Demo Data from SIGIR 2026 / reviewers in the wild / expert
Benjamin Coleman
dblp:217/2220
· DBLP profile ↗
18ranked-venue papers
6as first author
15since 2021 · last 2026
—ORCID · conflict
Domains — the database's venue-derived domains; a paper can count in several
Artificial intelligence and machine learning · 10 · 4 first-author · 9 since 2021Databases, data management, data science and information retrieval · 7 · 1 first-author · 6 since 2021Applied, interdisciplinary, general and emerging computing · 2 · 1 first-authorSecurity and privacy · 1 · 1 first-author · 1 since 2021Graphics, computer vision, multimedia, augmented reality and games · 1 · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Databases, data mining, and information retrieval
9 papers |
Information retrieval · 34% Recommender systems · 20% Data stream processing · 20% | |
| Artificial intelligence
3 papers |
Efficient and distributed learning · 66% Learning paradigms · 23% Deep learning architectures and training · 11% | |
| Theoretical computer science
2 papers |
Algorithms and data structures · 100% | |
| Computer architecture, parallel and distributed computing, and storage systems
2 papers |
Distributed systems · 38% Memory systems · 33% Parallel and multicore computing · 29% | |
| Interdisciplinary, comprehensive, and emerging computing
2 papers |
Bioinformatics and computational biology · 100% | |
| Network and information security
1 paper |
Privacy and data protection · 100% |
Topics — the 30 heaviest of 40, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Information retrieval › similarity search
nearest neighbor search |
1.2 | 2 | 2023 | DESSERT: An Efficient Algorithm for Vector Set Search with Vector Set Queries · NeurIPS 2023 Graph Reordering for Cache-Efficient Near Neighbor Search · NeurIPS 2022 |
Recommender systems › large language model-based recommendation
agentic recommender system |
1.0 | 1 | 2026 | Multi-Agentic Recommender Systems: Foundations, Perspectives, and Lessons from Large Scale Deployments in eCommerce · SIGIR 2026 |
Algorithms and data structures › data structure design › search structures › hashing
locality-sensitive hashing |
0.9 | 2 | 2021 | Practical Near Neighbor Search via Group Testing · NeurIPS 2021 Sub-linear Memory Sketches for Near Neighbor Search on Streaming Data · ICML 2020 |
Machine learning › Efficient and distributed learning › federated learning
client selection |
0.7 | 1 | 2023 | One-Pass Distribution Sketch for Measuring Data Heterogeneity in Federated Learning · NeurIPS 2023 |
Machine learning › Efficient and distributed learning › federated learning
data heterogeneity |
0.7 | 1 | 2023 | One-Pass Distribution Sketch for Measuring Data Heterogeneity in Federated Learning · NeurIPS 2023 |
Machine learning › Efficient and distributed learning › model compression
embedding compression |
0.7 | 1 | 2023 | Unified Embedding: Battle-Tested Feature Representations for Web-Scale ML Systems · NeurIPS 2023 |
Machine learning › Efficient and distributed learning
federated learning |
0.7 | 1 | 2023 | One-Pass Distribution Sketch for Measuring Data Heterogeneity in Federated Learning · NeurIPS 2023 |
Machine learning › Efficient and distributed learning
model compression |
0.7 | 1 | 2023 | Unified Embedding: Battle-Tested Feature Representations for Web-Scale ML Systems · NeurIPS 2023 |
Recommender systems › representation learning for recommendation
embedding-based recommendation |
0.7 | 1 | 2023 | Unified Embedding: Battle-Tested Feature Representations for Web-Scale ML Systems · NeurIPS 2023 |
Machine learning and data management
embedding tables |
0.7 | 1 | 2023 | Unified Embedding: Battle-Tested Feature Representations for Web-Scale ML Systems · NeurIPS 2023 |
Information retrieval
retrieval models |
0.7 | 1 | 2023 | DESSERT: An Efficient Algorithm for Vector Set Search with Vector Set Queries · NeurIPS 2023 |
Information retrieval › search engines
semantic search |
0.7 | 1 | 2023 | DESSERT: An Efficient Algorithm for Vector Set Search with Vector Set Queries · NeurIPS 2023 |
Machine learning › Learning paradigms › continual learning
catastrophic forgetting |
0.6 | 1 | 2022 | Retaining Knowledge for Learning with Dynamic Definition · NeurIPS 2022 |
Machine learning › Learning paradigms
continual learning |
