50 accepted papers
Improving antibody binding to an antigen without antibody-antigen structure information or antigen-specific data remains a critical challenge in therapeutic protein design. In this work, we propose \textbf{\textsc{AffinityEnhancer}}, a framework to improve the affinity of an antibody in a one-shot s…
Language models are increasingly capable and are being rapidly deployed on a population-level scale. As a result, the safety of these models is increasingly high-stakes. Fortunately, advances in alignment have significantly reduced the likelihood of harmful model outputs. However, when models are qu…
Diffusion and flow-based models benefit from simple regression losses, but inference (i.e, producing samples) incurs significant computational overhead because it requires integration. Consistency models address this overhead by directly learning the flow maps along the ODE trajectory, revealing a d…
Classical intuitions cast minimizing reverse KL as "mode seeking" and forward KL as "mass covering". In KL-regularized reinforcement learning, however, the regularizer determines _both_ the target distribution's shape _and_ the divergence being implicitly minimized, making its role more nuanced than…
Large language models (LLMs) are increasingly deployed in high-stakes domains, where free-text explanations such as chain-of-thought and post-hoc rationales are used to justify model outputs. Yet it remains unclear whether these explanations are _sufficient_, i.e., if they contain enough information…
Diffusion models have demonstrated remarkable performance in generative modeling, but generating samples with specific desiderata remains challenging. Existing solutions --- such as fine-tuning, best-of-n sampling, and gradient-based guidance --- are expensive, inefficient, or limited in applicabil…
Many applications that modern large language models (LLMs) are deployed on are retrieval tasks: the answer can be recovered from context and success is a matter of learning generalizable features from data. However, this is easier said than done. Overparametrized models trained on cross-entropy loss
Preference learning, or the task of aligning generative models to preference comparison data, has yet to reach the conceptual maturity of classification, density estimation, etc. To close this gap, this work presents a framework to understand preference learning starting from the sampling distributi…
Uncertainty-aware meta-learning aims not only for rapid adaptation to new tasks but also for reliable uncertainty estimation under limited supervision. Neural Processes (NPs) offer a flexible solution by learning implicit stochastic processes directly from data, often using a global latent variable…
Problems in fields such as healthcare, robotics, and finance requires reasoning about the value both of what decision or action to take and when to take it. The prevailing hope is that artificial intelligence will support such decisions by estimating the causal effect of policies such as how to trea…
Magnetic Resonance (MR) imaging, despite its proven diagnostic utility, remains an inaccessible imaging modality for disease surveillance at the population level. A major factor rendering MR inaccessible is lengthy scan times. An MR scanner collects measurements associated with the underlying anatom…
Contrastive learning methods, such as CLIP, leverage naturally paired data—for example, images and their corresponding text captions—to learn general representations that transfer efficiently to downstream tasks. While such approaches are generally applied to two modalities, domains such as robotics…
Feature attributions attempt to highlight what inputs drive predictive power. Good attributions or explanations are thus those that produce inputs that retain this predictive power; accordingly, evaluations of explanations score their quality of prediction. However, evaluations produce scores better…
Preference learning algorithms (e.g., RLHF and DPO) are frequently used to steer LLMs to produce generations that are more preferred by humans, but our understanding of their inner workings is still limited. In this work, we study the conventional wisdom that preference learning trains models to ass…
Generative models inspired by dynamical transport of measure -- such as flows and diffusions -- construct a continuous-time map between two probability densities. Conventionally, one of these is the target density, only accessible through samples, while the other is taken as a simple base density th…
Reversing a diffusion process by learning its score forms the heart of diffusion-based generative modeling and for estimating properties of scientific systems. The diffusion processes that are tractable center on linear processes with a Gaussian stationary distribution, limiting the kinds of models…
One straightforward metric to evaluate a survival prediction model is based on the Mean Absolute Error (MAE) – the average of the absolute difference between the time predicted by the model and the true event time, over all subjects. Unfortunately, this is challenging because, in practice, the test…
Conditional randomization tests (CRTs) assess whether a variable $x$ is predictive of another variable $y$, having observed covariates $z$. CRTs require fitting a large number of predictive models, which is often computationally intractable. Existing solutions to reduce the cost of CRTs typically sp…
Feature attribution methods identify which features of an input most influence a model’s output. Most widely-used feature attribution methods (such as SHAP, LIME, and Grad-CAM) are “class-dependent” methods in that they generate a feature attribution vector as a function of class. In this work, we d…
Common explanations for shortcut learning assume that the shortcut improves prediction only under the training distribution. Thus, models trained in the typical way by minimizing log-loss using gradient descent, which we call default-ERM, should utilize the shortcut. However, even when the stable fe…
Methods which utilize the outputs or feature representations of predictive models have emerged as promising approaches for out-of-distribution (OOD) detection of image inputs. However, as demonstrated in previous work, these methods struggle to detect OOD inputs that share nuisance values (e.g. back…
Diffusion-based generative models (DBGMs) perturb data to a target noise distribution and reverse this process to generate samples. The choice of noising process, or inference diffusion process, affects both likelihoods and sample quality. For example, extending the inference process with auxiliary…
Although Shapley values are theoretically appealing for explaining black-box models, they are costly to calculate and thus impractical in settings that involve large, high-dimensional models. To remedy this issue, we introduce FastSHAP, a new method for estimating Shapley values in a single forward…
In many prediction problems, spurious correlations are induced by a changing relationship between the label and a nuisance variable that is also correlated with the covariates. For example, in classifying animals in natural images, the background, which is a nuisance, can predict the type of animal.…
Permutation invariant neural networks are a promising tool for predictive modeling of set data. We show, however, that existing architectures struggle to perform well when they are deep. In this work, we mathematically and empirically analyze normalization layers and residual connections in the cont…
