NeurIPS 2023 Papers

Optimizing proper loss functions is popularly believed to yield predictors with good calibration properties; the intuition being that for such losses, the global optimum is to predict the ground-truth probabilities, which is indeed calibrated. However, typical machine learning models are trained to approximately minimize loss over restricted families of predictors, that are unlikely to contain the ground truth. Under what circumstances does optimizing proper loss over a restricted family yield calibrated models? What precise calibration guarantees does it give? In this work, we provide a rigorous answer to these questions. We replace the global optimality with a local optimality condition stipulating that the (proper) loss of the predictor cannot be reduced much by post-processing its predictions with a certain family of Lipschitz functions. We show that any predictor with this local optimality satisfies smooth calibration as defined in [Kakade and Foster, 2008, Błasiok et al., 2023]. Local optimality is plausibly satisfied by well-trained DNNs, which suggests an explanation for why they are calibrated from proper loss minimization alone. Finally, we show that the connection between local optimality and calibration error goes both ways: nearly calibrated predictors are also nearly locally optimal.

As Large Language Models (LLMs) become increasingly integrated into our everyday lives, understanding their ability to comprehend human mental states becomes critical for ensuring effective interactions. However, despite the recent attempts to assess the Theory-of-Mind (ToM) reasoning capabilities of LLMs, the degree to which these models can align with human ToM remains a nuanced topic of exploration. This is primarily due to two distinct challenges: (1) the presence of inconsistent results from previous evaluations, and (2) concerns surrounding the validity of existing evaluation methodologies. To address these challenges, we present a novel framework for procedurally generating evaluations with LLMs by populating causal templates. Using our framework, we create a new social reasoning benchmark (BigToM) for LLMs which consists of 25 controls and 5,000 model-written evaluations. We find that human participants rate the quality of our benchmark higher than previous crowd-sourced evaluations and comparable to expert-written evaluations. Using BigToM, we evaluate the social reasoning capabilities of a variety of LLMs and compare model performances with human performance. Our results suggest that GPT4 has ToM capabilities that mirror human inference patterns, though less reliable, while other LLMs struggle.

Classical analysis of convex and non-convex optimization methods often requires the Lipschitz continuity of the gradient, which limits the analysis to functions bounded by quadratics. Recent work relaxed this requirement to a non-uniform smoothness condition with the Hessian norm bounded by an affine function of the gradient norm, and proved convergence in the non-convex setting via gradient clipping, assuming bounded noise. In this paper, we further generalize this non-uniform smoothness condition and develop a simple, yet powerful analysis technique that bounds the gradients along the trajectory, thereby leading to stronger results for both convex and non-convex optimization problems. In particular, we obtain the classical convergence rates for (stochastic) gradient descent and Nesterov's accelerated gradient method in the convex and/or non-convex setting under this general smoothness condition. The new analysis approach does not require gradient clipping and allows heavy-tailed noise with bounded variance in the stochastic setting.

Graph Neural Networks (GNNs) are crucial for machine learning applications with graph-structured data, but their success depends on sufficient labeled data. We present a novel active learning (AL) method for GNNs, extending the Expected Model Change Maximization (EMCM) principle to improve prediction performance on unlabeled data. By presenting a Bayesian interpretation for the node embeddings generated by GNNs under the semi-supervised setting, we efficiently compute the closed-form EMCM acquisition function as the selection criterion for AL without re-training. Our method establishes a direct connection with expected prediction error minimization, offering theoretical guarantees for AL performance. Experiments demonstrate our method's effectiveness compared to existing approaches, in terms of both accuracy and efficiency.

We present a novel methodology aimed at optimizing the application of frozen large language models (LLMs) for resource-intensive vision-language (VL) pre-training. The current paradigm uses visual features as prompts to guide language models, with a focus on determining the most relevant visual features for corresponding text. Our approach diverges by concentrating on the language component, specifically identifying the optimal prompts to align with visual features. We introduce the Prompt-Transformer (P-Former), a model that predicts these ideal prompts, which is trained exclusively on linguistic data, bypassing the need for image-text pairings. This strategy subtly bifurcates the end-to-end VL training process into an additional, separate stage. Our experiments reveal that our framework significantly enhances the performance of a robust image-to-text baseline (BLIP-2), and effectively narrows the performance gap between models trained with either 4M or 129M image-text pairs. Importantly, our framework is modality-agnostic and flexible in terms of architectural design, as validated by its successful application in a video learning task using varied base modules. The code will be made available at https://github.com/yiren-jian/BLIText.