0.6 | 1 | 2022 | Retaining Knowledge for Learning with Dynamic Definition · NeurIPS 2022 |
Bioinformatics and computational biology › sequence analysis
genomic sequence analysis |
0.6 | 1 | 2022 | One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams · ICML 2022 |
Bioinformatics and computational biology › metagenomics
metagenome profiling |
0.6 | 1 | 2022 | One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams · ICML 2022 |
Data mining › sampling
diversity sampling |
0.6 | 1 | 2022 | One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams · ICML 2022 |
Information retrieval › similarity search › nearest neighbor search › approximate nearest neighbor search
graph-based approximate nearest neighbor search |
0.6 | 1 | 2022 | Graph Reordering for Cache-Efficient Near Neighbor Search · NeurIPS 2022 |
Data stream processing
stream sampling |
0.6 | 1 | 2022 | One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams · ICML 2022 |
Memory systems
cache |
0.6 | 1 | 2022 | Graph Reordering for Cache-Efficient Near Neighbor Search · NeurIPS 2022 |
Privacy and data protection
differential privacy |
0.5 | 1 | 2021 | A One-Pass Distributed and Private Sketch for Kernel Sums with Applications to Machine Learning at Scale · CCS 2021 |
Privacy and data protection
privacy-preserving machine learning |
0.5 | 1 | 2021 | A One-Pass Distributed and Private Sketch for Kernel Sums with Applications to Machine Learning at Scale · CCS 2021 |
Privacy and data protection › differential privacy › differentially private query answering › private data analysis
private sketching |
0.5 | 1 | 2021 | A One-Pass Distributed and Private Sketch for Kernel Sums with Applications to Machine Learning at Scale · CCS 2021 |
Distributed systems › peer-to-peer systems
consistent hashing |
0.5 | 1 | 2021 | Revisiting Consistent Hashing with Bounded Loads · AAAI 2021 |
Parallel and multicore computing
load balancing |
0.5 | 1 | 2021 | Revisiting Consistent Hashing with Bounded Loads · AAAI 2021 |
Algorithms and data structures › similarity search › nearest neighbor search
approximate nearest neighbor search |
0.5 | 1 | 2021 | Practical Near Neighbor Search via Group Testing · NeurIPS 2021 |
Algorithms and data structures
similarity search |
0.5 | 1 | 2021 | Practical Near Neighbor Search via Group Testing · NeurIPS 2021 |
Data mining › density estimation
kernel density estimation |
0.4 | 1 | 2020 | Sub-linear RACE Sketches for Approximate Kernel Density Estimation on Streaming Data · WWW 2020 |
Data stream processing
sketch |
0.4 | 1 | 2020 | Sub-linear RACE Sketches for Approximate Kernel Density Estimation on Streaming Data · WWW 2020 |
Data stream processing
sketch-based stream processing |
0.4 | 1 | 2020 | Sub-linear Memory Sketches for Near Neighbor Search on Streaming Data · ICML 2020 |
Methods — techniques the papers use, named apart from their topics
locality-sensitive hashing · 1.9unified embedding · 1.3feature multiplexing · 1.3reservoir sampling · 1.1graph reordering · 1.1coreset · 1.1multi-agent orchestration · 1.0large language model · 1.0sketching algorithm · 0.7retrieval tables · 0.7distribution sketch · 0.7approximate nearest neighbor search · 0.7universal function approximation · 0.6hash-based sparsity · 0.6HNSW · 0.6randomized contingency tables · 0.5one-pass streaming · 0.5minwise hashing · 0.5
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2026 | Down with the Hierarchy: The 'H' in HNSW Stands for "Hubs"
Blaise Munyampirwa, Vihan Lakshman, Benjamin Coleman |
ECIR (3) | 3 |
| 2026 | Multi-Agentic Recommender Systems: Foundations, Perspectives, and Lessons from Large Scale Deployments in eCommerceabstractThis tutorial covers topics on multi-agentic recommender systems — recommender systems augmented with Large Language Models (LLMs) and multi-agent orchestration to enable multi-step reasoning, tool use, and interactive decision-making. The tutorial emphasizes foundational concepts, reusable design patterns, and practical lessons learned from large-scale e-commerce deployments. Specifically, we first cover background and recent trends in generative recommender systems and their connection to agentic approaches. We then survey major deployment areas in industry and review the agent orchestration frameworks developed to support them. Finally, we present a project walkthrough that traces the full lifecycle of an agentic recommender system, from scoping and data definition through modeling, deployment, and monitoring, to provide actionable deployment insights. The tutorial bridges perspectives from information retrieval (IR), recommender systems (RecSys), and large-scale industrial practice. The accompanying material can be found at agenticrecsys.github.io. Reza Yousefi Maragheh, Yashar Deldjoo, Benjamin Coleman, Jason H. D. Cho, Chi Wang 0001 |
