Propensity Score Alignment of Unpaired Multimodal Data

Multimodal representation learning techniques typically rely on paired samples to learn common representations, but paired samples are challenging to collect in fields such as biology where measurement devices often destroy the samples. This paper presents an approach to address the challenge of aligning unpaired samples across disparate modalities in multimodal representation learning. We draw an analogy between potential outcomes in causal inference and potential views in multimodal observations, which allows us to use Rubin's framework to estimate a common space in which to match samples. Our approach assumes we collect samples that are experimentally perturbed by treatments, and uses this to estimate a propensity score from each modality, which encapsulates all shared information between a latent state and treatment and can be used to define a distance between samples. We experiment with two alignment techniques that leverage this distance -- shared nearest neighbours (SNN) and optimal transport (OT) matching -- and find that OT matching results in significant improvements over state-of-the-art alignment approaches in both a synthetic multi-modal setting and in real-world data from NeurIPS Multimodal Single-Cell Integration Challenge.

Object-centric architectures enable efficient causal representation learning

Causal representation learning has showed a variety of settings in which we can disentangle latent variables with identifiability guarantees (up to some reasonable equivalence class). Common to all of these approaches is the assumption that (1) the latent variables are represented as $d$-dimensional vectors, and (2) that the observations are the output of some injective generative function of these latent variables. While these assumptions appear benign, we show that when the observations are of multiple objects, the generative function is no longer injective and disentanglement fails in practice. We can address this failure by combining recent developments in object-centric learning and causal representation learning. By modifying the Slot Attention architecture arXiv:2006.15055, we develop an object-centric architecture that leverages weak supervision from sparse perturbations to disentangle each object's properties. This approach is more data-efficient in the sense that it requires significantly fewer perturbations than a comparable approach that encodes to a Euclidean space and we show that this approach successfully disentangles the properties of a set of objects in a series of simple image-based disentanglement experiments.

Sequential Underspecified Instrument Selection for Cause-Effect Estimation

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

DynGFN: Bayesian Dynamic Causal Discovery using Generative Flow Networks

Learning the causal structure of observable variables is a central focus for scientific discovery. Bayesian causal discovery methods tackle this problem by learning a posterior over the set of admissible graphs given our priors and observations. Existing methods primarily consider observations from static systems and assume the underlying causal structure takes the form of a directed acyclic graph (DAG). In settings with dynamic feedback mechanisms that regulate the trajectories of individual variables, this acyclicity assumption fails unless we account for time. We focus on learning Bayesian posteriors over cyclic graphs and treat causal discovery as a problem of sparse identification of a dynamical system. This imposes a natural temporal causal order between variables and captures cyclic feedback loops through time. Under this lens, we propose a new framework for Bayesian causal discovery for dynamical systems and present a novel generative flow network architecture (DynGFN) tailored for this task. Our results indicate that DynGFN learns posteriors that better encapsulate the distributions over admissible cyclic causal structures compared to counterpart state-of-the-art approaches.

GFlowNets for AI-Driven Scientific Discovery

Tackling the most pressing problems for humanity, such as the climate crisis and the threat of global pandemics, requires accelerating the pace of scientific discovery. While science has traditionally relied on trial and error and even serendipity to a large extent, the last few decades have seen a surge of data-driven scientific discoveries. However, in order to truly leverage large-scale data sets and high-throughput experimental setups, machine learning methods will need to be further improved and better integrated in the scientific discovery pipeline. A key challenge for current machine learning methods in this context is the efficient exploration of very large search spaces, which requires techniques for estimating reducible (epistemic) uncertainty and generating sets of diverse and informative experiments to perform. This motivated a new probabilistic machine learning framework called GFlowNets, which can be applied in the modeling, hypotheses generation and experimental design stages of the experimental science loop. GFlowNets learn to sample from a distribution given indirectly by a reward function corresponding to an unnormalized probability, which enables sampling diverse, high-reward candidates. GFlowNets can also be used to form efficient and amortized Bayesian posterior estimators for causal models conditioned on the already acquired experimental data. Having such posterior models can then provide estimators of epistemic uncertainty and information gain that can drive an experimental design policy. Altogether, here we will argue that GFlowNets can become a valuable tool for AI-driven scientific discovery, especially in scenarios of very large candidate spaces where we have access to cheap but inaccurate measurements or to expensive but accurate measurements. This is a common setting in the context of drug and material discovery, which we use as examples throughout the paper.

Monte Carlo Forest Search: UNSAT Solver Synthesis via Reinforcement learning

We introduce Monte Carlo Forest Search (MCFS), an offline algorithm for automatically synthesizing strong tree-search solvers for proving \emph{unsatisfiability} on given distributions, leveraging ideas from the Monte Carlo Tree Search (MCTS) algorithm that led to breakthroughs in AlphaGo. The crucial difference between proving unsatisfiability and existing applications of MCTS, is that policies produce trees rather than paths. Rather than finding a good path (solution) within a tree, the search problem becomes searching for a small proof tree within a forest of candidate proof trees. We introduce two key ideas to adapt to this setting. First, we estimate tree size with paths, via the unbiased approximation from Knuth (1975). Second, we query a strong solver at a user-defined depth rather than learning a policy across the whole tree, in order to focus our policy search on early decisions, which offer the greatest potential for reducing tree size. We then present MCFS-SAT, an implementation of MCFS for learning branching policies for solving the Boolean satisfiability (SAT) problem that required many modifications from AlphaGo. We matched or improved performance over a strong baseline on two well-known SAT distributions (\texttt{sgen}, \texttt{random}). Notably, we improved running time by 9\% on \texttt{sgen} over the \texttt{kcnfs} solver and even further over the strongest UNSAT solver from the 2021 SAT competition.

