ICML 2024 Papers

We investigate the potential of patent data for improving the antibody humanness prediction using a multi-stage, multi-loss training process. Humanness serves as a proxy for the immunogenic response to antibody therapeutics, one of the major causes of attrition in drug discovery and a challenging obstacle for their use in clinical settings. We pose the initial learning stage as a weakly-supervised contrastive-learning problem, where each antibody sequence is associated with possibly multiple identifiers of function and the objective is to learn an encoder that groups them according to their patented properties. We then freeze a part of the contrastive encoder and continue training it on the patent data using the cross-entropy loss to predict the humanness score of a given antibody sequence. We illustrate the utility of the patent data and our approach by performing inference on three different immunogenicity datasets, unseen during training. Our empirical results demonstrate that the learned model consistently outperforms the alternative baselines and establishes new state-of-the-art on five out of six inference tasks, irrespective of the used metric.

Pedestrian trajectory prediction aims to predict future trajectories based on observed trajectories. Current state-of-the-art methods often assume that the observed sequences of agents are complete, which is a strong assumption that overlooks inherent uncertainties. Understanding pedestrian behavior when dealing with missing values in the observed sequence is crucial for enhancing the performance of predictive models. In this work, we propose the MultiScale hypergraph for Trajectory Imputation and Prediction (MS-TIP), a novel approach that simultaneously addresses the imputation of missing observations and the prediction of future trajectories. Specifically, we leverage transformers with diagonal masked self-attention to impute incomplete observations. Further, our approach promotes complex interaction modeling through multi-scale hypergraphs, optimizing our trajectory prediction module to capture different types of interactions. With the inclusion of scenic attention, we learn contextual scene information, instead of sole reliance on coordinates. Additionally, our approach utilizes an intermediate control point and refinement module to infer future trajectories accurately. Extensive experiments validate the efficacy of MS-TIP in precisely predicting pedestrian future trajectories. Code is publicly available at https://github.com/Pranav-chib/MS-TIP.

Algorithmic predictions are increasingly used to inform the allocations of goods and interventions in the public sphere. In these domains, predictions serve as a means to an end. They provide stakeholders with insights into likelihood of future events as a means to improve decision making quality, and enhance social welfare. However, if maximizing welfare is the ultimate goal, prediction is only a small piece of the puzzle. There are various other policy levers a social planner might pursue in order to improve bottom-line outcomes, such as expanding access to available goods, or increasing the effect sizes of interventions. Given this broad range of design decisions, a basic question to ask is: What is the relative value of prediction in algorithmic decision making? How do the improvements in welfare arising from better predictions compare to those of other policy levers? The goal of our work is to initiate the formal study of these questions. Our main results are theoretical in nature. We identify simple, sharp conditions determining the relative value of prediction vis-à-vis expanding access, within several statistical models that are popular amongst quantitative social scientists. Furthermore, we illustrate how these theoretical insights can guide the design of algorithmic decision making systems in practice.

Approaches to predicting neuronal spike responses commonly use a Poisson learning objective. This objective quantizes responses into spike counts within a fixed summation interval, typically on the order of 10 to 100 milliseconds in duration; however, neuronal responses are often time accurate down to a few milliseconds, and Poisson models struggle to precisely model them at these timescales. We propose the concept of a spike distance function that maps points in time to the temporal distance to the nearest spike. We show that neural networks can be trained to approximate spike distance functions, and we present an efficient algorithm for inferring spike trains from the outputs of these models. Using recordings of chicken and frog retinal ganglion cells responding to visual stimuli, we compare the performance of our approach to that of Poisson models trained with various summation intervals. We show that our approach outperforms the use of Poisson models at spike train inference.

