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  1. Degeneracy in biological systems refers to a many-to-one mapping between physical structures and their functional (including psychological) outcomes. Despite the ubiquity of the phenomenon, traditional analytical tools for modeling degeneracy in neuroscience are extremely limited. In this study, we generated synthetic datasets to describe three situations of degeneracy in fMRI data to demonstrate the limitations of the current univariate approach. We describe a novel computational approach for the analysis referred to as neural topographic factor analysis (NTFA). NTFA is designed to capture variations in neural activity across task conditions and participants. The advantage of this discovery-oriented approach is to revealmore »whether and how experimental trials and participants cluster into task conditions and participant groups. We applied NTFA on simulated data, revealing the appropriate degeneracy assumption in all three situations and demonstrating NTFA’s utility in uncovering degeneracy. Lastly, we discussed the importance of testing degeneracy in fMRI data and the implications of applying NTFA to do so.« less
    Free, publicly-accessible full text available January 1, 2023
  2. III, H.D. ; Singh, A. (Ed.)
    We develop amortized population Gibbs (APG) samplers, a class of scalable methods that frame structured variational inference as adaptive importance sampling. APG samplers construct high-dimensional proposals by iterating over updates to lower-dimensional blocks of variables. We train each conditional proposal by minimizing the inclusive KL divergence with respect to the conditional posterior. To appropriately account for the size of the input data, we develop a new parameterization in terms of neural sufficient statistics. Experiments show that APG samplers can be used to train highly-structured deep generative models in an unsupervised manner, and achieve substantial improvements in inference accuracy relative tomore »standard autoencoding variational methods.« less
  3. Recent work has shown that fine-tuning large networks is surprisingly sensitive to changes in random seed(s). We explore the implications of this phenomenon for model fairness across demographic groups in clinical prediction tasks over electronic health records (EHR) in MIMIC-III —— the standard dataset in clinical NLP research. Apparent subgroup performance varies substantially for seeds that yield similar overall performance, although there is no evidence of a trade-off between overall and subgroup performance. However, we also find that the small sample sizes inherent to looking at intersections of minority groups and somewhat rare conditions limit our ability to accurately estimatemore »disparities. Further, we find that jointly optimizing for high overall performance and low disparities does not yield statistically significant improvements. Our results suggest that fairness work using MIMIC-III should carefully account for variations in apparent differences that may arise from stochasticity and small sample sizes.« less
  4. Ranzato, M. ; Beygelzimer, A. ; Dauphin, Y. ; Liang, P.S. ; Wortman Vaughan, J. (Ed.)
    We develop nested variational inference (NVI), a family of methods that learn proposals for nested importance samplers by minimizing an forward or reverse KL divergence at each level of nesting. NVI is applicable to many commonly-used importance sampling strategies and provides a mechanism for learning intermediate densities, which can serve as heuristics to guide the sampler. Our experiments apply NVI to (a) sample from a multimodal distribution using a learned annealing path (b) learn heuristics that approximate the likelihood of future observations in a hidden Markov model and (c) to perform amortized inference in hierarchical deep generative models. We observemore »that optimizing nested objectives leads to improved sample quality in terms of log average weight and effective sample size.« less
  5. Doshi-Velez, Finale ; Fackler, Jim ; Jung, Ken ; Kale, David ; Ranganath, Rajesh ; Wallace, Byron ; Wiens, Jenna (Ed.)
    Electronic Health Records (EHRs) provide vital contextual information to radiologists and other physicians when making a diagnosis. Unfortunately, because a given patient’s record may contain hundreds of notes and reports, identifying relevant information within these in the short time typically allotted to a case is very difficult. We propose and evaluate models that extract relevant text snippets from patient records to provide a rough case summary intended to aid physicians considering one or more diagnoses. This is hard because direct supervision (i.e., physician annotations of snippets relevant to specific diagnoses in medical records) is prohibitively expensive to collect at scale.more »We propose a distantly supervised strategy in which we use groups of International Classification of Diseases (ICD) codes observed in ‘future’ records as noisy proxies for ‘downstream’ diagnoses. Using this we train a transformer-based neural model to perform extractive summarization conditioned on potential diagnoses. This model defines an attention mechanism that is conditioned on potential diagnoses (queries) provided by the diagnosing physician. We train (via distant supervision) and evaluate variants of this model on EHR data from Brigham and Women’s Hospital in Boston and MIMIC-III (the latter to facilitate reproducibility). Evaluations performed by radiologists demonstrate that these distantly supervised models yield better extractive summaries than do unsupervised approaches. Such models may aid diagnosis by identifying sentences in past patient reports that are clinically relevant to a potential diagnosis. Code is available at https://github.com/dmcinerney/ehr-extraction-models.« less
  6. We present Variational Aspect-based Latent Topic Allocation (VALTA), a family of autoencoding topic models that learn aspect-based representations of reviews. VALTA defines a user-item encoder that maps bag-of-words vectors for combined reviews associated with each paired user; item onto structured embeddings, which in turn define per-aspect topic weights. We model individual reviews in a structured manner by inferring an aspect assignment for each sentence in a given review, where the per-aspect topic weights obtained by the user-item encoder serve to define a mixture over topics, conditioned on the aspect. The result is an autoencoding neural topic model for reviews, whichmore »can be trained in a fully unsupervised manner to learn topics that are structured into aspects. Experimental evaluation on large number of datasets demonstrates that aspects are interpretable, yield higher coherence scores than non-structured autoencoding topic model variants,; can be utilized to perform aspect-based comparison; genre discovery.« less
  7. Deep latent-variable models learn representations of high-dimensional data in an unsupervised manner. A number of recent efforts have focused on learning representations that disentangle statistically independent axes of variation by introducing modifications to the standard objective function. These approaches generally assume a simple diagonal Gaussian prior and as a result are not able to reliably disentangle discrete factors of variation. We propose a two-level hierarchical objective to control relative degree of statistical independence between blocks of variables and individual variables within blocks. We derive this objective as a generalization of the evidence lower bound, which allows us to explicitly representmore »the trade-offs between mutual information between data and representation, KL divergence between representation and prior, and coverage of the support of the empirical data distribution. Experiments on a variety of datasets demonstrate that our objective can not only disentangle discrete variables, but that doing so also improves disentanglement of other variables and, importantly, generalization even to unseen combinations of factors« less