Mehran Kazemi, Bahare Fatemi, Hritik Bansal, John Palowitch, Chrysovalantis Anastasiou, Sanket Vaibhav Mehta, Lalit K Jain, Virginia Aglietti, Disha Jindal, Peter Chen, Nishanth Dikkala, Gladys Tyen, Xin Liu, Uri Shalit, Silvia Chiappa, Kate Olszewska, Yi Tay, Vinh Q. Tran, Quoc V Le, Orhan Firat. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Merging datasets across institutions is a lengthy and costly procedure, especially when it involves private information. Data hosts may therefore want to prospectively gauge which datasets are most beneficial to merge with, without revealing sensitive information. For causal estimation this is particularly challenging as the value of a merge depends not only on reduction in epistemic uncertainty but also on improvement in overlap. To address this challenge, we introduce the first \emph{cryptographically secure} information-theoretic approach for quantifying the value of a merge in the context of heterogeneous treatment effect estimation. We do this by evaluating the \emph{Expected Information Gain} (EIG) using multi-party computation to ensure that no raw data is revealed. We further demonstrate that our approach can be combined with differential privacy (DP) to meet arbitrary privacy requirements whilst preserving more accurate computation compared to DP alone. To the best of our knowledge, this work presents the first privacy-preserving method for dataset acquisition tailored to causal estimation.Code is publicly available: \url{https://github.com/LucileTerminassian/causal_prospective_merge}.

Randomized Controlled Trials (RCTs) are the gold standard for evaluating the effect of new medical treatments. Treatments must pass stringent regulatory conditions in order to be approved for widespread use, yet even after the regulatory barriers are crossed, real-world challenges might arise: Who should get the treatment? What is its true clinical utility? Are there discrepancies in the treatment effectiveness across diverse and under-served populations? We introduce two new objectives for future clinical trials that integrate regulatory constraints and treatment policy value for both the entire population and under-served populations, thus answering some of the questions above in advance. Designed to meet these objectives, we formulate Randomize First Augment Next (RFAN), a new framework for designing Phase III clinical trials. Our framework consists of a standard randomized component followed by an adaptive one, jointly meant to efficiently and safely acquire and assign patients into treatment arms during the trial. Then, we propose strategies for implementing RFAN based on causal, deep Bayesian active learning. Finally, we empirically evaluate the performance of our framework using synthetic and real-world semi-synthetic datasets.

Tailoring treatments to individual needs is a central goal in fields such as medicine. A key step toward this goal is estimating Heterogeneous Treatment Effects (HTE)—the way treatments impact different subgroups. While crucial, HTE estimation is challenging with survival data, where time until an event (e.g., death) is key. Existing methods often assume complete observation, an assumption violated in survival data due to right-censoring, leading to bias and inefficiency. Cui et al. (2023) proposed a doubly-robust method for HTE estimation in survival data under no hidden confounders, combining a causal survival forest with an augmented inverse-censoring weighting estimator. However, we find it struggles under heavy censoring, which is common in rare-outcome problems such as Amyotrophic lateral sclerosis (ALS). Moreover, most current methods cannot handle instrumental variables, which are a crucial tool in the causal inference arsenal. We introduce Multiple Imputation for Survival Treatment Response (MISTR), a novel, general, and non-parametric method for estimating HTE in survival data. MISTR uses recursively imputed survival trees to handle censoring without directly modeling the censoring mechanism. Through extensive simulations and analysis of two real-world datasets—the AIDS Clinical Trials Group Protocol 175 and the Illinois unemployment dataset we show that MISTR outperforms prior methods under heavy censoring in the no-hidden-confounders setting, and extends to the instrumental variable setting. To our knowledge, MISTR is the first non-parametric approach for HTE estimation with unobserved confounders via instrumental variables.

Despite the impressive advancements in modern machine learning, achieving robustness in Domain Generalization (DG) tasks remains a significant challenge. In DG, models are expected to perform well on samples from unseen test distributions (also called domains), by learning from multiple related training distributions. Most existing approaches to this problem rely on single-valued predictions, which inherently limit their robustness. We argue that set-valued predictors could be leveraged to enhance robustness across unseen domains, while also taking into account that these sets should be as small as possible. We introduce a theoretical framework defining successful set prediction in the DG setting, focusing on meeting a predefined performance criterion across as many domains as possible, and provide theoretical insights into the conditions under which such domain generalization is achievable. We further propose a practical optimization method compatible with modern learning architectures, that balances robust performance on unseen domains with small prediction set sizes. We evaluate our approach on several real-world datasets from the WILDS benchmark, demonstrating its potential as a promising direction for robust domain generalization.

