Author name cluster

Ryan Adams

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

25 papers

1 author row

NeurIPS Conference 2025 Conference Paper

Space Group Equivariant Crystal Diffusion

Rees Chang
Angela Pak
Alex Guerra
Ni Zhan
Nick Richardson
Elif Ertekin
Ryan Adams

Accelerating inverse design of crystalline materials with generative models has significant implications for a range of technologies. Unlike other atomic systems, 3D crystals are invariant to discrete groups of isometries called the space groups. Crucially, these space group symmetries are known to heavily influence materials properties. We propose SGEquiDiff, a crystal generative model which naturally handles space group constraints with space group invariant likelihoods. SGEquiDiff consists of an SE(3)-invariant, telescoping discrete sampler of crystal lattices; permutation-invariant, transformer-based autoregressive sampling of Wyckoff positions, elements, and numbers of symmetrically unique atoms; and space group equivariant diffusion of atomic coordinates. We show that space group equivariant vector fields automatically live in the tangent spaces of the Wyckoff positions. SGEquiDiff achieves state-of-the-art performance on standard benchmark datasets as assessed by quantitative proxy metrics and quantum mechanical calculations. Our code is available at https: //github. com/rees-c/sgequidiff.

NeurIPS Conference 2019 Conference Paper

Discrete Object Generation with Reversible Inductive Construction

Ari Seff
Wenda Zhou
Farhan Damani
Abigail Doyle
Ryan Adams

The success of generative modeling in continuous domains has led to a surge of interest in generating discrete data such as molecules, source code, and graphs. However, construction histories for these discrete objects are typically not unique and so generative models must reason about intractably large spaces in order to learn. Additionally, structured discrete domains are often characterized by strict constraints on what constitutes a valid object and generative models must respect these requirements in order to produce useful novel samples. Here, we present a generative model for discrete objects employing a Markov chain where transitions are restricted to a set of local operations that preserve validity. Building off of generative interpretations of denoising autoencoders, the Markov chain alternates between producing 1) a sequence of corrupted objects that are valid but not from the data distribution, and 2) a learned reconstruction distribution that attempts to fix the corruptions while also preserving validity. This approach constrains the generative model to only produce valid objects, requires the learner to only discover local modifications to the objects, and avoids marginalization over an unknown and potentially large space of construction histories. We evaluate the proposed approach on two highly structured discrete domains, molecules and Laman graphs, and find that it compares favorably to alternative methods at capturing distributional statistics for a host of semantically relevant metrics.

NeurIPS Conference 2019 Conference Paper

SpArSe: Sparse Architecture Search for CNNs on Resource-Constrained Microcontrollers

Igor Fedorov
Ryan Adams
Matthew Mattina
Paul Whatmough

The vast majority of processors in the world are actually microcontroller units (MCUs), which find widespread use performing simple control tasks in applications ranging from automobiles to medical devices and office equipment. The Internet of Things (IoT) promises to inject machine learning into many of these every-day objects via tiny, cheap MCUs. However, these resource-impoverished hardware platforms severely limit the complexity of machine learning models that can be deployed. For example, although convolutional neural networks (CNNs) achieve state-of-the-art results on many visual recognition tasks, CNN inference on MCUs is challenging due to severe memory limitations. To circumvent the memory challenge associated with CNNs, various alternatives have been proposed that do fit within the memory budget of an MCU, albeit at the cost of prediction accuracy. This paper challenges the idea that CNNs are not suitable for deployment on MCUs. We demonstrate that it is possible to automatically design CNNs which generalize well, while also being small enough to fit onto memory-limited MCUs. Our Sparse Architecture Search method combines neural architecture search with pruning in a single, unified approach, which learns superior models on four popular IoT datasets. The CNNs we find are more accurate and up to 7. 4× smaller than previous approaches, while meeting the strict MCU working memory constraint.

