arXiv subjects

Christopher Ré

Publications and source records attributed to Christopher Ré.

At least 163 records · Page 9Linked to original sources

arXiv2017

SwellShark: A Generative Model for Biomedical Named Entity Recognition without Labeled Data

We present SwellShark, a framework for building biomedical named entity recognition (NER) systems quickly and without hand-labeled data. Our approach views biomedical resources like lexicons as function primitives for autogenerating weak supervision. We then use a generative model to unify and denoise this supervision and construct large-scale, probabilistically labeled datasets for training high-accuracy NER taggers. In three biomedical NER tasks, SwellShark achieves competitive scores with state-of-the-art supervised benchmarks using no hand-labeled training data. In a drug name extraction task using patient medical records, one domain expert using SwellShark achieved within 5.1% of a crowdsourced annotation approach -- which originally utilized 20 teams over the course of several weeks -- in 24 hours.

cs.CL↗

arXiv2017

HoloClean: Holistic Data Repairs with Probabilistic Inference

We introduce HoloClean, a framework for holistic data repairing driven by probabilistic inference. HoloClean unifies existing qualitative data repairing approaches, which rely on integrity constraints or external data sources, with quantitative data repairing methods, which leverage statistical properties of the input data. Given an inconsistent dataset as input, HoloClean automatically generates a probabilistic program that performs data repairing. Inspired by recent theoretical advances in probabilistic inference, we introduce a series of optimizations which ensure that inference over HoloClean's probabilistic model scales to instances with millions of tuples. We show that HoloClean scales to instances with millions of tuples and find data repairs with an average precision of ~90% and an average recall of above ~76% across a diverse array of datasets exhibiting different types of errors. This yields an average F1 improvement of more than 2x against state-of-the-art methods.

cs.DB↗

arXiv2017

GYM: A Multiround Join Algorithm In MapReduce

Multiround algorithms are now commonly used in distributed data processing systems, yet the extent to which algorithms can benefit from running more rounds is not well understood. This paper answers this question for a spectrum of rounds for the problem of computing the equijoin of $n$ relations. Specifically, given any query $Q$ with width $\w$, {\em intersection width} $\iw$, input size $\mathrm{IN}$, output size $\mathrm{OUT}$, and a cluster of machines with $M$ memory available per machine, we show that: (1) $Q$ can be computed in $O(n)$ rounds with $O(n\frac{(\mathrm{IN}^{\w} + \mathrm{OUT})^2}{M})$ communication cost. (2) $Q$ can be computed in $O(\log(n))$ rounds with $O(n\frac{(\mathrm{IN}^{\max(\w, 3\iw)} + \mathrm{OUT})^2}{M})$ communication cost. \end{itemize} Intersection width is a new notion of queries and generalized hypertree decompositions (GHDs) of queries we introduce to capture how connected the adjacent cyclic components of the GHDs are. We achieve our first result by introducing a distributed and generalized version of Yannakakis's algorithm, called GYM. GYM takes as input any GHD of $Q$ with width $\w$ and depth $d$, and computes $Q$ in $O(d + \log(n))$ rounds and $O(n\frac{(\mathrm{IN}^{\w} + \mathrm{OUT})^2}{M})$ communication cost. We achieve our second result by showing how to construct GHDs of $Q$ with width $\max(\w, 3\iw)$ and depth $O(\log(n))$. We describe another technique to construct GHDs with longer widths and shorter depths, demonstrating a spectrum of tradeoffs one can make between communication and the number of rounds.

cs.DB↗

arXiv2017

Data Programming: Creating Large Training Sets, Quickly

Large labeled training sets are the critical building blocks of supervised learning methods and are key enablers of deep learning techniques. For some applications, creating labeled training sets is the most time-consuming and expensive part of applying machine learning. We therefore propose a paradigm for the programmatic creation of training sets called data programming in which users express weak supervision strategies or domain heuristics as labeling functions, which are programs that label subsets of the data, but that are noisy and may conflict. We show that by explicitly representing this training set labeling process as a generative model, we can "denoise" the generated training set, and establish theoretically that we can recover the parameters of these generative models in a handful of settings. We then show how to modify a discriminative loss function to make it noise-aware, and demonstrate our method over a range of discriminative models including logistic regression and LSTMs. Experimentally, on the 2014 TAC-KBP Slot Filling challenge, we show that data programming would have led to a new winning score, and also show that applying data programming to an LSTM model leads to a TAC-KBP score almost 6 F1 points over a state-of-the-art LSTM baseline (and into second place in the competition). Additionally, in initial user studies we observed that data programming may be an easier way for non-experts to create machine learning models when training data is limited or unavailable.