We consider the task of learning how to act in collaboration with a human expert based on observational data. The task is motivated by high-stake scenarios such as healthcare and welfare where algorithmic action recommendations are made to a human expert, opening the option of deferring making a recommendation in cases where the human might act better on their own. This task is especially challenging when dealing with observational data, as using such data runs the risk of hidden confounders whose existence can lead to biased and harmful policies. However, unlike standard policy learning, the presence of a human expert can mitigate some of these risks. We build on the work of Mozannar and Sontag (2020) on consistent surrogate loss for learning with the option of deferral to an expert, where they solve a cost-sensitive supervised classification problem. Since we are solving a causal problem, where labels don’t exist, we use a causal model to learn costs which are robust to a bounded degree of hidden confounding. We prove that our approach can take advantage of the strengths of both the model and the expert to obtain a better policy than either. We demonstrate our results by conducting experiments on synthetic and semi-synthetic data and show the advantages of our method compared to baselines.

Estimating heterogeneous treatment effects from observational data is a crucial task across many fields, helping policy and decision-makers take better actions. There has been recent progress on robust and efficient methods for estimating the conditional average treatment effect (CATE) function, but these methods often do not take into account the risk of hidden confounding, which could arbitrarily and unknowingly bias any causal estimate based on observational data. We propose a meta-learner called the B-Learner, which can efficiently learn sharp bounds on the CATE function under limits on the level of hidden confounding. We derive the B-Learner by adapting recent results for sharp and valid bounds of the average treatment effect (Dorn et al., 2021) into the framework given by Kallus & Oprescu (2023) for robust and model-agnostic learning of conditional distributional treatment effects. The B-Learner can use any function estimator such as random forests and deep neural networks, and we prove its estimates are valid, sharp, efficient, and have a quasi-oracle property with respect to the constituent estimators under more general conditions than existing methods. Semi-synthetic experimental comparisons validate the theoretical findings, and we use real-world data demonstrate how the method might be used in practice.

Intensive care medicine is complex and resource-demanding. A critical and common challenge lies in inferring the underlying physiological state of a patient from partially observed data. Specifically for the cardiovascular system, clinicians use observables such as heart rate, arterial and venous blood pressures, as well as findings from the physical examination and ancillary tests to formulate a mental model and estimate hidden variables such as cardiac output, vascular resistance, filling pressures and volumes, and autonomic tone. Then, they use this mental model to derive the causes for instability and choose appropriate interventions. Not only this is a very hard problem due to the nature of the signals, but it also requires expertise and a clinician's ongoing presence at the bedside. Clinical decision support tools based on mechanistic dynamical models offer an appealing solution due to their inherent explainability, corollaries to the clinical mental process, and predictive power. With a translational motivation in mind, we developed iCVS: a simple, with high explanatory power, dynamical mechanistic model to infer hidden cardiovascular states. Full model estimation requires no prior assumptions on physiological parameters except age and weight, and the only inputs are arterial and venous pressure waveforms. iCVS also considers autonomic and non-autonomic modulations. To gain more information without increasing model complexity, both slow and fast timescales of the blood pressure traces are exploited, while the main inference and dynamic evolution are at the longer, clinically relevant, timescale of minutes. iCVS is designed to allow bedside deployment at pediatric and adult intensive care units and for retrospective investigation of cardiovascular mechanisms underlying instability. In this paper, we describe iCVS and inference system in detail, and using a dataset of critically-ill children, we provide initial indications to its ability to identify bleeding, distributive states, and cardiac dysfunction, in isolation and in combination.

