author
Co-Founder
,
Snorkel AI
Professor @ Stanford University
Christopher (Chris) Ré is a professor in the department of computer science at Stanford University. He is in the Stanford AI Lab and is affiliated with the Statistical Machine Learning Group. His recent work is to understand how software and hardware systems will change as a result of machine learning along with a continuing, petulant drive to work on math problems. Research from his group has been incorporated into scientific and humanitarian efforts, such as the fight against human trafficking, along with widely used products from technology and enterprise companies including Google Ads, Gmail, YouTube, and Apple.
He has co-founded four companies based on his research into machine learning systems, SambaNova and Snorkel, along with two companies that are now part of Apple, Lattice (DeepDive) in 2017, and Inductiv (HoloClean) in 2020.
His research contributions have spanned database theory, database systems, and machine learning. His work has won the best paper or test-of-time awards at the premier venues in each area. He still can’t believe he won the MacArthur Foundation Fellowship.
The latest from Chris
Leveraging Organizational Resources to Adapt Models to New Data Modalities
As applications in large organizations evolve, the machine learning (ML) models that power them must adapt the same predictive tasks to newly arising data modalities (e.g., a new video content launch in a social media application requires existing text or image models to extend to video). To solve this problem, organizations typically create ML pipelines from scratch. However, this fails to utilize the domain expertise and data they have cultivated from developing tasks for existing modalities. We demonstrate how organizational resources, in the form of aggregate statistics, knowledge bases, and existing services that operate over related tasks, enable teams to...
Research Paper
Leveraging Organizational Resources to Adapt Models to New Data Modalities
As applications in large organizations evolve, the machine learning (ML) models that power them must adapt the same predictive tasks to newly arising data modalities (e.g., a new video content launch in a social media application requires existing text or image models to extend to video). To solve this problem, organizations typically create ML pipelines from scratch. However, this fails…
Fast and Three-Rious: Speed up Weak Supervision With Triplet Methods
Weak supervision is a popular method for building machine learning models without relying on ground truth annotations. Instead, it generates probabilistic training labels by estimating the accuracies of multiple noisy labeling sources (e.g., heuristics, crowd workers). Existing approaches use latent variable estimation to model the noisy sources, but these methods can be computationally expensive, scaling superlinearly in the data. In this work, we show that, for a class of latent variable models highly applicable to weak supervision, we can find a closed-form solution to model parameters, obviating the need for iterative solutions like stochastic gradient descent (SGD). We use this...
Research Paper
Fast and Three-Rious: Speed up Weak Supervision With Triplet Methods
Weak supervision is a popular method for building machine learning models without relying on ground truth annotations. Instead, it generates probabilistic training labels by estimating the accuracies of multiple noisy labeling sources (e.g., heuristics, crowd workers). Existing approaches use latent variable estimation to model the noisy sources, but these methods can be computationally expensive, scaling superlinearly in the data. In…
Cross-Modal Data Programming Enables Rapid Medical Machine Learning
Labeling training datasets has become a key barrier to building medical machine learning models. One strategy is to generate training labels programmatically, for example by applying natural language processing pipelines to text reports associated with imaging studies. We propose cross-modal data programming, which generalizes this intuitive strategy in a theoretically-grounded way that enables simpler, clinician-driven input, reduces required labeling time, and improves with additional unlabeled data. In this approach, clinicians generate training labels for models defined over a target modality (e.g. images or time series) by writing rules over an auxiliary modality (e.g. text reports). The resulting technical challenge consists...
Research Paper
Cross-Modal Data Programming Enables Rapid Medical Machine Learning
Labeling training datasets has become a key barrier to building medical machine learning models. One strategy is to generate training labels programmatically, for example by applying natural language processing pipelines to text reports associated with imaging studies. We propose cross-modal data programming, which generalizes this intuitive strategy in a theoretically-grounded way that enables simpler, clinician-driven input, reduces required labeling time,…
Train and You’ll Miss It: Interactive Model Iteration With Weak Supervision…
Our goal is to enable machine learning systems to be trained interactively. This requires models that perform well and train quickly, without large amounts of hand-labeled data. We take a step forward in this direction by borrowing from weak supervision (WS), wherein models can be trained with noisy sources of signal instead of hand-labeled data. But WS relies on training downstream deep networks to extrapolate to unseen data points, which can take hours or days. Pre-trained embeddings can remove this requirement. We do not use the embeddings as features as in transfer learning (TL), which requires fine-tuning for high performance,...