Fluid prediction is a long-standing challenge due to the intrinsic high-dimensional non-linear dynamics. Previous methods usually utilize the non-linear modeling capability of deep models to directly estimate velocity fields for future prediction. However, skipping over inherent physical properties but directly learning superficial velocity fields will overwhelm the model from generating precise or physics-reliable results. In this paper, we propose the HelmFluid toward an accurate and interpretable predictor for fluid. Inspired by the Helmholtz theorem, we design a HelmDynamics block to learn Helmholtz dynamics, which decomposes fluid dynamics into more solvable curl-free and divergence-free parts, physically corresponding to potential and stream functions of fluid. By embedding the HelmDynamics block into a Multiscale Multihead Integral Architecture, HelmFluid can integrate learned Helmholtz dynamics along temporal dimension in multiple spatial scales to yield future fluid. Compared with previous velocity estimating methods, HelmFluid is faithfully derived from Helmholtz theorem and ravels out complex fluid dynamics with physically interpretable evidence. Experimentally, HelmFluid achieves consistent state-of-the-art in both numerical simulated and real-world observed benchmarks, even for scenarios with complex boundaries.

Predictor-based methods have substantially enhanced Neural Architecture Search (NAS) optimization. The efficacy of these predictors is largely influenced by the method of encoding neural network architectures. While traditional encodings used an adjacency matrix describing the graph structure of a neural network, novel encodings embrace a variety of approaches from unsupervised pretraining of latent representations to vectors of zero-cost proxies. In this paper, we categorize and investigate neural encodings from three main types: structural, learned, and score-based. Furthermore, we extend these encodings and introduce *unified encodings*, that extend NAS predictors to multiple search spaces. Our analysis draws from experiments conducted on over 1.5 million neural network architectures on NAS spaces such as NASBench-101 (NB101), NB201, NB301, Network Design Spaces (NDS), and TransNASBench-101. Building on our study, we present our predictor **FLAN**: **Fl**ow **A**ttention for **N**AS. FLAN integrates critical insights on predictor design, transfer learning, and *unified encodings* to enable more than an order of magnitude cost reduction for training NAS accuracy predictors. Our implementation and encodings for all neural networks are open-sourced at https://github.com/abdelfattah-lab/flan_nas.

The use of machine learning models to predict clinical outcomes from (longitudinal) electronic health record (EHR) data is becoming increasingly popular due to advances in deep architectures, representation learning, and the growing availability of large EHR datasets. Existing models generally assume access to the same data sources during both training and inference stages. However, this assumption is often challenged by the fact that real-world clinical datasets originate from various data sources (with distinct sets of covariates), which though can be available for training (in a research or retrospective setting), are more realistically only partially available (a subset of such sets) for inference when deployed. So motivated, we introduce Contrastive Learning for clinical Outcome Prediction with Partial data Sources (CLOPPS), that trains encoders to capture information across different data sources and then leverages them to build classifiers restricting access to a single data source. This approach can be used with existing cross-sectional or longitudinal outcome classification models. We present experiments on two real-world datasets demonstrating that CLOPPS consistently outperforms strong baselines in several practical scenarios.

We study the behavior of optimal ridge regularization and optimal ridge risk for out-of-distribution prediction, where the test distribution deviates arbitrarily from the train distribution. We establish general conditions that determine the sign of the optimal regularization level under covariate and regression shifts. These conditions capture the alignment between the covariance and signal structures in the train and test data and reveal stark differences compared to the in-distribution setting. For example, a negative regularization level can be optimal under covariate shift or regression shift, even when the training features are isotropic or the design is underparameterized. Furthermore, we prove that the optimally tuned risk is monotonic in the data aspect ratio, even in the out-of-distribution setting and when optimizing over negative regularization levels. In general, our results do not make any modeling assumptions for the train or the test distributions, except for moment bounds, and allow for arbitrary shifts and the widest possible range of (negative) regularization levels.

Conformal prediction is a statistical framework that generates prediction sets containing ground-truth labels with a desired coverage guarantee. The predicted probabilities produced by machine learning models are generally miscalibrated, leading to large prediction sets in conformal prediction. To address this issue, we propose a novel algorithm named $\textit{Sorted Adaptive Prediction Sets}$ (SAPS), which discards all the probability values except for the maximum softmax probability. The key idea behind SAPS is to minimize the dependence of the non-conformity score on the probability values while retaining the uncertainty information. In this manner, SAPS can produce compact prediction sets and communicate instance-wise uncertainty. Extensive experiments validate that SAPS not only lessens the prediction sets but also broadly enhances the conditional coverage rate of prediction sets.