Estimating the effects of continuous-valued interventions from observational data is a critically important task for climate science, healthcare, and economics. Recent work focuses on designing neural network architectures and regularization functions to allow for scalable estimation of average and individual-level dose-response curves from high-dimensional, large-sample data. Such methodologies assume ignorability (observation of all confounding variables) and positivity (observation of all treatment levels for every covariate value describing a set of units), assumptions problematic in the continuous treatment regime. Scalable sensitivity and uncertainty analyses to understand the ignorance induced in causal estimates when these assumptions are relaxed are less studied. Here, we develop a continuous treatment-effect marginal sensitivity model (CMSM) and derive bounds that agree with the observed data and a researcher-defined level of hidden confounding. We introduce a scalable algorithm and uncertainty-aware deep models to derive and estimate these bounds for high-dimensional, large-sample observational data. We work in concert with climate scientists interested in the climatological impacts of human emissions on cloud properties using satellite observations from the past 15 years. This problem is known to be complicated by many unobserved confounders.

We present the problem of reinforcement learning with exogenous termination. We define the Termination Markov Decision Process (TerMDP), an extension of the MDP framework, in which episodes may be interrupted by an external non-Markovian observer. This formulation accounts for numerous real-world situations, such as a human interrupting an autonomous driving agent for reasons of discomfort. We learn the parameters of the TerMDP and leverage the structure of the estimation problem to provide state-wise confidence bounds. We use these to construct a provably-efficient algorithm, which accounts for termination, and bound its regret. Motivated by our theoretical analysis, we design and implement a scalable approach, which combines optimism (w.r.t. termination) and a dynamic discount factor, incorporating the termination probability. We deploy our method on high-dimensional driving and MinAtar benchmarks. Additionally, we test our approach on human data in a driving setting. Our results demonstrate fast convergence and significant improvement over various baseline approaches.

Practitioners in diverse fields such as healthcare, economics and education are eager to apply machine learning to improve decision making. The cost and impracticality of performing experiments and a recent monumental increase in electronic record keeping has brought attention to the problem of evaluating decisions based on non-experimental observational data. This is the setting of this work. In particular, we study estimation of individual-level potential outcomes and causal effects---such as a single patient's response to alternative medication---from recorded contexts, decisions and outcomes. We give generalization bounds on the error in estimated outcomes based on distributional distance measures between re-weighted samples of groups receiving different treatments. We provide conditions under which our bounds are tight and show how they relate to results for unsupervised domain adaptation. Led by our theoretical results, we devise algorithms which learn representations and weighting functions that minimize our bounds by regularizing the representation's induced treatment group distance, and encourage sharing of information between treatment groups. Finally, an experimental evaluation on real and synthetic data shows the value of our proposed representation architecture and regularization scheme.

We study the problem of learning conditional average treatment effects (CATE) from high-dimensional, observational data with unobserved confounders. Unobserved confounders introduce ignorance—a level of unidentifiability—about an individual’s response to treatment by inducing bias in CATE estimates. We present a new parametric interval estimator suited for high-dimensional data, that estimates a range of possible CATE values when given a predefined bound on the level of hidden confounding. Further, previous interval estimators do not account for ignorance about the CATE associated with samples that may be underrepresented in the original study, or samples that violate the overlap assumption. Our interval estimator also incorporates model uncertainty so that practitioners can be made aware of such out-of-distribution data. We prove that our estimator converges to tight bounds on CATE when there may be unobserved confounding and assess it using semi-synthetic, high-dimensional datasets.

We propose to analyse the conditional distributional treatment effect (CoDiTE), which, in contrast to the more common conditional average treatment effect (CATE), is designed to encode a treatment’s distributional aspects beyond the mean. We first introduce a formal definition of the CoDiTE associated with a distance function between probability measures. Then we discuss the CoDiTE associated with the maximum mean discrepancy via kernel conditional mean embeddings, which, coupled with a hypothesis test, tells us whether there is any conditional distributional effect of the treatment. Finally, we investigate what kind of conditional distributional effect the treatment has, both in an exploratory manner via the conditional witness function, and in a quantitative manner via U-statistic regression, generalising the CATE to higher-order moments. Experiments on synthetic, semi-synthetic and real datasets demonstrate the merits of our approach.

Estimating personalized treatment effects from high-dimensional observational data is essential in situations where experimental designs are infeasible, unethical, or expensive. Existing approaches rely on fitting deep models on outcomes observed for treated and control populations. However, when measuring individual outcomes is costly, as is the case of a tumor biopsy, a sample-efficient strategy for acquiring each result is required. Deep Bayesian active learning provides a framework for efficient data acquisition by selecting points with high uncertainty. However, existing methods bias training data acquisition towards regions of non-overlapping support between the treated and control populations. These are not sample-efficient because the treatment effect is not identifiable in such regions. We introduce causal, Bayesian acquisition functions grounded in information theory that bias data acquisition towards regions with overlapping support to maximize sample efficiency for learning personalized treatment effects. We demonstrate the performance of the proposed acquisition strategies on synthetic and semi-synthetic datasets IHDP and CMNIST and their extensions, which aim to simulate common dataset biases and pathologies.