stat.ML↗

arXiv2017

EmptyHeaded: A Relational Engine for Graph Processing

There are two types of high-performance graph processing engines: low- and high-level engines. Low-level engines (Galois, PowerGraph, Snap) provide optimized data structures and computation models but require users to write low-level imperative code, hence ensuring that efficiency is the burden of the user. In high-level engines, users write in query languages like datalog (SociaLite) or SQL (Grail). High-level engines are easier to use but are orders of magnitude slower than the low-level graph engines. We present EmptyHeaded, a high-level engine that supports a rich datalog-like query language and achieves performance comparable to that of low-level engines. At the core of EmptyHeaded's design is a new class of join algorithms that satisfy strong theoretical guarantees but have thus far not achieved performance comparable to that of specialized graph processing engines. To achieve high performance, EmptyHeaded introduces a new join engine architecture, including a novel query optimizer and data layouts that leverage single-instruction multiple data (SIMD) parallelism. With this architecture, EmptyHeaded outperforms high-level approaches by up to three orders of magnitude on graph pattern queries, PageRank, and Single-Source Shortest Paths (SSSP) and is an order of magnitude faster than many low-level baselines. We validate that EmptyHeaded competes with the best-of-breed low-level engine (Galois), achieving comparable performance on PageRank and at most 3x worse performance on SSSP.

cs.DB↗

arXiv2016

Joins via Geometric Resolutions: Worst-case and Beyond

We present a simple geometric framework for the relational join. Using this framework, we design an algorithm that achieves the fractional hypertree-width bound, which generalizes classical and recent worst-case algorithmic results on computing joins. In addition, we use our framework and the same algorithm to show a series of what are colloquially known as beyond worst-case results. The framework allows us to prove results for data stored in Btrees, multidimensional data structures, and even multiple indices per table. A key idea in our framework is formalizing the inference one does with an index as a type of geometric resolution; transforming the algorithmic problem of computing joins to a geometric problem. Our notion of geometric resolution can be viewed as a geometric analog of logical resolution. In addition to the geometry and logic connections, our algorithm can also be thought of as backtracking search with memoization.

cs.DB↗

arXiv2016

Asynchrony begets Momentum, with an Application to Deep Learning

Asynchronous methods are widely used in deep learning, but have limited theoretical justification when applied to non-convex problems. We show that running stochastic gradient descent (SGD) in an asynchronous manner can be viewed as adding a momentum-like term to the SGD iteration. Our result does not assume convexity of the objective function, so it is applicable to deep learning systems. We observe that a standard queuing model of asynchrony results in a form of momentum that is commonly used by deep learning practitioners. This forges a link between queuing theory and asynchrony in deep learning systems, which could be useful for systems builders. For convolutional neural networks, we experimentally validate that the degree of asynchrony directly correlates with the momentum, confirming our main result. An important implication is that tuning the momentum parameter is important when considering different levels of asynchrony. We assert that properly tuned momentum reduces the number of steps required for convergence. Finally, our theory suggests new ways of counteracting the adverse effects of asynchrony: a simple mechanism like using negative algorithmic momentum can improve performance under high asynchrony. Since asynchronous methods have better hardware efficiency, this result may shed light on when asynchronous execution is more efficient for deep learning systems.

stat.ML↗

arXiv2016

SLiMFast: Guaranteed Results for Data Fusion and Source Reliability

We focus on data fusion, i.e., the problem of unifying conflicting data from data sources into a single representation by estimating the source accuracies. We propose SLiMFast, a framework that expresses data fusion as a statistical learning problem over discriminative probabilistic models, which in many cases correspond to logistic regression. In contrast to previous approaches that use complex generative models, discriminative models make fewer distributional assumptions over data sources and allow us to obtain rigorous theoretical guarantees. Furthermore, we show how SLiMFast enables incorporating domain knowledge into data fusion, yielding accuracy improvements of up to 50\% over state-of-the-art baselines. Building upon our theoretical results, we design an optimizer that obviates the need for users to manually select an algorithm for learning SLiMFast's parameters. We validate our optimizer on multiple real-world datasets and show that it can accurately predict the learning algorithm that yields the best data fusion results.