NeurIPS Conference 2018 Conference Paper

A Bayesian Nonparametric View on Count-Min Sketch

Diana Cai
Michael Mitzenmacher
Ryan Adams

The count-min sketch is a time- and memory-efficient randomized data structure that provides a point estimate of the number of times an item has appeared in a data stream. The count-min sketch and related hash-based data structures are ubiquitous in systems that must track frequencies of data such as URLs, IP addresses, and language n-grams. We present a Bayesian view on the count-min sketch, using the same data structure, but providing a posterior distribution over the frequencies that characterizes the uncertainty arising from the hash-based approximation. In particular, we take a nonparametric approach and consider tokens generated from a Dirichlet process (DP) random measure, which allows for an unbounded number of unique tokens. Using properties of the DP, we show that it is possible to straightforwardly compute posterior marginals of the unknown true counts and that the modes of these marginals recover the count-min sketch estimator, inheriting the associated probabilistic guarantees. Using simulated data with known ground truth, we investigate the properties of these estimators. Lastly, we also study a modified problem in which the observation stream consists of collections of tokens (i. e. , documents) arising from a random measure drawn from a stable beta process, which allows for power law scaling behavior in the number of unique tokens.

NeurIPS Conference 2017 Conference Paper

PASS-GLM: polynomial approximate sufficient statistics for scalable Bayesian GLM inference

Jonathan Huggins
Ryan Adams
Tamara Broderick

Generalized linear models (GLMs)---such as logistic regression, Poisson regression, and robust regression---provide interpretable models for diverse data types. Probabilistic approaches, particularly Bayesian ones, allow coherent estimates of uncertainty, incorporation of prior information, and sharing of power across experiments via hierarchical models. In practice, however, the approximate Bayesian methods necessary for inference have either failed to scale to large data sets or failed to provide theoretical guarantees on the quality of inference. We propose a new approach based on constructing polynomial approximate sufficient statistics for GLMs (PASS-GLM). We demonstrate that our method admits a simple algorithm as well as trivial streaming and distributed extensions that do not compound error across computations. We provide theoretical guarantees on the quality of point (MAP) estimates, the approximate posterior, and posterior mean and uncertainty estimates. We validate our approach empirically in the case of logistic regression using a quadratic approximation and show competitive performance with stochastic gradient descent, MCMC, and the Laplace approximation in terms of speed and multiple measures of accuracy---including on an advertising data set with 40 million data points and 20, 000 covariates.

NeurIPS Conference 2017 Conference Paper

Reducing Reparameterization Gradient Variance

Andrew Miller
Nick Foti
Alexander D'Amour
Ryan Adams

Optimization with noisy gradients has become ubiquitous in statistics and machine learning. Reparameterization gradients, or gradient estimates computed via the ``reparameterization trick, '' represent a class of noisy gradients often used in Monte Carlo variational inference (MCVI). However, when these gradient estimators are too noisy, the optimization procedure can be slow or fail to converge. One way to reduce noise is to generate more samples for the gradient estimate, but this can be computationally expensive. Instead, we view the noisy gradient as a random variable, and form an inexpensive approximation of the generating procedure for the gradient sample. This approximation has high correlation with the noisy gradient by construction, making it a useful control variate for variance reduction. We demonstrate our approach on a non-conjugate hierarchical model and a Bayesian neural net where our method attained orders of magnitude (20-2{, }000$\times$) reduction in gradient variance resulting in faster and more stable optimization.

NeurIPS Conference 2016 Conference Paper

Bayesian latent structure discovery from multi-neuron recordings

Scott Linderman
Ryan Adams
Jonathan Pillow

Neural circuits contain heterogeneous groups of neurons that differ in type, location, connectivity, and basic response properties. However, traditional methods for dimensionality reduction and clustering are ill-suited to recovering the structure underlying the organization of neural circuits. In particular, they do not take advantage of the rich temporal dependencies in multi-neuron recordings and fail to account for the noise in neural spike trains. Here we describe new tools for inferring latent structure from simultaneously recorded spike train data using a hierarchical extension of a multi-neuron point process model commonly known as the generalized linear model (GLM). Our approach combines the GLM with flexible graph-theoretic priors governing the relationship between latent features and neural connectivity patterns. Fully Bayesian inference via Pólya-gamma augmentation of the resulting model allows us to classify neurons and infer latent dimensions of circuit organization from correlated spike trains. We demonstrate the effectiveness of our method with applications to synthetic data and multi-neuron recordings in primate retina, revealing latent patterns of neural types and locations from spike trains alone.