This paper tackles the challenge of detecting unreliable behavior in regression algorithms, which may arise from intrinsic variability (e.g., aleatoric uncertainty) or modeling errors (e.g., model uncertainty). First, we formally introduce the notion of unreliability in regression, i.e., when the output of the regressor exceeds a specified discrepancy (or error). Then, using powerful tools for probabilistic modeling, we estimate the discrepancy density, and we measure its statistical diversity using our proposed metric for statistical dissimilarity. In turn, this allows us to derive a data-driven score that expresses the uncertainty of the regression outcome. We show empirical improvements in error detection for multiple regression tasks, consistently outperforming popular baseline approaches, and contributing to the broader field of uncertainty quantification and safe machine learning systems.

In this paper, we focus on the problem of conformal prediction with conditional guarantees. Prior work has shown that it is impossible to construct nontrivial prediction sets with full conditional coverage guarantees. A wealth of research has considered relaxations of full conditional guarantees, relying on some *predefined* uncertainty structures. Departing from this line of thinking, we propose Partition Learning Conformal Prediction (PLCP), a framework to improve conditional validity of prediction sets through *learning* uncertainty-guided features from the calibration data. We implement PLCP efficiently with alternating gradient descent, utilizing off-the-shelf machine learning models. We further analyze PLCP theoretically and provide conditional guarantees for infinite and finite sample sizes. Finally, our experimental results over four real-world and synthetic datasets show the superior performance of PLCP compared to state-of-the-art methods in terms of coverage and length in both classification and regression scenarios.

We investigate the accuracy of prediction in deterministic learning dynamics of zero-sum games with random initializations, specifically focusing on observer uncertainty and its relationship to the evolution of covariances. Zero-sum games are a prominent field of interest in machine learning due to their various applications. Concurrently, the accuracy of prediction in dynamical systems from mechanics has long been a classic subject of investigation since the discovery of the Heisenberg Uncertainty Principle. This principle employs covariance and standard deviation of particle states to measure prediction accuracy. In this study, we bring these two approaches together to analyze the Follow-the-Regularized-Leader (FTRL) algorithm in two-player zero-sum games. We provide growth rates of covariance information for continuous-time FTRL, as well as its two canonical discretization methods (Euler and Symplectic). A Heisenberg-type inequality is established for FTRL. Our analysis and experiments also show that employing Symplectic discretization enhances the accuracy of prediction in learning dynamics.

Algorithmic predictions are emerging as a promising solution concept for efficiently allocating societal resources. Fueling their use is an underlying assumption that such systems are necessary to identify individuals for interventions. We propose a principled framework for assessing this assumption: Using a simple mathematical model, we evaluate the efficacy of prediction-based allocations in settings where individuals belong to larger units such as hospitals, neighborhoods, or schools. We find that prediction-based allocations outperform baseline methods using aggregate unit-level statistics only when between-unit inequality is low and the intervention budget is high. Our results hold for a wide range of settings for the price of prediction, treatment effect heterogeneity, and unit-level statistics' learnability. Combined, we highlight the potential limits to improving the efficacy of interventions through prediction.

In addressing the challenge of Crystal Structure Prediction (CSP), symmetry-aware deep learning models, particularly diffusion models, have been extensively studied, which treat CSP as a conditional generation task. However, ensuring permutation, rotation, and periodic translation equivariance during diffusion process remains incompletely addressed. In this work, we propose EquiCSP, a novel equivariant diffusion-based generative model. We not only address the overlooked issue of lattice permutation equivariance in existing models, but also develop a unique noising algorithm that rigorously maintains periodic translation equivariance throughout both training and inference processes. Our experiments indicate that EquiCSP significantly surpasses existing models in terms of generating accurate structures and demonstrates faster convergence during the training process.