Out-of-domain (OOD) generalization is a significant challenge for machine learning models. Many techniques have been proposed to overcome this challenge, often focused on learning models with certain invariance properties. In this work, we draw a link between OOD performance and model calibration, arguing that calibration across multiple domains can be viewed as a special case of an invariant representation leading to better OOD generalization. Specifically, we show that under certain conditions, models which achieve \emph{multi-domain calibration} are provably free of spurious correlations. This leads us to propose multi-domain calibration as a measurable and trainable surrogate for the OOD performance of a classifier. We therefore introduce methods that are easy to apply and allow practitioners to improve multi-domain calibration by training or modifying an existing model, leading to better performance on unseen domains. Using four datasets from the recently proposed WILDS OOD benchmark, as well as the Colored MNIST, we demonstrate that training or tuning models so they are calibrated across multiple domains leads to significantly improved performance on unseen test domains. We believe this intriguing connection between calibration and OOD generalization is promising from both a practical and theoretical point of view.

We study linear contextual bandits with access to a large, confounded, offline dataset that was sampled from some fixed policy. We show that this problem is closely related to a variant of the bandit problem with side information. We construct a linear bandit algorithm that takes advantage of the projected information, and prove regret bounds. Our results demonstrate the ability to take advantage of confounded offline data. Particularly, we prove regret bounds that improve current bounds by a factor related to the visible dimensionality of the contexts in the data. Our results indicate that confounded offline data can significantly improve online learning algorithms. Finally, we demonstrate various characteristics of our approach through synthetic simulations.

Abstract Understanding predictions made by deep neural networks is notoriously difficult, but also crucial to their dissemination. As all machine learning–based methods, they are as good as their training data, and can also capture unwanted biases. While there are tools that can help understand whether such biases exist, they do not distinguish between correlation and causation, and might be ill-suited for text-based models and for reasoning about high level language concepts. A key problem of estimating the causal effect of a concept of interest on a given model is that this estimation requires the generation of counterfactual examples, which is challenging with existing generation technology. To bridge that gap, we propose CausaLM, a framework for producing causal model explanations using counterfactual language representation models. Our approach is based on fine-tuning of deep contextualized embedding models with auxiliary adversarial tasks derived from the causal graph of the problem. Concretely, we show that by carefully choosing auxiliary adversarial pre-training tasks, language representation models such as BERT can effectively learn a counterfactual representation for a given concept of interest, and be used to estimate its true causal effect on model performance. A byproduct of our method is a language representation model that is unaffected by the tested concept, which can be useful in mitigating unwanted bias ingrained in the data.

OBJECTIVE: The spread of coronavirus disease 2019 (COVID-19) has led to severe strain on hospital capacity in many countries. We aim to develop a model helping planners assess expected COVID-19 hospital resource utilization based on individual patient characteristics. MATERIALS AND METHODS: We develop a model of patient clinical course based on an advanced multistate survival model. The model predicts the patient's disease course in terms of clinical states-critical, severe, or moderate. The model also predicts hospital utilization on the level of entire hospitals or healthcare systems. We cross-validated the model using a nationwide registry following the day-by-day clinical status of all hospitalized COVID-19 patients in Israel from March 1 to May 2, 2020 (n = 2703). RESULTS: Per-day mean absolute errors for predicted total and critical care hospital bed utilization were 4.72 ± 1.07 and 1.68 ± 0.40, respectively, over cohorts of 330 hospitalized patients; areas under the curve for prediction of critical illness and in-hospital mortality were 0.88 ± 0.04 and 0.96 ± 0.04, respectively. We further present the impact of patient influx scenarios on day-by-day healthcare system utilization. We provide an accompanying R software package. DISCUSSION: The proposed model accurately predicts total and critical care hospital utilization. The model enables evaluating impacts of patient influx scenarios on utilization, accounting for the state of currently hospitalized patients and characteristics of incoming patients. We show that accurate hospital load predictions were possible using only a patient's age, sex, and day-by-day clinical state (critical, severe, or moderate). CONCLUSIONS: The multistate model we develop is a powerful tool for predicting individual-level patient outcomes and hospital-level utilization.