NeurIPS Conference 2016 Conference Paper

Composing graphical models with neural networks for structured representations and fast inference

Matthew Johnson
David Duvenaud
Alex Wiltschko
Ryan Adams
Sandeep Datta

We propose a general modeling and inference framework that combines the complementary strengths of probabilistic graphical models and deep learning methods. Our model family composes latent graphical models with neural network observation likelihoods. For inference, we use recognition networks to produce local evidence potentials, then combine them with the model distribution using efficient message-passing algorithms. All components are trained simultaneously with a single stochastic variational inference objective. We illustrate this framework by automatically segmenting and categorizing mouse behavior from raw depth video, and demonstrate several other example models.

NeurIPS Conference 2015 Conference Paper

A Gaussian Process Model of Quasar Spectral Energy Distributions

Andrew Miller
Albert Wu
Jeff Regier
Jon McAuliffe
Dustin Lang
Mr. Prabhat
David Schlegel
Ryan Adams

We propose a method for combining two sources of astronomical data, spectroscopy and photometry, that carry information about sources of light (e. g. , stars, galaxies, and quasars) at extremely different spectral resolutions. Our model treats the spectral energy distribution (SED) of the radiation from a source as a latent variable that jointly explains both photometric and spectroscopic observations. We place a flexible, nonparametric prior over the SED of a light source that admits a physically interpretable decomposition, and allows us to tractably perform inference. We use our model to predict the distribution of the redshift of a quasar from five-band (low spectral resolution) photometric data, the so called ``photo-z'' problem. Our method shows that tools from machine learning and Bayesian statistics allow us to leverage multiple resolutions of information to make accurate predictions with well-characterized uncertainties.

NeurIPS Conference 2015 Conference Paper

Convolutional Networks on Graphs for Learning Molecular Fingerprints

David Duvenaud
Dougal Maclaurin
Jorge Iparraguirre
Rafael Bombarell
Timothy Hirzel
Alan Aspuru-Guzik
Ryan Adams

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

NeurIPS Conference 2015 Conference Paper

Dependent Multinomial Models Made Easy: Stick-Breaking with the Polya-gamma Augmentation

Scott Linderman
Matthew Johnson
Ryan Adams

Many practical modeling problems involve discrete data that are best represented as draws from multinomial or categorical distributions. For example, nucleotides in a DNA sequence, children's names in a given state and year, and text documents are all commonly modeled with multinomial distributions. In all of these cases, we expect some form of dependency between the draws: the nucleotide at one position in the DNA strand may depend on the preceding nucleotides, children's names are highly correlated from year to year, and topics in text may be correlated and dynamic. These dependencies are not naturally captured by the typical Dirichlet-multinomial formulation. Here, we leverage a logistic stick-breaking representation and recent innovations in P\'{o}lya-gamma augmentation to reformulate the multinomial distribution in terms of latent variables with jointly Gaussian likelihoods, enabling us to take advantage of a host of Bayesian inference techniques for Gaussian models with minimal overhead.

AAAI Conference 2015 Conference Paper

Graph-Sparse LDA: A Topic Model with Structured Sparsity

Finale Doshi-Velez
Byron Wallace
Ryan Adams

Topic modeling is a powerful tool for uncovering latent structure in many domains, including medicine, finance, and vision. The goals for the model vary depending on the application: sometimes the discovered topics are used for prediction or another downstream task. In other cases, the content of the topic may be of intrinsic scientific interest. Unfortunately, even when one uses modern sparse techniques, discovered topics are often difficult to interpret due to the high dimensionality of the underlying space. To improve topic interpretability, we introduce Graph-Sparse LDA, a hierarchical topic model that uses knowledge of relationships between words (e. g. , as encoded by an ontology). In our model, topics are summarized by a few latent concept-words from the underlying graph that explain the observed words. Graph- Sparse LDA recovers sparse, interpretable summaries on two real-world biomedical datasets while matching state-of-the-art prediction performance.

