealth of low-dimensional and cluster structure in image and document datasets.
Exploration by Learning Diverse Skills through Successor State Representations
Authors: Paul-Antoine LE TOLGUENEC; Yann BESSE; Florent Teichteil-Königsbuch; Dennis George Wilson; Emmanuel Rachelson
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: The ability to perform different skills can encourage agents to explore. In this work, we aim to construct a set of diverse skills that uniformly cover the state space. We propose a formalization of this search for diverse skills, building on a previous definition based on the mutual information between states and skills. We consider the distribution of states reached by a policy conditioned on each skill and leverage the successor state representation to maximize the difference between these skill distributions. We call this approach LEADS: Learning Diverse Skills through Successor State Representations. We demonstrate our approach on a set of maze navigation and robotic control tasks which show that our method is capable of constructing a diverse set of skills which exhaustively cover the state space without relying on reward or exploration bonuses. Our findings demonstrate that this new formalization promotes more robust and efficient exploration by combining mutual information maximization and exploration bonuses.
SpecExec: Massively Parallel Speculative Decoding For Interactive LLM Inference on Consumer Devices
Authors: Ruslan Svirschevski; Avner May; Zhuoming Chen; Beidi Chen; Zhihao Jia; Max Ryabinin
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: As large language models gain widespread adoption, running them efficiently becomes a crucial task. Recent works on LLM inference use speculative decoding to achieve extreme speedups. However, most of these works implicitly design their algorithms for high-end datacenter hardware. In this work, we ask the opposite question: how fast can we run LLMs on consumer machines? Consumer GPUs can no longer fit the largest available models and must offload them to RAM or SSD. With parameter offloading, hundreds or thousands of tokens can be processed in batches within the same time as just one token, making it a natural fit for speculative decoding. We propose SpecExec (Speculative Execution), a simple parallel decoding method that can generate up to 20 tokens per target model iteration for popular LLM families.  SpecExec takes the most probable continuations from the draft model to build a "cache" tree for the target model, which then gets validated in a single pass. Using SpecExec, we demonstrate inference of 50B+ parameter LLMs on consumer GPUs with RAM offloading at 4--6 tokens per second with 4-bit quantization or 2--3 tokens per second with 16-bit weights. Our code is available at https://github.com/yandex-research/specexec .
Interpretable Generalized Additive Models for Datasets with Missing Values
Authors: Hayden McTavish; Jon Donnelly; Margo Seltzer; Cynthia Rudin
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Many important datasets contain samples that are missing one or more feature values. Maintaining the interpretability of machine learning models in the presence of such missing data is challenging. Singly or multiply imputing missing values complicates the model’s mapping from features to labels. On the other hand, reasoning on indicator variables that represent missingness introduces a potentially large number of additional terms, sacrificing sparsity. We solve these problems with M-GAM, a sparse, generalized, additive modeling approach that incorporates missingness indicators and their interaction terms while maintaining sparsity through $\ell_0$ regularization. We show that M-GAM provides similar or superior accuracy to prior methods while significantly improving sparsity relative to either imputation or naïve inclusion of indicator variables.
The Feature Speed Formula: a flexible approach to scale hyper-parameters of deep neural networks
Authors: Lénaïc Chizat; Praneeth Netrapalli
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Deep learning succeeds by doing hierarchical feature learning, yet tuning hyper-parameters (HP) such as initialization scales, learning rates etc., only give indirect control over this behavior. In this paper, we introduce a key notion to predict and control feature learning: the angle $\theta_\ell$ between the feature updates and the backward pass (at layer index $\ell$). We show that the magnitude of feature updates after one GD step, at any training time, can be expressed via a simple and general *feature speed formula* in terms of this angle $\theta_\ell$, the loss decay, and the magnitude of the backward pass. This angle $\theta_\ell$ is controlled by the conditioning of the layer-to-layer Jacobians and at random initialization, it is determined by the spectrum of a certain kernel, which coincides with the Neural Tangent Kernel when $\ell=\text{depth}$. Given $\theta_\ell$, the feature speed formula provides us with rules to adjust HPs (scales and learning rates) so as to satisfy certain dynamical properties, such as feature learning and loss decay. We investigate the implications of our approach for ReLU MLPs and ResNets in the large width-then-depth limit. Relying on prior work, we show that in ReLU MLPs with iid initialization, the angle degenerates with depth as $\cos(\theta_\ell)=\Theta(1/\sqrt{\ell})$. In contrast, ResNets with branch scale  $O(1/\sqrt{\text{depth}})$ maintain a non-degenerate angle $\cos(\theta_\ell)=\Theta(1)$. We use these insights to recover key properties of known HP scalings (such as $\mu$P), and also introduce a new HP scaling for large depth ReLU MLPs with favorable theoretical properties.
