NeurIPS 2024 Papers

Survival prediction often involves estimating the time-to-event distribution from censored datasets. Previous approaches have focused on enhancing discrimination and marginal calibration. In this paper, we highlight the significance of *conditional calibration* for real-world applications – especially its role in individual decision-making. We propose a method based on conformal prediction that uses the model’s predicted individual survival probability at that instance’s observed time. This method effectively improves the model’s marginal and conditional calibration, without compromising discrimination. We provide asymptotic theoretical guarantees for both marginal and conditional calibration and test it extensively across 15 diverse real-world datasets, demonstrating the method’s practical effectiveness and versatility in various settings.

We develop a method to generate prediction sets with a guaranteed coverage rate that is robust to corruptions in the training data, such as missing or noisy variables. Our approach builds on conformal prediction, a powerful framework to construct prediction sets that are valid under the i.i.d assumption. Importantly, naively applying conformal prediction does not provide reliable predictions in this setting, due to the distribution shift induced by the corruptions. To account for the distribution shift, we assume access to privileged information (PI). The PI is formulated as additional features that explain the distribution shift, however, they are only available during training and absent at test time. We approach this problem by introducing a novel generalization of weighted conformal prediction and support our method with theoretical coverage guarantees. Empirical experiments on both real and synthetic datasets indicate that our approach achieves a valid coverage rate and constructs more informative predictions compared to existing methods, which are not supported by theoretical guarantees.

Machine learning catalyzes a revolution in chemical and biological science. However, its efficacy is heavily dependent on the availability of labeled data, and annotating biochemical data is extremely laborious. To surmount this data sparsity challenge, we present an instructive learning algorithm named InstructMol to measure pseudo-labels' reliability and help the target model leverage large-scale unlabeled data. InstructMol does not require transferring knowledge between multiple domains, which avoids the potential gap between the pretraining and fine-tuning stages. We demonstrated the high accuracy of InstructMol on several real-world molecular datasets and out-of-distribution (OOD) benchmarks.

Top-down Bird's Eye View (BEV) maps are a popular perception representation for ground robot navigation due to their richness and flexibility for downstream tasks. While recent methods have shown promise for predicting BEV maps from First-Person View (FPV) images, their generalizability is limited to small regions captured by current autonomous vehicle-based datasets. In this context, we show that a more scalable approach towards generalizable map prediction can be enabled by using two large-scale crowd-sourced mapping platforms, Mapillary for FPV images and OpenStreetMap for BEV semantic maps. We introduce Map It Anywhere (MIA), a data engine that enables seamless curation and modeling of labeled map prediction data from existing open-source map platforms. Using our MIA data engine, we display the ease of automatically collecting a 1.2 million FPV & BEV pair dataset encompassing diverse geographies, landscapes, environmental factors, camera models & capture scenarios. We further train a simple camera model-agnostic model on this data for BEV map prediction. Extensive evaluations using established benchmarks and our dataset show that the data curated by MIA enables effective pretraining for generalizable BEV map prediction, with zero-shot performance far exceeding baselines trained on existing datasets by 35%. Our analysis highlights the promise of using large-scale public maps for developing & testing generalizable BEV perception, paving the way for more robust autonomous navigation. Website: mapitanywhere.github.io

Graph Neural Networks have achieved remarkable accuracy in semi-supervised node classification tasks. However, these results lack reliable uncertainty estimates. Conformal prediction methods provide a theoretical guarantee for node classification tasks, ensuring that the conformal prediction set contains the ground-truth label with a desired probability (e.g., 95\%). In this paper, we empirically show that for each node, aggregating the non-conformity scores of nodes with the same label can improve the efficiency of conformal prediction sets while maintaining valid marginal coverage. This observation motivates us to propose a novel algorithm named $\textit{Similarity-Navigated Adaptive Prediction Sets}$ (SNAPS), which aggregates the non-conformity scores based on feature similarity and structural neighborhood. The key idea behind SNAPS is that nodes with high feature similarity or direct connections tend to have the same label. By incorporating adaptive similar nodes information, SNAPS can generate compact prediction sets and increase the singleton hit ratio (correct prediction sets of size one). Moreover, we theoretically provide a finite-sample coverage guarantee of SNAPS. Extensive experiments demonstrate the superiority of SNAPS, improving the efficiency of prediction sets and singleton hit ratio while maintaining valid coverage.