NeurIPS Conference 2015 Conference Paper

Spectral Representations for Convolutional Neural Networks

Oren Rippel
Jasper Snoek
Ryan Adams

Discrete Fourier transforms provide a significant speedup in the computation of convolutions in deep learning. In this work, we demonstrate that, beyond its advantages for efficient computation, the spectral domain also provides a powerful representation in which to model and train convolutional neural networks (CNNs). We employ spectral representations to introduce a number of innovations to CNN design. First, we propose spectral pooling, which performs dimensionality reduction by truncating the representation in the frequency domain. This approach preserves considerably more information per parameter than other pooling strategies and enables flexibility in the choice of pooling output dimensionality. This representation also enables a new form of stochastic regularization by randomized modification of resolution. We show that these methods achieve competitive results on classification and approximation tasks, without using any dropout or max-pooling. Finally, we demonstrate the effectiveness of complex-coefficient spectral parameterization of convolutional filters. While this leaves the underlying model unchanged, it results in a representation that greatly facilitates optimization. We observe on a variety of popular CNN configurations that this leads to significantly faster convergence during training.

NeurIPS Conference 2014 Conference Paper

A framework for studying synaptic plasticity with neural spike train data

Scott Linderman
Christopher Stock
Ryan Adams

Learning and memory in the brain are implemented by complex, time-varying changes in neural circuitry. The computational rules according to which synaptic weights change over time are the subject of much research, and are not precisely understood. Until recently, limitations in experimental methods have made it challenging to test hypotheses about synaptic plasticity on a large scale. However, as such data become available and these barriers are lifted, it becomes necessary to develop analysis techniques to validate plasticity models. Here, we present a highly extensible framework for modeling arbitrary synaptic plasticity rules on spike train data in populations of interconnected neurons. We treat synaptic weights as a (potentially nonlinear) dynamical system embedded in a fully-Bayesian generalized linear model (GLM). In addition, we provide an algorithm for inferring synaptic weight trajectories alongside the parameters of the GLM and of the learning rules. Using this method, we perform model comparison of two proposed variants of the well-known spike-timing-dependent plasticity (STDP) rule, where nonlinear effects play a substantial role. On synthetic data generated from the biophysical simulator NEURON, we show that we can recover the weight trajectories, the pattern of connectivity, and the underlying learning rules.

NeurIPS Conference 2013 Conference Paper

A Determinantal Point Process Latent Variable Model for Inhibition in Neural Spiking Data

Jasper Snoek
Richard Zemel
Ryan Adams

Point processes are popular models of neural spiking behavior as they provide a statistical distribution over temporal sequences of spikes and help to reveal the complexities underlying a series of recorded action potentials. However, the most common neural point process models, the Poisson process and the gamma renewal process, do not capture interactions and correlations that are critical to modeling populations of neurons. We develop a novel model based on a determinantal point process over latent embeddings of neurons that effectively captures and helps visualize complex inhibitory and competitive interaction. We show that this model is a natural extension of the popular generalized linear model to sets of interacting neurons. The model is extended to incorporate gain control or divisive normalization, and the modulation of neural spiking based on periodic phenomena. Applied to neural spike recordings from the rat hippocampus, we see that the model captures inhibitory relationships, a dichotomy of classes of neurons, and a periodic modulation by the theta rhythm known to be present in the data.

NeurIPS Conference 2013 Conference Paper

Contrastive Learning Using Spectral Methods

James Zou
Daniel Hsu
David Parkes
Ryan Adams

In many natural settings, the analysis goal is not to characterize a single data set in isolation, but rather to understand the difference between one set of observations and another. For example, given a background corpus of news articles together with writings of a particular author, one may want a topic model that explains word patterns and themes specific to the author. Another example comes from genomics, in which biological signals may be collected from different regions of a genome, and one wants a model that captures the differential statistics observed in these regions. This paper formalizes this notion of contrastive learning for mixture models, and develops spectral algorithms for inferring mixture components specific to a foreground data set when contrasted with a background data set. The method builds on recent moment-based estimators and tensor decompositions for latent variable models, and has the intuitive feature of using background data statistics to appropriately modify moments estimated from foreground data. A key advantage of the method is that the background data need only be coarsely modeled, which is important when the background is too complex, noisy, or not of interest. The method is demonstrated on applications in contrastive topic modeling and genomic sequence analysis.