Weakly Supervised Representation Learning with Sparse Perturbations

The theory of representation learning aims to build methods that provably invert the data generating process with minimal domain knowledge or any source of supervision. Most prior approaches require strong distributional assumptions on the latent variables and weak supervision (auxiliary information such as timestamps) to provide provable identification guarantees. In this work, we show that if one has weak supervision from observations generated by sparse perturbations of the latent variables--e.g. images in a reinforcement learning environment where actions move individual sprites--identification is achievable under unknown continuous latent distributions. We show that if the perturbations are applied only on mutually exclusive blocks of latents, we identify the latents up to those blocks. We also show that if these perturbation blocks overlap, we identify latents up to the smallest blocks shared across perturbations. Consequently, if there are blocks that intersect in one latent variable only, then such latents are identified up to permutation and scaling. We propose a natural estimation procedure based on this theory and illustrate it on low-dimensional synthetic and image-based experiments.

Properties from Mechanisms: An Equivariance Perspective on Identifiable Representation Learning

A key goal of unsupervised representation learning is "inverting" a data generating process to recover its latent properties. Existing work that provably achieves this goal relies on strong assumptions on relationships between the latent variables (e.g., independence conditional on auxiliary information). In this paper, we take a very different perspective on the problem and ask, "Can we instead identify latent properties by leveraging knowledge of the mechanisms that govern their evolution?" We provide a complete characterization of the sources of non-identifiability as we vary knowledge about a set of possible mechanisms. In particular, we prove that if we know the exact mechanisms under which the latent properties evolve, then identification can be achieved up to any equivariances that are shared by the underlying mechanisms. We generalize this characterization to settings where we only know some hypothesis class over possible mechanisms, as well as settings where the mechanisms are stochastic. We demonstrate the power of this mechanism-based perspective by showing that we can leverage our results to generalize existing identifiable representation learning results. These results suggest that by exploiting inductive biases on mechanisms, it is possible to design a range of new identifiable representation learning approaches.

The Perils of Learning Before Optimizing

Formulating real-world optimization problems often begins with making predictions from historical data (e.g., an optimizer that aims to recommend fast routes relies upon travel-time predictions). Typically, learning the prediction model used to generate the optimization problem and solving that problem are performed in two separate stages. Recent work has showed how such prediction models can be learned end-to-end by differentiating through the optimization task. Such methods often yield empirical improvements, which are typically attributed to end-to-end making better error tradeoffs than the standard loss function used in a two-stage solution. We refine this explanation and more precisely characterize when end-to-end can improve performance. When prediction targets are stochastic, a two-stage solution must make an a priori choice about which statistics of the target distribution to model -- we consider expectations over prediction targets -- while an end-to-end solution can make this choice adaptively. We show that the performance gap between a two-stage and end-to-end approach is closely related to the \emph{price of correlation} concept in stochastic optimization and show the implications of some existing POC results for our predict-then-optimize problem. We then consider a novel and particularly practical setting, where coefficients in the objective function depend on multiple prediction targets. We give explicit constructions where (1) two-stage performs unboundedly worse than end-to-end; and (2) two-stage is optimal. We identify a large set of real-world applications whose objective functions rely on multiple prediction targets but which nevertheless deploy two-stage solutions. We also use simulations to experimentally quantify performance gaps.

Exemplar Guided Active Learning

We consider the problem of wisely using a limited budget to label a small subset of a large unlabeled dataset. We are motivated by the NLP problem of word sense disambiguation. For any word, we have a set of candidate labels from a knowledge base, but the label set is not necessarily representative of what occurs in the data: there may exist labels in the knowledge base that very rarely occur in the corpus because the sense is rare in modern English; and conversely there may exist true labels that do not exist in our knowledge base. Our aim is to obtain a classifier that performs as well as possible on examples of each "common class" that occurs with frequency above a given threshold in the unlabeled set while annotating as few examples as possible from "rare classes" whose labels occur with less than this frequency. The challenge is that we are not informed which labels are common and which are rare, and the true label distribution may exhibit extreme skew. We describe an active learning approach that (1) explicitly searches for rare classes by leveraging the contextual embedding spaces provided by modern language models, and (2) incorporates a stopping rule that ignores classes once we prove that they occur below our target threshold with high probability. We prove that our algorithm only costs logarithmically more than a hypothetical approach that knows all true label frequencies and show experimentally that incorporating automated search can significantly reduce the number of samples needed to reach target accuracy levels.