This work studies the problem of batch off-policy evaluation for Reinforcement Learning in partially observable environments. Off-policy evaluation under partial observability is inherently prone to bias, with risk of arbitrarily large errors. We define the problem of off-policy evaluation for Partially Observable Markov Decision Processes (POMDPs) and establish what we believe is the first off-policy evaluation result for POMDPs. In addition, we formulate a model in which observed and unobserved variables are decoupled into two dynamic processes, called a Decoupled POMDP. We show how off-policy evaluation can be performed under this new model, mitigating estimation errors inherent to general POMDPs. We demonstrate the pitfalls of off-policy evaluation in POMDPs using a well-known off-policy method, Importance Sampling, and compare it with our result on synthetic medical data.

We investigate the use of a non-parametric independence measure, the Hilbert-Schmidt Independence Criterion (HSIC), as a loss-function for learning robust regression and classification models. This loss-function encourages learning models where the distribution of the residuals between the label and the model prediction is statistically independent of the distribution of the instances themselves. This loss-function was first proposed by \citet{mooij2009regression} in the context of learning causal graphs. We adapt it to the task of learning for unsupervised covariate shift: learning on a source domain without access to any instances or labels from the unknown target domain, but with the assumption that $p(y|x)$ (the conditional probability of labels given instances) remains the same in the target domain. We show that the proposed loss is expected to give rise to models that generalize well on a class of target domains characterised by the complexity of their description within a reproducing kernel Hilbert space. Experiments on unsupervised covariate shift tasks demonstrate that models learned with the proposed loss-function outperform models learned with standard loss functions, achieving state-of-the-art results on a challenging cell-microscopy unsupervised covariate shift task.

People easily recognize new visual categories that are new combinations of known components. This compositional generalization capacity is critical for learning in real-world domains like vision and language because the long tail of new combinations dominates the distribution. Unfortunately, learning systems struggle with compositional generalization because they often build on features that are correlated with class labels even if they are not "essential" for the class. This leads to consistent misclassification of samples from a new distribution, like new combinations of known components. Here we describe an approach for compositional generalization that builds on causal ideas. First, we describe compositional zero-shot learning from a causal perspective, and propose to view zero-shot inference as finding "which intervention caused the image?". Second, we present a causal-inspired embedding model that learns disentangled representations of elementary components of visual objects from correlated (confounded) training data. We evaluate this approach on two datasets for predicting new combinations of attribute-object pairs: A well-controlled synthesized images dataset and a real world dataset which consists of fine-grained types of shoes. We show improvements compared to strong baselines.

Recommending the best course of action for an individual is a major application of individual-level causal effect estimation. This application is often needed in safety-critical domains such as healthcare, where estimating and communicating uncertainty to decision-makers is crucial. We introduce a practical approach for integrating uncertainty estimation into a class of state-of-the-art neural network methods used for individual-level causal estimates. We show that our methods enable us to deal gracefully with situations of "no-overlap", common in high-dimensional data, where standard applications of causal effect approaches fail. Further, our methods allow us to handle covariate shift, where the train and test distributions differ, common when systems are deployed in practice. We show that when such a covariate shift occurs, correctly modeling uncertainty can keep us from giving overconfident and potentially harmful recommendations. We demonstrate our methodology with a range of state-of-the-art models. Under both covariate shift and lack of overlap, our uncertainty-equipped methods can alert decision makers when predictions are not to be trusted while outperforming standard methods that use the propensity score to identify lack of overlap.