cs.DB↗

arXiv2016

Omnivore: An Optimizer for Multi-device Deep Learning on CPUs and GPUs

We study the factors affecting training time in multi-device deep learning systems. Given a specification of a convolutional neural network, our goal is to minimize the time to train this model on a cluster of commodity CPUs and GPUs. We first focus on the single-node setting and show that by using standard batching and data-parallel techniques, throughput can be improved by at least 5.5x over state-of-the-art systems on CPUs. This ensures an end-to-end training speed directly proportional to the throughput of a device regardless of its underlying hardware, allowing each node in the cluster to be treated as a black box. Our second contribution is a theoretical and empirical study of the tradeoffs affecting end-to-end training time in a multiple-device setting. We identify the degree of asynchronous parallelization as a key factor affecting both hardware and statistical efficiency. We see that asynchrony can be viewed as introducing a momentum term. Our results imply that tuning momentum is critical in asynchronous parallel configurations, and suggest that published results that have not been fully tuned might report suboptimal performance for some configurations. For our third contribution, we use our novel understanding of the interaction between system and optimization dynamics to provide an efficient hyperparameter optimizer. Our optimizer involves a predictive model for the total time to convergence and selects an allocation of resources to minimize that time. We demonstrate that the most popular distributed deep learning systems fall within our tradeoff space, but do not optimize within the space. By doing this optimization, our prototype runs 1.9x to 12x faster than the fastest state-of-the-art systems.

cs.DC↗

arXiv2016

Sub-sampled Newton Methods with Non-uniform Sampling

We consider the problem of finding the minimizer of a convex function $F: \mathbb R^d \rightarrow \mathbb R$ of the form $F(w) := \sum_{i=1}^n f_i(w) + R(w)$ where a low-rank factorization of $\nabla^2 f_i(w)$ is readily available. We consider the regime where $n \gg d$. As second-order methods prove to be effective in finding the minimizer to a high-precision, in this work, we propose randomized Newton-type algorithms that exploit \textit{non-uniform} sub-sampling of $\{\nabla^2 f_i(w)\}_{i=1}^{n}$, as well as inexact updates, as means to reduce the computational complexity. Two non-uniform sampling distributions based on {\it block norm squares} and {\it block partial leverage scores} are considered in order to capture important terms among $\{\nabla^2 f_i(w)\}_{i=1}^{n}$. We show that at each iteration non-uniformly sampling at most $\mathcal O(d \log d)$ terms from $\{\nabla^2 f_i(w)\}_{i=1}^{n}$ is sufficient to achieve a linear-quadratic convergence rate in $w$ when a suitable initial point is provided. In addition, we show that our algorithms achieve a lower computational complexity and exhibit more robustness and better dependence on problem specific quantities, such as the condition number, compared to similar existing methods, especially the ones based on uniform sampling. Finally, we empirically demonstrate that our methods are at least twice as fast as Newton's methods with ridge logistic regression on several real datasets.

math.OC↗

arXiv2016

Parallel SGD: When does averaging help?

Consider a number of workers running SGD independently on the same pool of data and averaging the models every once in a while -- a common but not well understood practice. We study model averaging as a variance-reducing mechanism and describe two ways in which the frequency of averaging affects convergence. For convex objectives, we show the benefit of frequent averaging depends on the gradient variance envelope. For non-convex objectives, we illustrate that this benefit depends on the presence of multiple globally optimal points. We complement our findings with multicore experiments on both synthetic and real data.

stat.ML↗

arXiv2016

Ensuring Rapid Mixing and Low Bias for Asynchronous Gibbs Sampling

Gibbs sampling is a Markov chain Monte Carlo technique commonly used for estimating marginal distributions. To speed up Gibbs sampling, there has recently been interest in parallelizing it by executing asynchronously. While empirical results suggest that many models can be efficiently sampled asynchronously, traditional Markov chain analysis does not apply to the asynchronous case, and thus asynchronous Gibbs sampling is poorly understood. In this paper, we derive a better understanding of the two main challenges of asynchronous Gibbs: bias and mixing time. We show experimentally that our theoretical results match practical outcomes.

cs.LG↗

arXiv2016

Scan Order in Gibbs Sampling: Models in Which it Matters and Bounds on How Much

Gibbs sampling is a Markov Chain Monte Carlo sampling technique that iteratively samples variables from their conditional distributions. There are two common scan orders for the variables: random scan and systematic scan. Due to the benefits of locality in hardware, systematic scan is commonly used, even though most statistical guarantees are only for random scan. While it has been conjectured that the mixing times of random scan and systematic scan do not differ by more than a logarithmic factor, we show by counterexample that this is not the case, and we prove that that the mixing times do not differ by more than a polynomial factor under mild conditions. To prove these relative bounds, we introduce a method of augmenting the state space to study systematic scan using conductance.

