Recent efforts to improve the interpretability of deep neural networks use saliency to characterize the importance of input features to predictions made by models. Work on interpretability using saliency-based methods on Recurrent Neural Networks (RNNs) has mostly targeted language tasks, and their applicability to time series data is less understood. In this work we analyze saliency-based methods for RNNs, both classical and gated cell architectures. We show that RNN saliency vanishes over time, biasing detection of salient features only to later time steps and are, therefore, incapable of reliably detecting important features at arbitrary time intervals. To address this vanishing saliency problem, we propose a novel RNN cell structure (input-cell attention), which can extend any RNN cell architecture.

Cookies are designed to enable more accurate identification and tracking of user behavior, in turn allowing for more personalized ads and better performing ad campaigns. Given the additional information that is recorded, questions related to privacy and fairness naturally arise. How does a user's consent decision influence how much the system can learn about their demographic and tastes? Is the impact of a user's consent decision on the recommender system's ability to learn about their latent attributes uniform across demographics? We investigate these questions in the context of an engagement-driven recommender system using simulation. We empirically demonstrate that when consent rates exhibit demographic-dependence, user consent has a disparate impact on the recommender agent's ability to estimate users' latent attributes. In particular, we find that when consent rates are demographic-dependent, a user disagreeing to share their cookie may counter-intuitively cause the recommender agent to know more about the user than if the user agreed to share their cookie. Furthermore, the gap in base consent rates across demographics serves as an amplifier: users from the lower consent rate demographic who agree to cookie sharing generally experience higher estimation errors than the same users from the higher consent rate demographic, and conversely for users who choose to disagree to cookie sharing, with these differences increasing in consent rate gap. We discuss the need for new notions of fairness that encourage consistency between a user's privacy decisions and the system's ability to estimate their latent attributes.

The Kalman filter (KF) is one of the most widely used tools for data assimilation and sequential estimation. In this work, we show that the state estimates from the KF in a standard linear dynamical system setting are equivalent to those given by the KF in a transformed system, with infinite process noise (i.e., a ``flat prior'') and an augmented measurement space. This reformulation---which we refer to as augmented measurement sensor fusion (SF)---is conceptually interesting, because the transformed system here is seemingly static (as there is effectively no process model), but we can still capture the state dynamics inherent to the KF by folding the process model into the measurement space. Further, this reformulation of the KF turns out to be useful in settings in which past states are observed eventually (at some lag). Here, when the measurement noise covariance is estimated by the empirical covariance, we show that the state predictions from SF are equivalent to those from a regression of past states on past measurements, subject to particular linear constraints (reflecting the relationships encoded in the measurement map). This allows us to port standard ideas (say, regularization methods) in regression over to dynamical systems. For example, we can posit multiple candidate process models, fold all of them into the measurement model, transform to the regression perspective, and apply $\ell_1$ penalization to perform process model selection. We give various empirical demonstrations, and focus on an application to nowcasting the weekly incidence of influenza in the US.

Nonlinear embedding manifold learning methods provide invaluable visual insights into a structure of high-dimensional data. However, due to a complicated nonconvex objective function, these methods can easily get stuck in local minima and their embedding quality can be poor. We propose a natural extension to several manifold learning methods aimed at identifying pressured points, i.e. points stuck in the poor local minima and have poor embedding quality. We show that the objective function can be decreased by temporarily allowing these points to make use of an extra dimension in the embedding space. Our method is able to improve the objective function value of existing methods even after they get stuck in a poor local minimum.

Diffusion Models (DMs) are state-of-the-art generative models that learn a reversible corruption process from iterative noise addition and denoising. They are the backbone of many generative AI applications, such as text-to-image conditional generation. However, recent studies have shown that basic unconditional DMs (e.g., DDPM and DDIM) are vulnerable to backdoor injection, a type of output manipulation attack triggered by a maliciously embedded pattern at model input. This paper presents a unified backdoor attack framework (VillanDiffusion) to expand the current scope of backdoor analysis for DMs. Our framework covers mainstream unconditional and conditional DMs (denoising-based and score-based) and various training-free samplers for holistic evaluations. Experiments show that our unified framework facilitates the backdoor analysis of different DM configurations and provides new insights into caption-based backdoor attacks on DMs.