Inference of Neural Dynamics Using Switching Recurrent Neural Networks
Authors: Yongxu Zhang; Shreya Saxena
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Neural population activity often exhibits distinct dynamical features across time, which may correspond to distinct internal processes or behavior. Linear methods and variations thereof, such as Hidden Markov Model (HMM) and Switching Linear Dynamical System (SLDS), are often employed to identify discrete states with evolving neural dynamics. However, these techniques may not be able to capture the underlying nonlinear dynamics associated with neural propagation. Recurrent Neural Networks (RNNs) are commonly used to model neural dynamics thanks to their nonlinear characteristics. In our work, we develop Switching Recurrent Neural Networks (SRNN), RNNs with weights that switch across time, to reconstruct switching dynamics of neural time-series data. We apply these models to simulated data as well as cortical neural activity across mice and monkeys, which allows us to automatically detect discrete states that lead to the identification of varying neural dynamics. In a monkey reaching dataset with electrophysiology recordings, a mouse self-initiated lever pull dataset with widefield calcium recordings, and a mouse self-initiated decision making dataset with widefield calcium recording, SRNNs are able to automatically identify discrete states with distinct nonlinear neural dynamics. The inferred switches are aligned with the behavior, and the reconstructions show that the recovered neural dynamics are distinct across different stages of the behavior. We show that the neural dynamics have behaviorally-relevant switches across time and we are able to use SRNNs to successfully capture these switches and the corresponding dynamical features.
Mutli-Armed Bandits with Network Interference
Authors: Abhineet Agarwal; Anish Agarwal; Lorenzo Masoero; Justin Whitehouse
Venue: NeurIPS 2024 (NeurIPS 2024 poster)

Abstract: Online experimentation with interference is a common challenge in modern applications such as e-commerce and adaptive clinical trials in medicine. For example, in online marketplaces, the revenue of a good depends on discounts applied to competing goods. Statistical inference with interference is widely studied in the offline setting, but far less is known about how to adaptively assign treatments to minimize regret. We address this gap by studying a multi-armed bandit (MAB) problem where a learner (e-commerce platform) sequentially assigns one of possible $\mathcal{A}$ actions (discounts) to $N$ units (goods) over $T$ rounds to minimize regret (maximize revenue). Unlike traditional MAB problems, the reward of each unit depends on the treatments assigned to other units, i.e., there is *interference* across the underlying network of units. With $\mathcal{A}$ actions and $N$ units, minimizing regret is combinatorially difficult since the action space grows as $\mathcal{A}^N$. To overcome this issue, we study a *sparse network interference* model, where the reward of a unit is only affected by the treatments assigned to $s$ neighboring units. We use tools from discrete Fourier analysis to develop a sparse linear representation of the unit-specific reward $r_n: [\mathcal{A}]^N \rightarrow \mathbb{R} $, and propose simple, linear regression-based algorithms to minimize regret. Importantly, our algorithms achieve provably low regret both when the learner observes the interference neighborhood for all units and when it is unknown. This significantly generalizes other works on this topic which impose strict conditions on the strength of interference on a *known* network, and also compare regret to a markedly weaker optimal action. 
Empirically, we corroborate our theoretical findings via numerical simulations.
Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling
Authors: Yuanqi Du; Michael Plainer; Rob Brekelmans; Chenru Duan; Frank Noe; Carla P Gomes; Alan Aspuru-Guzik; Kirill Neklyudov
Venue: NeurIPS 2024 (NeurIPS 2024 spotlight)

Abstract: Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational challenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the question of conditioning the process to reach a given endpoint or desired rare event is definitively answered by Doob's $h$-transform. However, the naive estimation of this transform is infeasible, as it requires simulating sufficiently many forward trajectories to estimate rare event probabilities. In this work, we propose a variational formulation of Doob's $h$-transform as an optimization problem over trajectories between a given initial point and the desired ending point. To solve this optimization, we propose a simulation-free training objective with a model parameterization that imposes the desired boundary conditions by design. Our approach significantly reduces the search space over trajectories and avoids expensive trajectory simulation and inefficient importance sampling estimators which are required in existing methods. We demonstrate the ability of our method to find feasible transition paths on real-world molecular simulation and protein folding tasks.