NeurIPS Conference 2013 Conference Paper

Message Passing Inference with Chemical Reaction Networks

Nils Napp
Ryan Adams

Recent work on molecular programming has explored new possibilities for computational abstractions with biomolecules, including logic gates, neural networks, and linear systems. In the future such abstractions might enable nanoscale devices that can sense and control the world at a molecular scale. Just as in macroscale robotics, it is critical that such devices can learn about their environment and reason under uncertainty. At this small scale, systems are typically modeled as chemical reaction networks. In this work, we develop a procedure that can take arbitrary probabilistic graphical models, represented as factor graphs over discrete random variables, and compile them into chemical reaction networks that implement inference. In particular, we show that marginalization based on sum-product message passing can be implemented in terms of reactions between chemical species whose concentrations represent probabilities. We show algebraically that the steady state concentration of these species correspond to the marginal distributions of the random variables in the graph and validate the results in simulations. As with standard sum-product inference, this procedure yields exact results for tree-structured graphs, and approximate solutions for loopy graphs.

NeurIPS Conference 2013 Conference Paper

Multi-Task Bayesian Optimization

Kevin Swersky
Jasper Snoek
Ryan Adams

Bayesian optimization has recently been proposed as a framework for automatically tuning the hyperparameters of machine learning models and has been shown to yield state-of-the-art performance with impressive ease and efficiency. In this paper, we explore whether it is possible to transfer the knowledge gained from previous optimizations to new tasks in order to find optimal hyperparameter settings more efficiently. Our approach is based on extending multi-task Gaussian processes to the framework of Bayesian optimization. We show that this method significantly speeds up the optimization process when compared to the standard single-task approach. We further propose a straightforward extension of our algorithm in order to jointly minimize the average error across multiple tasks and demonstrate how this can be used to greatly speed up $k$-fold cross-validation. Lastly, our most significant contribution is an adaptation of a recently proposed acquisition function, entropy search, to the cost-sensitive and multi-task settings. We demonstrate the utility of this new acquisition function by utilizing a small dataset in order to explore hyperparameter settings for a large dataset. Our algorithm dynamically chooses which dataset to query in order to yield the most information per unit cost.

NeurIPS Conference 2012 Conference Paper

Cardinality Restricted Boltzmann Machines

Kevin Swersky
Ilya Sutskever
Daniel Tarlow
Richard Zemel
Russ Salakhutdinov
Ryan Adams

The Restricted Boltzmann Machine (RBM) is a popular density model that is also good for extracting features. A main source of tractability in RBM models is the model's assumption that given an input, hidden units activate independently from one another. Sparsity and competition in the hidden representation is believed to be beneficial, and while an RBM with competition among its hidden units would acquire some of the attractive properties of sparse coding, such constraints are not added due to the widespread belief that the resulting model would become intractable. In this work, we show how a dynamic programming algorithm developed in 1981 can be used to implement exact sparsity in the RBM's hidden units. We then expand on this and show how to pass derivatives through a layer of exact sparsity, which makes it possible to fine-tune a deep belief network (DBN) consisting of RBMs with sparse hidden layers. We show that sparsity in the RBM's hidden layer improves the performance of both the pre-trained representations and of the fine-tuned model.

NeurIPS Conference 2012 Conference Paper

Practical Bayesian Optimization of Machine Learning Algorithms

Jasper Snoek
Hugo Larochelle
Ryan Adams

The use of machine learning algorithms frequently involves careful tuning of learning parameters and model hyperparameters. Unfortunately, this tuning is often a “black art” requiring expert experience, rules of thumb, or sometimes brute-force search. There is therefore great appeal for automatic approaches that can optimize the performance of any given learning algorithm to the problem at hand. In this work, we consider this problem through the framework of Bayesian optimization, in which a learning algorithm’s generalization performance is modeled as a sample from a Gaussian process (GP). We show that certain choices for the nature of the GP, such as the type of kernel and the treatment of its hyperparameters, can play a crucial role in obtaining a good optimizer that can achieve expert-level performance. We describe new algorithms that take into account the variable cost (duration) of learning algorithm experiments and that can leverage the presence of multiple cores for parallel experimentation. We show that these proposed algorithms improve on previous automatic procedures and can reach or surpass human expert-level optimization for many algorithms including Latent Dirichlet Allocation, Structured SVMs and convolutional neural networks.