Model-based reinforcement learning (MBRL) is a promising route to sample-efficient policy optimization. However, a known vulnerability of reconstruction-based MBRL consists of scenarios in which detailed aspects of the world are highly predictable, but irrelevant to learning a good policy. Such scenarios can lead the model to exhaust its capacity on meaningless content, at the cost of neglecting important environment dynamics. While existing approaches attempt to solve this problem, we highlight its continuing impact on leading MBRL methods ---including DreamerV3 and DreamerPro--- with a novel environment where background distractions are intricate, predictable, and useless for planning future actions. To address this challenge we develop a method for focusing the capacity of the world model through a synergy of a pretrained segmentation model, a task-aware reconstruction loss, and adversarial learning. Our method outperforms a variety of other approaches designed to reduce the impact of distractors, and is an advance towards robust model-based reinforcement learning.

Optimal transport (OT) is a general framework for finding a minimum-cost transport plan, or coupling, between probability distributions, and has many applications in machine learning. A key challenge in applying OT to massive datasets is the quadratic scaling of the coupling matrix with the size of the dataset. [Forrow et al. 2019] introduced a factored coupling for the k-Wasserstein barycenter problem, which [Scetbon et al. 2021] adapted to solve the primal low-rank OT problem. We derive an alternative parameterization of the low-rank problem based on the _latent coupling_ (LC) factorization previously introduced by [Lin et al. 2021] generalizing [Forrow et al. 2019]. The LC factorization has multiple advantages for low-rank OT including decoupling the problem into three OT problems and greater flexibility and interpretability. We leverage these advantages to derive a new algorithm _Factor Relaxation with Latent Coupling_ (FRLC), which uses _coordinate_ mirror descent to compute the LC factorization. FRLC handles multiple OT objectives (Wasserstein, Gromov-Wasserstein, Fused Gromov-Wasserstein), and marginal constraints (balanced, unbalanced, and semi-relaxed) with linear space complexity. We provide theoretical results on FRLC, and demonstrate superior performance on diverse applications -- including graph clustering and spatial transcriptomics -- while demonstrating its interpretability.

Recently developed quasi-Bayesian (QB) methods \cite{fong2023martingale} proposed a stimulating change of paradigm in Bayesian computation by directly constructing the Bayesian predictive distribution through recursion, removing the need for expensive computations involved in sampling the Bayesian posterior distribution. This has proved to be data-efficient for univariate predictions, however, existing constructions for higher dimensional densities are only possible by relying on restrictive assumptions on the model's multivariate structure. Here, we propose a wholly different approach to extend Quasi-Bayesian prediction to high dimensions through the use of Sklar's theorem, by decomposing the predictive distribution into one-dimensional predictive marginals and a high-dimensional copula. We use the efficient recursive QB construction for the one-dimensional marginals and model the dependence using highly expressive vine copulas. Further, we tune hyperparameters using robust divergences (eg. energy score) and show that our proposed Quasi-Bayesian Vine (QB-Vine) is a fully non-parametric density estimator with \emph{an analytical form} and convergence rate independent of the dimension of the data in some situations. Our experiments illustrate that the QB-Vine is appropriate for high dimensional distributions ($\sim$64), needs very few samples to train ($\sim$200) and outperforms state-of-the-art methods with analytical forms for density estimation and supervised tasks by a considerable margin.

Conformal Prediction (CP) is a distribution-free uncertainty estimation framework that constructs prediction sets guaranteed to contain the true answer with a user-specified probability. Intuitively, the size of the prediction set encodes a general notion of uncertainty, with larger sets associated with higher degrees of uncertainty. In this work, we leverage information theory to connect conformal prediction to other notions of uncertainty. More precisely, we prove three different ways to upper bound the intrinsic uncertainty, as described by the conditional entropy of the target variable given the inputs, by combining CP with information theoretical inequalities. Moreover, we demonstrate two direct and useful applications of such connection between conformal prediction and information theory: (i) more principled and effective conformal training objectives that generalize previous approaches and enable end-to-end training of machine learning models from scratch, and (ii) a natural mechanism to incorporate side information into conformal prediction. We empirically validate both applications in centralized and federated learning settings, showing our theoretical results translate to lower inefficiency (average prediction set size) for popular CP methods.

Feature attribution methods explain black-box machine learning (ML) models by assigning importance scores to input features. These methods can be computationally expensive for large ML models. To address this challenge, there have been increasing efforts to develop amortized explainers, where a ML model is trained to efficiently approximate computationally expensive feature attribution scores. Despite their efficiency, amortized explainers can produce misleading explanations. In this paper, we propose selective explanations to (i) detect when amortized explainers generate inaccurate explanations and (ii) improve the approximation of the explanation using a technique we call explanations with initial guess. Selective explanations allow practitioners to specify the fraction of samples that receive explanations with initial guess, offering a principled way to bridge the gap between amortized explainers (one inference) and more computationally costly approximations (multiple inferences). Our experiments on various models and datasets demonstrate that feature attributions via selective explanations strike a favorable balance between explanation quality and computational efficiency.