SIGIR | 3 |
| 2024 | Improving Data Efficiency for Recommenders and LLMsabstractIn recent years, massive transformer-based architectures have driven breakthrough performance in practical applications like autoregressive text-generation (LLMs) and click-prediction (recommenders). A common recipe for success is to train large models on massive web-scale datasets [3, 15], e.g., modern recommenders are trained on billions of user-item click events, and LLMs are trained on trillions of tokens extracted from the public internet. We are close to hitting the computational and economical limits of scaling up the size of these models, and we expect the next frontier of gains to come from improving the: (i) data quality of the training dataset, and (ii) data efficiency of the extremely expensive training procedure. Inspired by this shift, we present a set of “data-centric” techniques for recommendation and language models that summarizes a dataset into a terse data summary, which is both (i) high-quality, i.e., trains better quality models, and (ii) improves the data-efficiency of the overall training procedure. We propose techniques from two disparate data frameworks: (i) data selection (a.k.a., coreset construction) methods that sample portions of the dataset using grounded heuristics, and (ii) data distillation techniques that generate synthetic examples which are optimized to retain the signals needed for training high-quality models. Overall, this work sheds light on the challenges and opportunities offered by data optimization in web-scale systems, a particularly relevant focus as the recommendation community grapples with the grand challenge of leveraging LLMs. Noveen Sachdeva, Benjamin Coleman, Wang-Cheng Kang, Jianmo Ni, James Caverlee, Lichan Hong, Ed H. Chi, Zhiyuan Cheng 0002 |
RecSys | 2 |
| 2023 | BOLT: An Automated Deep Learning Framework for Training and Deploying Large-Scale Search and Recommendation Models on Commodity CPU HardwareabstractEfficient large-scale neural network training and inference on commodity CPU hardware is of immense practical significance in democratizing deep learning (DL) capabilities. Presently, the process of training massive models consisting of hundreds of millions to billions of parameters requires the extensive use of specialized hardware accelerators, such as GPUs, which are only accessible to a limited number of institutions with considerable financial resources. Moreover, there is often an alarming carbon footprint associated with training and deploying these models. In this paper, we take a step towards addressing these challenges by introducing BOLT, a sparse deep learning library for training large-scale search and recommendation models on standard CPU hardware. BOLT provides a flexible, high-level API for constructing models that will be familiar to users of existing popular DL frameworks. By automatically tuning specialized hyperparameters, BOLT also abstracts away the algorithmic details of sparse network training. We evaluate BOLT on a number of information retrieval tasks including product recommendations, text classification, graph neural networks, and personalization. We find that our proposed system achieves competitive performance with state-of-the-art techniques at a fraction of the cost and energy consumption and an order-of-magnitude faster inference time. BOLT has also been successfully deployed by multiple businesses to address critical problems, and we highlight one customer case study in the field of e-commerce. Nicholas Meisburger, Vihan Lakshman, Benito Geordie, Joshua Engels, David Torres Ramos, Pratik Pranav, Benjamin Coleman, Benjamin Meisburger, Shubh Gupta, Yashwanth Adunukota, Tharun Medini, Anshumali Shrivastava |
CIKM | 7 |