cs.LG↗

arXiv2016

Old Techniques for New Join Algorithms: A Case Study in RDF Processing

Recently there has been significant interest around designing specialized RDF engines, as traditional query processing mechanisms incur orders of magnitude performance gaps on many RDF workloads. At the same time researchers have released new worst-case optimal join algorithms which can be asymptotically better than the join algorithms in traditional engines. In this paper we apply worst-case optimal join algorithms to a standard RDF workload, the LUBM benchmark, for the first time. We do so using two worst-case optimal engines: (1) LogicBlox, a commercial database engine, and (2) EmptyHeaded, our prototype research engine with enhanced worst-case optimal join algorithms. We show that without any added optimizations both LogicBlox and EmptyHeaded outperform two state-of-the-art specialized RDF engines, RDF-3X and TripleBit, by up to 6x on cyclic join queries-the queries where traditional optimizers are suboptimal. On the remaining, less complex queries in the LUBM benchmark, we show that three classic query optimization techniques enable EmptyHeaded to compete with RDF engines, even when there is no asymptotic advantage to the worst-case optimal approach. We validate that our design has merit as EmptyHeaded outperforms MonetDB by three orders of magnitude and LogicBlox by two orders of magnitude, while remaining within an order of magnitude of RDF-3X and TripleBit.

cs.DB↗

arXiv2015

Aggregations over Generalized Hypertree Decompositions

We study a class of aggregate-join queries with multiple aggregation operators evaluated over annotated relations. We show that straightforward extensions of standard multiway join algorithms and generalized hypertree decompositions (GHDs) provide best-known runtime guarantees. In contrast, prior work uses bespoke algorithms and data structures and does not match these guarantees. Our extensions to the standard techniques are a pair of simple tests that (1) determine if two orderings of aggregation operators are equivalent and (2) determine if a GHD is compatible with a given ordering. These tests provide a means to find an optimal GHD that, when provided to standard join algorithms, will correctly answer a given aggregate-join query. The second class of our contributions is a pair of complete characterizations of (1) the set of orderings equivalent to a given ordering and (2) the set of GHDs compatible with some equivalent ordering. We show by example that previous approaches are incomplete. The key technical consequence of our characterizations is a decomposition of a compatible GHD into a set of (smaller) {\em unconstrained} GHDs, i.e. into a set of GHDs of sub-queries without aggregations. Since this decomposition is comprised of unconstrained GHDs, we are able to connect to the wide literature on GHDs for join query processing, thereby obtaining improved runtime bounds, MapReduce variants, and an efficient method to find approximately optimal GHDs.

cs.DB↗

arXiv2015

Building a Large-scale Multimodal Knowledge Base System for Answering Visual Queries

The complexity of the visual world creates significant challenges for comprehensive visual understanding. In spite of recent successes in visual recognition, today's vision systems would still struggle to deal with visual queries that require a deeper reasoning. We propose a knowledge base (KB) framework to handle an assortment of visual queries, without the need to train new classifiers for new tasks. Building such a large-scale multimodal KB presents a major challenge of scalability. We cast a large-scale MRF into a KB representation, incorporating visual, textual and structured data, as well as their diverse relations. We introduce a scalable knowledge base construction system that is capable of building a KB with half billion variables and millions of parameters in a few hours. Our system achieves competitive results compared to purpose-built models on standard recognition and retrieval tasks, while exhibiting greater flexibility in answering richer visual queries.

cs.CV↗

arXiv2015

Taming the Wild: A Unified Analysis of Hogwild!-Style Algorithms

Stochastic gradient descent (SGD) is a ubiquitous algorithm for a variety of machine learning problems. Researchers and industry have developed several techniques to optimize SGD's runtime performance, including asynchronous execution and reduced precision. Our main result is a martingale-based analysis that enables us to capture the rich noise models that may arise from such techniques. Specifically, we use our new analysis in three ways: (1) we derive convergence rates for the convex case (Hogwild!) with relaxed assumptions on the sparsity of the problem; (2) we analyze asynchronous SGD algorithms for non-convex matrix problems including matrix completion; and (3) we design and analyze an asynchronous SGD algorithm, called Buckwild!, that uses lower-precision arithmetic. We show experimentally that our algorithms run efficiently for a variety of problems on modern hardware.

cs.LG↗

arXiv2015

Rapidly Mixing Gibbs Sampling for a Class of Factor Graphs Using Hierarchy Width

Gibbs sampling on factor graphs is a widely used inference technique, which often produces good empirical results. Theoretical guarantees for its performance are weak: even for tree structured graphs, the mixing time of Gibbs may be exponential in the number of variables. To help understand the behavior of Gibbs sampling, we introduce a new (hyper)graph property, called hierarchy width. We show that under suitable conditions on the weights, bounded hierarchy width ensures polynomial mixing time. Our study of hierarchy width is in part motivated by a class of factor graph templates, hierarchical templates, which have bounded hierarchy width---regardless of the data used to instantiate them. We demonstrate a rich application from natural language processing in which Gibbs sampling provably mixes rapidly and achieves accuracy that exceeds human volunteers.

cs.LG↗