Spiking Neural Networks (SNNs) are considered promising brain-inspired energy-efficient models due to their event-driven computing paradigm. The spatiotemporal spike patterns used to convey information in SNNs consist of both rate coding and temporal coding, where the temporal coding is crucial to biological-plausible learning rules such as spike-timing-dependent-plasticity. The time-based training strategy is proposed to better utilize the temporal information in SNNs and learn in an asynchronous fashion. However, some recent works train SNNs by the time-based scheme with rate-coding-dominated loss functions. In this paper, we first map rate-based loss functions to time-based counterparts and explain why they are also applicable to the time-based training scheme. After that, we infer that loss functions providing adequate positive overall gradients help training by theoretical analysis. Based on this, we propose the enhanced counting loss to replace the commonly used mean square counting loss. In addition, we transfer the training of scale factor in weight standardization into thresholds. Experiments show that our approach outperforms previous time-based training methods in most datasets. Our work provides insights for training SNNs with time-based schemes and offers a fresh perspective on the correlation between rate coding and temporal coding. Our code is available at https://github.com/zhuyaoyu/SNN-temporal-training-losses.

Through considerable effort and intuition, several recent works have reverse-engineered nontrivial behaviors of transformer models. This paper systematizes the mechanistic interpretability process they followed. First, researchers choose a metric and dataset that elicit the desired model behavior. Then, they apply activation patching to find which abstract neural network units are involved in the behavior. By varying the dataset, metric, and units under investigation, researchers can understand the functionality of each component. We automate one of the process' steps: finding the connections between the abstract neural network units that form a circuit. We propose several algorithms and reproduce previous interpretability results to validate them. For example, the ACDC algorithm rediscovered 5/5 of the component types in a circuit in GPT-2 Small that computes the Greater-Than operation. ACDC selected 68 of the 32,000 edges in GPT-2 Small, all of which were manually found by previous work. Our code is available at https://github.com/ArthurConmy/Automatic-Circuit-Discovery

In appropriate frameworks, automatic differentiation is transparent to the user, at the cost of being a significant computational burden when the number of operations is large. For iterative algorithms, implicit differentiation alleviates this issue but requires custom implementation of Jacobian evaluation. In this paper, we study one-step differentiation, also known as Jacobian-free backpropagation, a method as easy as automatic differentiation and as performant as implicit differentiation for fast algorithms (e.g. superlinear optimization methods). We provide a complete theoretical approximation analysis with specific examples (Newton's method, gradient descent) along with its consequences in bilevel optimization. Several numerical examples illustrate the well-foundness of the one-step estimator.

Language models pretrained on large collections of tabular data have demonstrated their effectiveness in several downstream tasks. However, many of these models do not take into account the row/column permutation invariances, hierarchical structure, etc. that exist in tabular data. To alleviate these limitations, we propose HyTrel, a tabular language model, that captures the permutation invariances and three more structural properties of tabular data by using hypergraphs--where the table cells make up the nodes and the cells occurring jointly together in each row, column, and the entire table are used to form three different types of hyperedges. We show that HyTrel is maximally invariant under certain conditions for tabular data, i.e., two tables obtain the same representations via HyTrel iff the two tables are identical up to permutation. Our empirical results demonstrate that HyTrel consistently outperforms other competitive baselines on four downstream tasks with minimal pretraining, illustrating the advantages of incorporating inductive biases associated with tabular data into the representations. Finally, our qualitative analyses showcase that HyTrel can assimilate the table structure to generate robust representations for the cells, rows, columns, and the entire table.