| 2023 | Unified Embedding: Battle-Tested Feature Representations for Web-Scale ML SystemsabstractLearning high-quality feature embeddings efficiently and effectively is critical for the performance of web-scale machine learning systems. A typical model ingests hundreds of features with vocabularies on the order of millions to billions of tokens. The standard approach is to represent each feature value as a $d$-dimensional embedding, which introduces hundreds of billions of parameters for extremely high-cardinality features. This bottleneck has led to substantial progress in alternative embedding algorithms. Many of these methods, however, make the assumption that each feature uses an independent embedding table. This work introduces a simple yet highly effective framework, Feature Multiplexing, where one single representation space is used for many different categorical features. Our theoretical and empirical analysis reveals that multiplexed embeddings can be decomposed into components from each constituent feature, allowing models to distinguish between features. We show that multiplexed representations give Pareto-optimal space-accuracy tradeoffs for three public benchmark datasets. Further, we propose a highly practical approach called Unified Embedding with three major benefits: simplified feature configuration, strong adaptation to dynamic data distributions, and compatibility with modern hardware. Unified embedding gives significant improvements in offline and online metrics compared to highly competitive baselines across five web-scale search, ads, and recommender systems, where it serves billions of users across the world in industry-leading products. Benjamin Coleman, Wang-Cheng Kang, Matthew Fahrbach, Lichan Hong, Ed H. Chi, Zhiyuan Cheng 0002 |
NeurIPS | 1 |
| 2023 | DESSERT: An Efficient Algorithm for Vector Set Search with Vector Set QueriesabstractWe study the problem of $\text{\emph{vector set search}}$ with $\text{\emph{vector set queries}}$. This task is analogous to traditional near-neighbor search, with the exception that both the query and each element in the collection are $\text{\textit{sets}}$ of vectors. We identify this problem as a core subroutine for semantic search applications and find that existing solutions are unacceptably slow. Towards this end, we present a new approximate search algorithm, DESSERT ($\text{\bf D}$ESSERT $\text{\bf E}$ffeciently $\text{\bf S}$earches $\text{\bf S}$ets of $\text{\bf E}$mbeddings via $\text{\bf R}$etrieval $\text{\bf T}$ables). DESSERT is a general tool with strong theoretical guarantees and excellent empirical performance. When we integrate DESSERT into ColBERT, a state-of-the-art semantic search model, we find a 2-5x speedup on the MS MARCO and LoTTE retrieval benchmarks with minimal loss in recall, underscoring the effectiveness and practical applicability of our proposal. Joshua Engels, Benjamin Coleman, Vihan Lakshman, Anshumali Shrivastava |
NeurIPS | 2 |
| 2023 | One-Pass Distribution Sketch for Measuring Data Heterogeneity in Federated LearningabstractFederated learning (FL) is a machine learning paradigm where multiple client devices train models collaboratively without data exchange. Data heterogeneity problem is naturally inherited in FL since data in different clients follow diverse distributions. To mitigate the negative influence of data heterogeneity, we need to start by measuring it across clients. However, the efficient measurement between distributions is a challenging problem, especially in high dimensionality. In this paper, we propose a one-pass distribution sketch to represent the client data distribution. Our sketching algorithm only requires a single pass of the client data, which is efficient in terms of time and memory. Moreover, we show in both theory and practice that the distance between two distribution sketches represents the divergence between their corresponding distributions. Furthermore, we demonstrate with extensive experiments that our distribution sketch improves the client selection in the FL training. We also showcase that our distribution sketch is an efficient solution to the cold start problem in FL for new clients with unlabeled data. Zichang Liu, Zhaozhuo Xu, Benjamin Coleman, Anshumali Shrivastava |
NeurIPS | 3 |