The Tanimoto coefficient is commonly used to measure the similarity between molecules represented as discrete fingerprints,either as a distance metric or a positive definite kernel. While many kernel methods can be accelerated using random feature approximations, at present there is a lack of such approximations for the Tanimoto kernel. In this paper we propose two kinds of novel random features to allow this kernel to scale to large datasets, and in the process discover a novel extension of the kernel to real-valued vectors. We theoretically characterize these random features, and provide error bounds on the spectral norm of the Gram matrix. Experimentally, we show that these random features are effective at approximating the Tanimoto coefficient of real-world datasetsand are useful for molecular property prediction and optimization tasks. Future updates to this work will be available at http://arxiv.org/abs/2306.14809.

We study the performance of optimistic regret-minimization algorithms for both minimizing regret in, and computing Nash equilibria of, zero-sum extensive-form games. In order to apply these algorithms to extensive-form games, a distance-generating function is needed. We study the use of the dilated entropy and dilated Euclidean distance functions. For the dilated Euclidean distance function we prove the first explicit bounds on the strong-convexity parameter for general treeplexes. Furthermore, we show that the use of dilated distance-generating functions enable us to decompose the mirror descent algorithm, and its optimistic variant, into local mirror descent algorithms at each information set. This decomposition mirrors the structure of the counterfactual regret minimization framework, and enables important techniques in practice, such as distributed updates and pruning of cold parts of the game tree. Our algorithms provably converge at a rate of $T^{-1}$, which is superior to prior counterfactual regret minimization algorithms. We experimentally compare to the popular algorithm CFR+, which has a theoretical convergence rate of $T^{-0.5}$ in theory, but is known to often converge at a rate of $T^{-1}$, or better, in practice. We give an example matrix game where CFR+ experimentally converges at a relatively slow rate of $T^{-0.74}$,

Protein design holds immense potential for optimizing naturally occurring proteins, with broad applications in drug discovery, material design, and sustainability. However, computational methods for protein engineering are confronted with significant challenges, such as an expansive design space, sparse functional regions, and a scarcity of available labels. These issues are further exacerbated in practice by the fact most real-life design scenarios necessitate the simultaneous optimization of multiple properties. In this work, we introduce ProteinNPT, a non-parametric transformer variant tailored to protein sequences and particularly suited to label-scarce and multi-task learning settings. We first focus on the supervised fitness prediction setting and develop several cross-validation schemes which support robust performance assessment. We subsequently reimplement prior top-performing baselines, introduce several extensions of these baselines by integrating diverse branches of the protein engineering literature, and demonstrate that ProteinNPT consistently outperforms all of them across a diverse set of protein property prediction tasks. Finally, we demonstrate the value of our approach for iterative protein design across extensive in silico Bayesian optimization and conditional sampling experiments.

Protein-ligand binding prediction is a fundamental problem in AI-driven drug discovery. Previous work focused on supervised learning methods for small molecules where binding affinity data is abundant, but it is hard to apply the same strategy to other ligand classes like antibodies where labelled data is limited. In this paper, we explore unsupervised approaches and reformulate binding energy prediction as a generative modeling task. Specifically, we train an energy-based model on a set of unlabelled protein-ligand complexes using SE(3) denoising score matching (DSM) and interpret its log-likelihood as binding affinity. Our key contribution is a new equivariant rotation prediction network called Neural Euler's Rotation Equations (NERE) for SE(3) DSM. It predicts a rotation by modeling the force and torque between protein and ligand atoms, where the force is defined as the gradient of an energy function with respect to atom coordinates. Using two protein-ligand and antibody-antigen binding affinity prediction benchmarks, we show that NERE outperforms all unsupervised baselines (physics-based potentials and protein language models) in both cases and surpasses supervised baselines in the antibody case.

We consider the graph matching/similarity problem of determining how similar two given graphs $G_0,G_1$ are and recovering the permutation $\pi$ on the vertices of $G_1$ that minimizes the symmetric difference between the edges of $G_0$ and $\pi(G_1)$. Graph matching/similarity has applications for pattern matching, vision, social network anonymization, malware analysis, and more. We give the first efficient algorithms proven to succeed in the correlated Erdös-Rényi model (Pedarsani and Grossglauser, 2011). Specifically, we give a polynomial time algorithm for the graph similarity/hypothesis testing task which works for every constant level of correlation between the two graphs that can be arbitrarily close to zero. We also give a quasi-polynomial ($n^{O(\log n)}$ time) algorithm for the graph matching task of recovering the permutation minimizing the symmetric difference in this model. This is the first algorithm to do so without requiring as additional input a ``seed'' of the values of the ground truth permutation on at least $n^{\Omega(1)}$ vertices. Our algorithms follow a general framework of counting the occurrences of subgraphs from a particular family of graphs allowing for tradeoffs between efficiency and accuracy.