Research Paper
Train and You’ll Miss It: Interactive Model Iteration With Weak Supervision…
Our goal is to enable machine learning systems to be trained interactively. This requires models that perform well and train quickly, without large amounts of hand-labeled data. We take a step forward in this direction by borrowing from weak supervision (WS), wherein models can be trained with noisy sources of signal instead of hand-labeled data. But WS relies on training…
Cardiac Imaging of Aortic Valve Area From 34 287 UK Biobank Participants Reveals Novel Genetic Associations and Shared Genetic Comorbidity With Multiple Disease Phenotypes
Background: The aortic valve is an important determinant of cardiovascular physiology and anatomic location of common human diseases. Methods: From a sample of 34 287 white British ancestry participants, we estimated functional aortic valve area by planimetry from prospectively obtained cardiac magnetic resonance imaging sequences of the aortic valve. Aortic valve area measurements were submitted to genome-wide association testing, followed by polygenic risk scoring and phenome-wide screening, to identify genetic comorbidities. Results: A genome-wide association study of aortic valve area in these UK Biobank participants showed 3 significant associations, indexed by rs71190365 (chr13:50764607, DLEU1, P=1.8×10−9), rs35991305 (chr12:94191968, CRADD, P=3.4×10−8), and chr17:45013271:C:T...
Research Paper
Cardiac Imaging of Aortic Valve Area From 34 287 UK Biobank Participants Reveals Novel Genetic Associations and Shared Genetic Comorbidity With Multiple Disease Phenotypes
Background: The aortic valve is an important determinant of cardiovascular physiology and anatomic location of common human diseases. Methods: From a sample of 34 287 white British ancestry participants, we estimated functional aortic valve area by planimetry from prospectively obtained cardiac magnetic resonance imaging sequences of the aortic valve. Aortic valve area measurements were submitted to genome-wide association testing, followed by…
Low-Dimensional Hyperbolic Knowledge Graph Embeddings
Knowledge graph (KG) embeddings learn lowdimensional representations of entities and relations to predict missing facts. KGs often exhibit hierarchical and logical patterns which must be preserved in the embedding space. For hierarchical data, hyperbolic embedding methods have shown promise for high-fidelity and parsimonious representations. However, existing hyperbolic embedding methods do not account for the rich logical patterns in KGs. In this work, we introduce a class of hyperbolic KG embedding models that simultaneously capture hierarchical and logical patterns. Our approach combines hyperbolic reflections and rotations with attention to model complex relational patterns. Experimental results on standard KG benchmarks show that...
Research Paper
Low-Dimensional Hyperbolic Knowledge Graph Embeddings
Knowledge graph (KG) embeddings learn lowdimensional representations of entities and relations to predict missing facts. KGs often exhibit hierarchical and logical patterns which must be preserved in the embedding space. For hierarchical data, hyperbolic embedding methods have shown promise for high-fidelity and parsimonious representations. However, existing hyperbolic embedding methods do not account for the rich logical patterns in KGs. In…
Ivy: Instrumental Variable Synthesis for Causal Inference
A popular way to estimate the causal effect of a variable x on y from observational data is to use an instrumental variable (IV): a third variable z that affects y only through x. The more strongly z is associated with x, the more reliable the estimate is, but such strong IVs are difficult to find. Instead, practitioners combine more commonly available IV candidates—which are not necessarily strong, or even valid, IVs—into a single "summary" that is plugged into causal effect estimators in place of an IV. In genetic epidemiology, such approaches are known as allele scores. Allele scores require...
Research Paper
Ivy: Instrumental Variable Synthesis for Causal Inference
A popular way to estimate the causal effect of a variable x on y from observational data is to use an instrumental variable (IV): a third variable z that affects y only through x. The more strongly z is associated with x, the more reliable the estimate is, but such strong IVs are difficult to find. Instead, practitioners combine more…
Extracting chemical reactions from text using Snorkel
BACKGROUND: Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of the biomedical literature. Conventional text mining pipelines provide tools to automatically extract entities and relationships from the scientific literature, and partially replace expert curation, but such machine learning frameworks often require a large amount of labeled training data and thus lack scalability for both larger document corpora and new relationship types. RESULTS: We developed an application of Snorkel, a weakly supervised learning framework, for extracting chemical reaction relationships from...
Research Paper
Extracting chemical reactions from text using Snorkel
BACKGROUND: Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of the biomedical literature. Conventional text mining pipelines provide tools to automatically extract entities and relationships from the scientific literature, and partially replace expert curation, but such machine learning frameworks…
AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature
The diagnosis of Mendelian disorders requires labor-intensive literature research. Trained clinicians can spend hours looking for the right publication(s) supporting a single gene that best explains a patient’s disease. AMELIE (Automatic Mendelian Literature Evaluation) greatly accelerates this process. AMELIE parses all 29 million PubMed abstracts and downloads and further parses hundreds of thousands of full-text articles in search of information supporting the causality and associated phenotypes of most published genetic variants. AMELIE then prioritizes patient candidate variants for their likelihood of explaining any patient’s given set of phenotypes. Diagnosis of singleton patients (without relatives’ exomes) is the most time-consuming scenario,...
Research Paper
AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature
The diagnosis of Mendelian disorders requires labor-intensive literature research. Trained clinicians can spend hours looking for the right publication(s) supporting a single gene that best explains a patient’s disease. AMELIE (Automatic Mendelian Literature Evaluation) greatly accelerates this process. AMELIE parses all 29 million PubMed abstracts and downloads and further parses hundreds of thousands of full-text articles in search of information…