Fact-checking is extensively studied in the context of misinformation and disinformation, addressing objective inaccuracies. However, a softer form of misinformation involves responses that are factually correct but lack certain features such as clarity and relevance. This challenge is prevalent in formal Question-Answer (QA) settings such as press conferences in finance, politics, sports, and other domains, where subjective answers can obscure transparency. Despite this, there is a lack of manually annotated datasets for subjective features across multiple dimensions. To address this gap, we introduce SubjECTive-QA, a human annotated dataset on Earnings Call Transcripts' (ECTs) QA sessions as the answers given by company representatives are often open to subjective interpretations and scrutiny. The dataset includes 49,446 annotations for long-form QA pairs across six features: Assertive, Cautious, Optimistic, Specific, Clear, and Relevant. These features are carefully selected to encompass the key attributes that reflect the tone of the answers provided during QA sessions across different domains. Our findings are that the best-performing Pre-trained Language Model (PLM), RoBERTa-base, has similar weighted F1 scores to Llama-3-70b-Chat on features with lower subjectivity, such as Relevant and Clear, with a mean difference of 2.17% in their weighted F1 scores. The models perform significantly better on features with higher subjectivity, such as Specific and Assertive, with a mean difference of 10.01% in their weighted F1 scores. Furthermore, testing SubjECTive-QA's generalizability using QAs from White House Press Briefings and Gaggles yields an average weighted F1 score of 65.97% using our best models for each feature, demonstrating broader applicability beyond the financial domain. SubjECTive-QA is publicly available under the CC BY 4.0 license.

This paper studies a risk minimization problem with decision dependent data distribution. The problem pertains to the performative prediction setting in which a trained model can affect the outcome estimated by the model. Such dependency creates a feedback loop that influences the stability of optimization algorithms such as stochastic gradient descent (SGD). We present the first study on performative prediction with smooth but possibly non-convex loss. We analyze a greedy deployment scheme with SGD (SGD-GD). Note that in the literature, SGD-GD is often studied with strongly convex loss. We first propose the definition of stationary performative stable (SPS) solutions through relaxing the popular performative stable condition. We then prove that SGD-GD converges to a biased SPS solution in expectation. We consider two conditions of sensitivity on the distribution shifts: (i) the sensitivity is characterized by Wasserstein-1 distance and the loss is Lipschitz w.r.t.~data samples, or (ii) the sensitivity is characterized by total variation (TV) divergence and the loss is bounded. In both conditions, the bias levels are proportional to the stochastic gradient's variance and sensitivity level. Our analysis is extended to a lazy deployment scheme where models are deployed once per several SGD updates, and we show that it converges to an SPS solution with reduced bias. Numerical experiments corroborate our theories.

Counterfactual Regret Minimization (CFR) and its variants are widely recognized as effective algorithms for solving extensive-form imperfect information games. Recently, many improvements have been focused on enhancing the convergence speed of the CFR algorithm. However, most of these variants are not applicable under Monte Carlo (MC) conditions, making them unsuitable for training in large-scale games. We introduce a new MC-based algorithm for solving extensive-form imperfect information games, called MCCFVFP (Monte Carlo Counterfactual Value-Based Fictitious Play). MCCFVFP combines CFR’s counterfactual value calculations with fictitious play’s best response strategy, leveraging the strengths of fictitious play to gain significant advantages in games with a high proportion of dominated strategies. Experimental results show that MCCFVFP achieved convergence speeds approximately 20\%$\sim$50\% faster than the most advanced MCCFR variants in games like poker and other test games.

We study the fractal structure of language, aiming to provide a precise formalism for quantifying properties that may have been previously suspected but not formally shown. We establish that language is: (1) self-similar, exhibiting complexities at all levels of granularity, with no particular characteristic context length, and (2) long-range dependent (LRD), with a Hurst parameter of approximately 0.7. Based on these findings, we argue that short-term patterns/dependencies in language, such as in paragraphs, mirror the patterns/dependencies over larger scopes, like entire documents. This may shed some light on how next-token prediction can capture the structure of text across multiple levels of granularity, from words and clauses to broader contexts and intents. In addition, we carry out an extensive analysis across different domains and architectures, showing that fractal parameters are robust. Finally, we demonstrate that the tiny variations in fractal parameters seen across LLMs improve upon perplexity-based bits-per-byte (BPB) in predicting their downstream performance. We hope these findings offer a fresh perspective on language and the mechanisms underlying the success of LLMs.