Large repositories of medical data, such as Electronic Medical Record (EMR) data, are recognized as promising sources for knowledge discovery. Effective analysis of such repositories often necessitate a thorough understanding of dependencies in the data. For example, if the patient age is ignored, then one might wrongly conclude a causal relationship between cataract and hypertension. Such confounding variables are often identified by causal graphs, where variables are connected by causal relationships. Current approaches to automatically building such graphs are based on text analysis over medical literature; yet, the result is typically a large graph of low precision. There are statistical methods for constructing causal graphs from observational data, but they are less suitable for dealing with a large number of covariates, which is the case in EMR data. Consequently, confounding variables are often identified by medical domain experts via a manual, expensive, and time-consuming process. We present a novel approach for automatically constructing causal graphs between medical conditions. The first part is a novel graph-based method to better capture causal relationships implied by medical literature, especially in the presence of multiple causal factors. Yet even after using these advanced text-analysis methods, the text data still contains many weak or uncertain causal connections. Therefore, we construct a second graph for these terms based on an EMR repository of over 1.5M patients. We combine the two graphs, leaving only edges that have both medical-text-based and observational evidence. We examine several strategies to carry out our approach, and compare the precision of the resulting graphs using medical experts. Our results show a significant improvement in the precision of any of our methods compared to the state of the art.

Observational data is increasingly used as a means for making individual-level causal predictions and intervention recommendations. The foremost challenge of causal inference from observational data is hidden confounding, whose presence cannot be tested in data and can invalidate any causal conclusion. Experimental data does not suffer from confounding but is usually limited in both scope and scale. We introduce a novel method of using limited experimental data to correct the hidden confounding in causal effect models trained on larger observational data, even if the observational data does not fully overlap with the experimental data. Our method makes strictly weaker assumptions than existing approaches, and we prove conditions under which it yields a consistent estimator. We demonstrate our method's efficacy using real-world data from a large educational experiment.

Gaussian state space models have been used for decades as generative models of sequential data. They admit an intuitive probabilistic interpretation, have a simple functional form, and enjoy widespread adoption. We introduce a unified algorithm to efficiently learn a broad class of linear and non-linear state space models, including variants where the emission and transition distributions are modeled by deep neural networks. Our learning algorithm simultaneously learns a compiled inference network and the generative model, leveraging a structured variational approximation parameterized by recurrent neural networks to mimic the posterior distribution. We apply the learning algorithm to both synthetic and real-world datasets, demonstrating its scalability and versatility. We find that using the structured approximation to the posterior results in models with significantly higher held-out likelihood.

There is intense interest in applying machine learning to problems of causal inference in fields such as healthcare, economics and education. In particular, individual-level causal inference has important applications such as precision medicine. We give a new theoretical analysis and family of algorithms for predicting individual treatment effect (ITE) from observational data, under the assumption known as strong ignorability. The algorithms learn a “balanced” representation such that the induced treated and control distributions look similar, and we give a novel and intuitive generalization-error bound showing the expected ITE estimation error of a representation is bounded by a sum of the standard generalization-error of that representation and the distance between the treated and control distributions induced by the representation. We use Integral Probability Metrics to measure distances between distributions, deriving explicit bounds for the Wasserstein and Maximum Mean Discrepancy (MMD) distances. Experiments on real and simulated data show the new algorithms match or outperform the state-of-the-art.

Learning individual-level causal effects from observational data, such as inferring the most effective medication for a specific patient, is a problem of growing importance for policy makers. The most important aspect of inferring causal effects from observational data is the handling of confounders, factors that affect both an intervention and its outcome. A carefully designed observational study attempts to measure all important confounders. However, even if one does not have direct access to all confounders, there may exist noisy and uncertain measurement of proxies for confounders. We build on recent advances in latent variable modeling to simultaneously estimate the unknown latent space summarizing the confounders and the causal effect. Our method is based on Variational Autoencoders (VAE) which follow the causal structure of inference with proxies. We show our method is significantly more robust than existing methods, and matches the state-of-the-art on previous benchmarks focused on individual treatment effects.

Observational studies are rising in importance due to the widespread accumulation of data in fields such as healthcare, education, employment and ecology. We consider the task of answering counterfactual questions such as, “Would this patient have lower blood sugar had she received a different medication?". We propose a new algorithmic framework for counterfactual inference which brings together ideas from domain adaptation and representation learning. In addition to a theoretical justification, we perform an empirical comparison with previous approaches to causal inference from observational data. Our deep learning algorithm significantly outperforms the previous state-of-the-art.