When deploying machine learning estimators in science and engineering (SAE) domains, it is critical to avoid failed estimations that can have disastrous consequences, e.g., in aero engine design. This work focuses on detecting and correcting failed state estimations before adopting them in SAE inverse problems, by utilizing simulations and performance metrics guided by physical laws. We suggest to flag a machine learning estimation when its physical model error exceeds a feasible threshold, and propose a novel approach, GEESE, to correct it through optimization, aiming at delivering both low error and high efficiency. The key designs of GEESE include (1) a hybrid surrogate error model to provide fast error estimations to reduce simulation cost and to enable gradient based backpropagation of error feedback, and (2) two generative models to approximate the probability distributions of the candidate states for simulating the exploitation and exploration behaviours. All three models are constructed as neural networks. GEESE is tested on three real-world SAE inverse problems and compared to a number of state-of-the-art optimization/search approaches. Results show that it fails the least number of times in terms of finding a feasible state correction, and requires physical evaluations less frequently in general.

We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new representation of protein structure, relies on a novel architecture for aligned proteins, and utilizes strong diffusion priors to improve the denoising process. Our approach improves protein diffusion by taking advantage of domain knowledge and physics-based constraints; handles sequence-length changes; and reduces memory complexity by an order of magnitude, enabling backbone and side chain generation. We validate AbDiffuser in silico and in vitro. Numerical experiments showcase the ability of AbDiffuser to generate antibodies that closely track the sequence and structural properties of a reference set. Laboratory experiments confirm that all 16 HER2 antibodies discovered were expressed at high levels and that 57.1% of the selected designs were tight binders.

In this paper we offer a new perspective on the well established agglomerative clustering algorithm, focusing on recovery of hierarchical structure. We recommend a simple variant of the standard algorithm, in which clusters are merged by maximum average dot product and not, for example, by minimum distance or within-cluster variance. We demonstrate that the tree output by this algorithm provides a bona fide estimate of generative hierarchical structure in data, under a generic probabilistic graphical model. The key technical innovations are to understand how hierarchical information in this model translates into tree geometry which can be recovered from data, and to characterise the benefits of simultaneously growing sample size and data dimension. We demonstrate superior tree recovery performance with real data over existing approaches such as UPGMA, Ward's method, and HDBSCAN.

In practice, encoding invariances into models improves sample complexity. In this work, we study this phenomenon from a theoretical perspective. In particular, we provide minimax optimal rates for kernel ridge regression on compact manifolds, with a target function that is invariant to a group action on the manifold. Our results hold for any smooth compact Lie group action, even groups of positive dimension. For a finite group, the gain effectively multiplies the number of samples by the group size. For groups of positive dimension, the gain is observed by a reduction in the manifold's dimension, in addition to a factor proportional to the volume of the quotient space. Our proof takes the viewpoint of differential geometry, in contrast to the more common strategy of using invariant polynomials. This new geometric viewpoint on learning with invariances may be of independent interest.

Many of the most commonly explored natural language processing (NLP) information extraction tasks can be thought of as evaluations of declarative knowledge, or fact-based information extraction. Procedural knowledge extraction, i.e., breaking down a described process into a series of steps, has received much less attention, perhaps in part due to the lack of structured datasets that capture the knowledge extraction process from end-to-end. To address this unmet need, we present FlaMBé (Flow annotations for Multiverse Biological entities), a collection of expert-curated datasets across a series of complementary tasks that capture procedural knowledge in biomedical texts. This dataset is inspired by the observation that one ubiquitous source of procedural knowledge that is described as unstructured text is within academic papers describing their methodology. The workflows annotated in FlaMBé are from texts in the burgeoning field of single cell research, a research area that has become notorious for the number of software tools and complexity of workflows used. Additionally, FlaMBé provides, to our knowledge, the largest manually curated named entity recognition (NER) and disambiguation (NED) datasets for tissue/cell type, a fundamental biological entity that is critical for knowledge extraction in the biomedical research domain. Beyond providing a valuable dataset to enable further development of NLP models for procedural knowledge extraction, automating the process of workflow mining also has important implications for advancing reproducibility in biomedical research.