The Mixture of Experts (MoE) paradigm provides a powerful way to decompose dense layers into smaller, modular computations often more amenable to human interpretation, debugging, and editability. However, a major challenge lies in the computational cost of scaling the number of experts high enough to achieve fine-grained specialization. In this paper, we propose the Multilinear Mixture of Experts (μMoE) layer to address this, focusing on vision models. μMoE layers enable scalable expert specialization by performing an implicit computation on prohibitively large weight tensors entirely in factorized form. Consequently, μMoEs (1) avoid the restrictively high inference-time costs of dense MoEs, yet (2) do not inherit the training issues of the popular sparse MoEs' discrete (non-differentiable) expert routing. We present both qualitative and quantitative evidence that scaling μMoE layers when fine-tuning foundation models for vision tasks leads to more specialized experts at the class-level, further enabling manual bias correction in CelebA attribute classification. Finally, we show qualitative results demonstrating the expert specialism achieved when pre-training large GPT2 and MLP-Mixer models with parameter-matched μMoE blocks at every layer, maintaining comparable accuracy. Our code is available at: https://github.com/james-oldfield/muMoE.

In density functional theory, charge density is the core attribute of atomic systems from which all chemical properties can be derived. Machine learning methods are promising in significantly accelerating charge density prediction, yet existing approaches either lack accuracy or scalability. We propose a recipe that can achieve both. In particular, we identify three key ingredients: (1) representing the charge density with atomic and virtual orbitals (spherical fields centered at atom/virtual coordinates); (2) using expressive and learnable orbital basis sets (basis function for the spherical fields); and (3) using high-capacity equivariant neural network architecture. Our method achieves state-of-the-art accuracy while being more than an order of magnitude faster than existing methods. Furthermore, our method enables flexible efficiency-accuracy trade-offs by adjusting the model/basis sizes.

There has been significant interest in "extreme" compression of large language models (LLMs), i.e. to 1-2 bits per parameter, which allows such models to be executed efficiently on resource-constrained devices. Existing work focused on improved one-shot quantization techniques and weight representations; yet, purely post-training approaches are reaching diminishing returns in terms of the accuracy-vs-bit-width trade-off. State-of-the-art quantization methods such as QuIP# and AQLM include fine-tuning (part of) the compressed parameters over a limited amount of calibration data; however, such fine-tuning techniques over compressed weights often make exclusive use of straight-through estimators (STE), whose performance is not well-understood in this setting. In this work, we question the use of STE for extreme LLM compression, showing that it can be sub-optimal, and perform a systematic study of quantization-aware fine-tuning strategies for LLMs. We propose PV-Tuning - a representation-agnostic framework that generalizes and improves upon existing fine-tuning strategies, and provides convergence guarantees in restricted cases. On the practical side, when used for 1-2 bit vector quantization, PV-Tuning outperforms prior techniques for highly-performant models such as Llama and Mistral. Using PV-Tuning, we achieve the first Pareto-optimal quantization for Llama-2 family models at 2 bits per parameter.

Message Passing Neural Networks (MPNNs) have emerged as the {\em de facto} standard in graph representation learning. However, when it comes to link prediction, they are not always superior to simple heuristics such as Common Neighbor (CN). This discrepancy stems from a fundamental limitation: while MPNNs excel in node-level representation, they stumble with encoding the joint structural features essential to link prediction, like CN. To bridge this gap, we posit that, by harnessing the orthogonality of input vectors, pure message-passing can indeed capture joint structural features. Specifically, we study the proficiency of MPNNs in approximating CN heuristics. Based on our findings, we introduce the Message Passing Link Predictor (MPLP), a novel link prediction model. MPLP taps into quasi-orthogonal vectors to estimate link-level structural features, all while preserving the node-level complexities. We conduct experiments on benchmark datasets from various domains, where our method consistently outperforms the baseline methods, establishing new state-of-the-arts.

Single-cell transcriptomics has revolutionized our understanding of cellular heterogeneity and drug perturbation effects. However, its high cost and the vast chemical space of potential drugs present barriers to experimentally characterizing the effect of chemical perturbations in all the myriad cell types of the human body. To overcome these limitations, several groups have proposed using machine learning methods to directly predict the effect of chemical perturbations either across cell contexts or chemical space. However, advances in this field have been hindered by a lack of well-designed evaluation datasets and benchmarks. To drive innovation in perturbation modeling, the Open Problems Perturbation Prediction (OP3) benchmark introduces a framework for predicting the effects of small molecule perturbations on cell type-specific gene expression. OP3 leverages the Open Problems in Single-cell Analysis benchmarking infrastructure and is enabled by a new single-cell perturbation dataset, encompassing 146 compounds tested on human blood cells. The benchmark includes diverse data representations, evaluation metrics, and winning methods from our "Single-cell perturbation prediction: generalizing experimental interventions to unseen contexts" competition at NeurIPS 2023. We envision that the OP3 benchmark and competition will drive innovation in single-cell perturbation prediction by improving the accessibility, visibility, and feasibility of this challenge, thereby promoting the impact of machine learning in drug discovery.