Optimizing over the set of orthogonal matrices is a central component in problems like sparse-PCA or tensor decomposition. Unfortunately, such optimization is hard since simple operations on orthogonal matrices easily break orthogonality, and correcting orthogonality usually costs a large amount of computation. Here we propose a framework for optimizing orthogonal matrices, that is the parallel of coordinate-descent in Euclidean spaces. It is based on \em Givens-rotations, a fast-to-compute operation that affects a small number of entries in the learned matrix, and preserves orthogonality. We show two applications of this approach: an algorithm for tensor decompositions used in learning mixture models, and an algorithm for sparse-PCA. We study the parameter regime where a Givens rotation approach converges faster and achieves a superior model on a genome-wide brain-wide mRNA expression dataset.

The role of musical influence has long been debated by scholars and critics in the humanities, but never in a data-driven way. In this work we approach the question of influence by applying topic-modeling tools (Blei & Lafferty, 2006; Gerrish & Blei, 2010) to a dataset of 24941 songs by 9222 artists, from the years 1922 to 2010. We find the models to be significantly correlated with a human-curated influence measure, and to clearly outperform a baseline method. Further using the learned model to study properties of influence, we find that musical influence and musical innovation are not monotonically correlated. However, we do find that the most influential songs were more innovative during two time periods: the early 1970’s and the mid 1990’s.

MOTIVATION: High-spatial resolution imaging datasets of mammalian brains have recently become available in unprecedented amounts. Images now reveal highly complex patterns of gene expression varying on multiple scales. The challenge in analyzing these images is both in extracting the patterns that are most relevant functionally and in providing a meaningful representation that allows neuroscientists to interpret the extracted patterns. RESULTS: Here, we present FuncISH--a method to learn functional representations of neural in situ hybridization (ISH) images. We represent images using a histogram of local descriptors in several scales, and we use this representation to learn detectors of functional (GO) categories for every image. As a result, each image is represented as a point in a low-dimensional space whose axes correspond to meaningful functional annotations. The resulting representations define similarities between ISH images that can be easily explained by functional categories. We applied our method to the genomic set of mouse neural ISH images available at the Allen Brain Atlas, finding that most neural biological processes can be inferred from spatial expression patterns with high accuracy. Using functional representations, we predict several gene interaction properties, such as protein-protein interactions and cell-type specificity, more accurately than competing methods based on global correlations. We used FuncISH to identify similar expression patterns of GABAergic neuronal markers that were not previously identified and to infer new gene function based on image-image similarities. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

When learning models that are represented in matrix forms, enforcing a low-rank constraint can dramatically improve the memory and run time complexity, while providing a natural regularization of the model. However, naive approaches for minimizing functions over the set of low-rank matrices are either prohibitively time consuming (repeated singular value decomposition of the matrix) or numerically unstable (optimizing a factored representation of the low rank matrix). We build on recent advances in optimization over manifolds, and describe an iterative online learning procedure, consisting of a gradient step, followed by a second-order retraction back to the manifold. While the ideal retraction is hard to compute, and so is the projection operator that approximates it, we describe another second-order retraction that can be computed efficiently, with run time and memory complexity of O((n+m)k) for a rank-k matrix of dimension m x n, given rank one gradients. We use this algorithm, LORETA, to learn a matrix-form similarity measure over pairs of documents represented as high dimensional vectors. LORETA improves the mean average precision over a passive- aggressive approach in a factorized model, and also improves over a full model trained over pre-selected features using the same memory requirements. LORETA also showed consistent improvement over standard methods in a large (1600 classes) multi-label image classification task.

Learning a measure of similarity between pairs of objects is a fundamental problem in machine learning. It stands in the core of classification methods like kernel machines, and is particularly useful for applications like searching for images that are similar to a given image or finding videos that are relevant to a given video. In these tasks, users look for objects that are not only visually similar but also semantically related to a given object. Unfortunately, current approaches for learning similarity may not scale to large datasets with high dimensionality, especially when imposing metric constraints on the learned similarity. We describe OASIS, a method for learning pairwise similarity that is fast and scales linearly with the number of objects and the number of non-zero features. Scalability is achieved through online learning of a bilinear model over sparse representations using a large margin criterion and an efficient hinge loss cost. OASIS is accurate at a wide range of scales: on a standard benchmark with thousands of images, it is more precise than state-of-the-art methods, and faster by orders of magnitude. On 2 million images collected from the web, OASIS can be trained within 3 days on a single CPU. The non-metric similarities learned by OASIS can be transformed into metric similarities, achieving higher precisions than similarities that are learned as metrics in the first place. This suggests an approach for learning a metric from data that is larger by an order of magnitude than was handled before.