Neural networks whose weights are the output of a predictor (HyperNetworks) achieve excellent performance on many tasks. In ConvNets, kernel prediction layers are a popular type of HyperNetwork. Previous theoretical work has argued that a hierarchy of multiplicative interactions exists in which gating is at the bottom and full weight prediction, as in HyperNetworks, is at the top. In this paper, we constructively demonstrate an equivalence between gating combined with fixed weight layers and weight prediction, relativizing the notion of a hierarchy of multiplicative interactions. We further derive an equivalence between a restricted type of HyperNetwork and factorization machines. Finally, we find empirically that gating layers can learn to imitate weight prediction layers with an SGD variant and show a novel practical application in image denoising using kernel prediction networks. Our reformulation of predicted kernels, combining fixed layers and gating, reduces memory requirements.

Conformal prediction (CP) can convert any model's output into prediction sets guaranteed to include the true label with any user-specified probability. However, same as the model itself, CP is vulnerable to adversarial test examples (evasion) and perturbed calibration data (poisoning). We derive provably robust sets by bounding the worst-case change in conformity scores. Our tighter bounds lead to more efficient sets. We cover both continuous and discrete (sparse) data and our guarantees work both for evasion and poisoning attacks (on both features and labels).

Differential privacy (DP) offers a theoretical upper bound on the potential privacy leakage of an algorithm, while empirical auditing establishes a practical lower bound. Auditing techniques exist for DP training algorithms. However machine learning can also be made private at inference. We propose the first framework for auditing private prediction where we instantiate adversaries with varying poisoning and query capabilities. This enables us to study the privacy leakage of four private prediction algorithms: PATE (Papernot et al., 2016), CaPC (Choquette-Choo et al., 2020), PromptPATE (Duan et al., 2023), and Private-kNN (Zhu et al., 2020). To conduct our audit, we introduce novel techniques to empirically evaluate privacy leakage in terms of Renyi DP. Our experiments show that (i) the privacy analysis of private prediction can be improved, (ii) algorithms which are easier to poison lead to much higher privacy leakage, and (iii) the privacy leakage is significantly lower for adversaries without query control than those with full control.

Spatio-temporal point processes (STPPs) are potent mathematical tools for modeling and predicting events with both temporal and spatial features. Despite their versatility, most existing methods for learning STPPs either assume a restricted form of the spatio-temporal distribution, or suffer from inaccurate approximations of the intractable integral in the likelihood training objective. These issues typically arise from the normalization term of the probability density function. Moreover, existing works only provide point prediction for events without quantifying their uncertainty, such as confidence intervals for the event's arrival time and confidence regions for the event's location, which is crucial given the considerable randomness of the data. To tackle these challenges, we introduce SMASH: a Score MAtching-based pSeudolikeliHood estimator for learning marked STPPs. Specifically, our framework adopts a normalization-free objective by estimating the pseudolikelihood of marked STPPs through score-matching and predicts confidence intervals/regions for event time and location by generating samples through a score-based sampling algorithm. The superior performance of our proposed framework is demonstrated through extensive experiments on both point and confidence interval/region prediction of events.

Private everlasting prediction (PEP), recently introduced by Naor et al. [2023], is a model for differentially private learning in which the learner never publicly releases a hypothesis. Instead, it provides black-box access to a "prediction oracle" that can predict the labels of an *endless stream* of unlabeled examples drawn from the underlying distribution. Importantly, PEP provides privacy both for the initial training set and for the endless stream of classification queries. We present two conceptual modifications to the definition of PEP, as well as new constructions exhibiting significant improvements over prior work. Specifically, we incorporate robustness against poisoning attacks into the definition of PEP; we present a relaxed privacy definition, suitable for PEP, that allows us to disconnect the privacy parameter $\delta$ from the number of total time steps $T$; and we present new constructions for axis-aligned rectangles and decision-stumps exhibiting improved sample complexity and runtime.