NeurIPS Conference 2012 Conference Paper

Priors for Diversity in Generative Latent Variable Models

James Kwok
Ryan Adams

Probabilistic latent variable models are one of the cornerstones of machine learning. They offer a convenient and coherent way to specify prior distributions over unobserved structure in data, so that these unknown properties can be inferred via posterior inference. Such models are useful for exploratory analysis and visualization, for building density models of data, and for providing features that can be used for later discriminative tasks. A significant limitation of these models, however, is that draws from the prior are often highly redundant due to i. i. d. assumptions on internal parameters. For example, there is no preference in the prior of a mixture model to make components non-overlapping, or in topic model to ensure that co-ocurring words only appear in a small number of topics. In this work, we revisit these independence assumptions for probabilistic latent variable models, replacing the underlying i. i. d. \ prior with a determinantal point process (DPP). The DPP allows us to specify a preference for diversity in our latent variables using a positive definite kernel function. Using a kernel between probability distributions, we are able to define a DPP on probability measures. We show how to perform MAP inference with DPP priors in latent Dirichlet allocation and in mixture models, leading to better intuition for the latent variable representation and quantitatively improved unsupervised feature extraction, without compromising the generative aspects of the model.

NeurIPS Conference 2012 Conference Paper

Probabilistic n-Choose-k Models for Classification and Ranking

Kevin Swersky
Brendan Frey
Daniel Tarlow
Richard Zemel
Ryan Adams

In categorical data there is often structure in the number of variables that take on each label. For example, the total number of objects in an image and the number of highly relevant documents per query in web search both tend to follow a structured distribution. In this paper, we study a probabilistic model that explicitly includes a prior distribution over such counts, along with a count-conditional likelihood that deﬁnes probabilities over all subsets of a given size. When labels are binary and the prior over counts is a Poisson-Binomial distribution, a standard logistic regression model is recovered, but for other count distributions, such priors induce global dependencies and combinatorics that appear to complicate learning and inference. However, we demonstrate that simple, efﬁcient learning procedures can be derived for more general forms of this model. We illustrate the utility of the formulation by exploring applications to multi-object classiﬁcation, learning to rank, and top-K classiﬁcation.

NeurIPS Conference 2010 Conference Paper

Slice sampling covariance hyperparameters of latent Gaussian models

Iain Murray
Ryan Adams

The Gaussian process (GP) is a popular way to specify dependencies between random variables in a probabilistic model. In the Bayesian framework the covariance structure can be specified using unknown hyperparameters. Integrating over these hyperparameters considers different possible explanations for the data when making predictions. This integration is often performed using Markov chain Monte Carlo (MCMC) sampling. However, with non-Gaussian observations standard hyperparameter sampling approaches require careful tuning and may converge slowly. In this paper we present a slice sampling approach that requires little tuning while mixing well in both strong- and weak-data regimes.

NeurIPS Conference 2010 Conference Paper

Tree-Structured Stick Breaking for Hierarchical Data

Zoubin Ghahramani
Michael Jordan
Ryan Adams

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

NeurIPS Conference 2008 Conference Paper

The Gaussian Process Density Sampler

Iain Murray
David MacKay
Ryan Adams

We present the Gaussian Process Density Sampler (GPDS), an exchangeable generative model for use in nonparametric Bayesian density estimation. Samples drawn from the GPDS are consistent with exact, independent samples from a fixed density function that is a transformation of a function drawn from a Gaussian process prior. Our formulation allows us to infer an unknown density from data using Markov chain Monte Carlo, which gives samples from the posterior distribution over density functions and from the predictive distribution on data space. We can also infer the hyperparameters of the Gaussian process. We compare this density modeling technique to several existing techniques on a toy problem and a skull-reconstruction task.