Targeted protein degradation techniques, such as PROteolysis TArgeting Chimeras (PROTACs), have emerged as powerful tools for selectively removing disease-causing proteins. One challenging problem in this field is designing a linker to connect different molecular fragments to form a stable drug-candidate molecule. Existing models for linker design assume that the relative positions of the fragments are known, which may not be the case in real scenarios. In this work, we address a more general problem where the poses of the fragments are *unknown* in 3D space. We develop a 3D equivariant diffusion model that jointly learns the generative process of both fragment poses and the 3D structure of the linker. By viewing fragments as rigid bodies, we design a fragment pose prediction module inspired by the Newton-Euler equations in rigid body mechanics. Empirical studies on ZINC and PROTAC-DB datasets demonstrate that our model can generate chemically valid, synthetically-accessible, and low-energy molecules under both unconstrained and constrained generation settings.

We present Prompt Diffusion, a framework for enabling in-context learning in diffusion-based generative models. Given a pair of task-specific example images, such as depth from/to image and scribble from/to image, and a text guidance, our model automatically understands the underlying task and performs the same task on a new query image following the text guidance. To achieve this, we propose a vision-language prompt that can model a wide range of vision-language tasks and a diffusion model that takes it as input. The diffusion model is trained jointly on six different tasks using these prompts. The resulting Prompt Diffusion model becomes the first diffusion-based vision-language foundation model capable of in-context learning. It demonstrates high-quality in-context generation for the trained tasks and effectively generalizes to new, unseen vision tasks using their respective prompts. Our model also shows compelling text-guided image editing results. Our framework aims to facilitate research into in-context learning for computer vision. We share our code and pre-trained models at https://github.com/Zhendong-Wang/Prompt-Diffusion.

Modern neural language models that are widely used in various NLP tasks risk memorizing sensitive information from their training data. Understanding this memorization is important in real world applications and also from a learning-theoretical perspective. An open question in previous studies of language model memorization is how to filter out ``common'' memorization. In fact, most memorization criteria strongly correlate with the number of occurrences in the training set, capturing memorized familiar phrases, public knowledge, templated texts, or other repeated data. We formulate a notion of counterfactual memorization which characterizes how a model's predictions change if a particular document is omitted during training. We identify and study counterfactually-memorized training examples in standard text datasets. We estimate the influence of each memorized training example on the validation set and on generated texts, showing how this can provide direct evidence of the source of memorization at test time.

Many common types of data can be represented as functions that map coordinates to signal values, such as pixel locations to RGB values in the case of an image. Based on this view, data can be compressed by overfitting a compact neural network to its functional representation and then encoding the network weights. However, most current solutions for this are inefficient, as quantization to low-bit precision substantially degrades the reconstruction quality. To address this issue, we propose overfitting variational Bayesian neural networks to the data and compressing an approximate posterior weight sample using relative entropy coding instead of quantizing and entropy coding it. This strategy enables direct optimization of the rate-distortion performance by minimizing the $\beta$-ELBO, and target different rate-distortion trade-offs for a given network architecture by adjusting $\beta$. Moreover, we introduce an iterative algorithm for learning prior weight distributions and employ a progressive refinement process for the variational posterior that significantly enhances performance. Experiments show that our method achieves strong performance on image and audio compression while retaining simplicity.

We consider the problem of estimating the causal effect of a treatment on an outcome in linear structural causal models (SCM) with latent confounders when we have access to a single proxy variable. Several methods (such as difference-in-difference (DiD) estimator or negative outcome control) have been proposed in this setting in the literature. However, these approaches require either restrictive assumptions on the data generating model or having access to at least two proxy variables. We propose a method to estimate the causal effect using cross moments between the treatment, the outcome, and the proxy variable. In particular, we show that the causal effect can be identified with simple arithmetic operations on the cross moments if the latent confounder in linear SCM is non-Gaussian. In this setting, DiD estimator provides an unbiased estimate only in the special case where the latent confounder has exactly the same direct causal effects on the outcomes in the pre-treatment and post-treatment phases. This translates to the common trend assumption in DiD, which we effectively relax. Additionally, we provide an impossibility result that shows the causal effect cannot be identified if the observational distribution over the treatment, the outcome, and the proxy is jointly Gaussian. Our experiments on both synthetic and real-world datasets showcase the effectiveness of the proposed approach in estimating the causal effect.