The holdout randomization test (HRT) discovers a set of covariates most predictive of a response. Given the covariate distribution, HRTs can explicitly control the false discovery rate (FDR). However, if this distribution is unknown and must be estimated from data, HRTs can inflate the FDR. To allev…
While the need for interpretable machine learning has been established, many common approaches are slow, lack fidelity, or hard to evaluate. Amortized explanation methods reduce the cost of providing interpretations by learning a global selector model that returns feature importances for a single in…
Deep models trained through maximum likelihood have achieved state-of-the-art results for survival analysis. Despite this training scheme, practitioners evaluate models under other criteria, such as binary classification losses at a chosen set of time horizons, e.g. Brier score (BS) and Bernoulli lo…
Recent results in supervised learning suggest that while overparameterized models have the capacity to overfit, they in fact generalize quite well. We ask whether the same phenomenon occurs for offline contextual bandits. Our results are mixed. Value-based algorithms benefit from the same generaliza…
Most prior approaches to offline reinforcement learning (RL) have taken an iterative actor-critic approach involving off-policy evaluation. In this paper we show that simply doing one step of constrained/regularized policy improvement using an on-policy Q estimate of the behavior policy performs sur…
Deep generative models (DGMs) seem a natural fit for detecting out-of-distribution (OOD) inputs, but such models have been shown to assign higher probabilities or densities to OOD images than images from the training distribution. In this work, we explain why this behavior should be attributed to mo…
Causal inference relies on two fundamental assumptions: ignorability and positivity. We study causal inference when the true confounder value can be expressed as a function of the observed data; we call this setting estimation with functional confounders (EFC). In this setting ignorability is satisf…
Predictive modeling often uses black box machine learning methods, such as deep neural networks, to achieve state-of-the-art performance. In scientific domains, the scientist often wishes to discover which features are actually important for making the predictions. These discoveries may lead to cost…
Causal effect estimation relies on separating the variation in the outcome into parts due to the treatment and due to the confounders. To achieve this separation, practitioners often use external sources of randomness that only influence the treatment called instrumental variables (IVs). We study va…
Survival analysis models the distribution of time until an event of interest, such as discharge from the hospital or admission to the ICU. When a model’s predicted number of events within any time interval is similar to the observed number, it is called well-calibrated. A survival model’s calibratio…
Energy-based models (EBMs) are powerful probabilistic models, but suffer from intractable sampling and density evaluation due to the partition function. As a result, inference in EBMs relies on approximate sampling algorithms, leading to a mismatch between the model and inference. Motivated by this,…
Programming languages allow us to express complex predicates, but existing inference methods are unable to condition probabilistic models on most of them. To support a broader class of predicates, we develop an inference procedure called predicate exchange, which softens predicates. A soft predicate…
Learning domain-invariant representations has become a popular approach to unsupervised domain adaptation and is often justified by invoking a particular suite of theoretical results. We argue that there are two significant flaws in such arguments. First, the results in question hold only for a fixe…
Variational inference transforms posterior inference into parametric optimization thereby enabling the use of latent variable models where otherwise impractical. However, variational inference can be finicky when different variational parameters control variables that are strongly correlated under t…
Recurrent neural networks (RNNs) are powerful models of sequential data. They have been successfully used in domains such as text and speech. However, RNNs are susceptible to overfitting; regularization is important. In this paper we develop Noisin, a new method for regularizing RNNs. Noisin injects…
Variational inference is a powerful approach for approximate posterior inference. However, it is sensitive to initialization and can be subject to poor local optima. In this paper, we develop proximity variational inference (PVI). PVI is a new method for optimizing the variational objective that con…
Many recent advances in large scale probabilistic inference rely on variational methods. The success of variational approaches depends on (i) formulating a flexible parametric family of distributions, and (ii) optimizing the parameters to find the member of this family that most closely approximates…
Implicit probabilistic models are a flexible class of models defined by a simulation process for data. They form the basis for models which encompass our understanding of the physical word. Despite this fundamental nature, the use of implicit models remains limited due to challenge in positing compl…
Variational inference (VI) is widely used as an efficient alternative to Markov chain Monte Carlo. It posits a family of approximating distributions $q$ and finds the closest member to the exact posterior $p$. Closeness is usually measured via a divergence $D(q || p)$ from $q$ to $p$. While successf…
Black box variational inference allows researchers to easily prototype and evaluate an array of models. Recent advances allow such algorithms to scale to high dimensions. However, a central question remains: How to specify an expressive variational distribution that maintains efficient computation?…
Variational inference is an umbrella term for algorithms which cast Bayesian inference as optimization. Classically, variational inference uses the Kullback-Leibler divergence to define the optimization. Though this divergence has been widely used, the resultant posterior approximation can suffer fr…
Variational inference (VI) combined with data subsampling enables approximate posterior inference with large data sets for otherwise intractable models, but suffers from poor local optima. We first formulate a deterministic annealing approach for the generic class of conditionally conjugate exponent…
Variational inference is a scalable technique for approximate Bayesian inference. Deriving variational inference algorithms requires tedious model-specific calculations; this makes it difficult for non-experts to use. We propose an automatic variational inference algorithm, automatic differentiati…
We describe deep exponential families (DEFs), a class of latent variable models that are inspired by the hidden structures used in deep neural networks. DEFs capture a hierarchy of dependencies between latent variables, and are easily generalized to many settings through exponential families. We per…
Many modern data analysis problems involve inferences from streaming data. However, streaming data is not easily amenable to the standard probabilistic modeling approaches, which assume that we condition on finite data. We develop population variational Bayes, a new approach for using Bayesian model…