| 2023 | Efficient Data Representation Learning in Google-scale Systemsabstract"Garbage in, Garbage out" is a familiar maxim to ML practitioners and researchers, because the quality of a learned data representation is highly crucial to the quality of any ML model that consumes it as an input. To handle systems that serve billions of users at millions of queries per second (QPS), we need representation learning algorithms with significantly improved efficiency. At Google, we have dedicated thousands of iterations to develop a set of powerful techniques that efficiently learn high quality data representations. We have thoroughly validated these methods through offline evaluation, online A/B testing, and deployed these in over 50 models across major Google products. In this paper, we consider a generalized data representation learning problem that allows us to identify feature embeddings and crosses as common challenges. We propose two solutions, including: 1. Multi-size Unified Embedding to learn high-quality embeddings; and 2. Deep Cross Network V2 for learning effective feature crosses. We discuss the practical challenges we encountered and solutions we developed during deployment to production systems, compare with SOTA methods, and report offline and online experimental results. This work sheds light on the challenges and opportunities for developing next-gen algorithms for web-scale systems. Zhiyuan Cheng 0002, Wang-Cheng Kang, Benjamin Coleman, Yin Zhang 0011, Jianmo Ni, Jonathan Valverde, Lichan Hong, Ed H. Chi |
RecSys | 4 |
| 2022 | One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence StreamsabstractA popular approach to reduce the size of a massive dataset is to apply efficient online sampling to the stream of data as it is read or generated. Online sampling routines are currently restricted to variations of reservoir sampling, where each sample is selected uniformly and independently of other samples. This renders them unsuitable for large-scale applications in computational biology, such as metagenomic community profiling and protein function annotation, which suffer from severe class imbalance. To maintain a representative and diverse sample, we must identify and preferentially select data that are likely to belong to rare classes. We argue that existing schemes for diversity sampling have prohibitive overhead for large-scale problems and high-throughput streams. We propose an efficient sampling routine that uses an online representation of the data distribution as a prefilter to retain elements from rare groups. We apply this method to several genomic data analysis tasks and demonstrate significant speedup in downstream analysis without sacrificing the quality of the results. Because our algorithm is 2x faster and uses 1000x less memory than coreset, reservoir and sketch-based alternatives, we anticipate that it will become a useful preprocessing step for applications with large-scale streaming data. Benjamin Coleman, Benito Geordie, Li Chou, Ryan A. Leo Elworth, Todd J. Treangen, Anshumali Shrivastava |
ICML | 1 |
| 2022 | Graph Reordering for Cache-Efficient Near Neighbor SearchabstractGraph search is one of the most successful algorithmic trends in near neighbor search. Several of the most popular and empirically successful algorithms are, at their core, a greedy walk along a pruned near neighbor graph. However, graph traversal applications often suffer from poor memory access patterns, and near neighbor search is no exception to this rule. Our measurements show that popular search indices such as the hierarchical navigable small-world graph (HNSW) can have poor cache miss performance. To address this issue, we formulate the graph traversal problem as a cache hit maximization task and propose multiple graph reordering as a solution. Graph reordering is a memory layout optimization that groups commonly-accessed nodes together in memory. We mathematically formalize the connection between the graph layout and the cache complexity of search. We present exhaustive experiments applying several reordering algorithms to a leading graph-based near neighbor method based on the HNSW index. We find that reordering improves the query time by up to 40%, we present analysis and improvements for existing graph layout methods, and we demonstrate that the time needed to reorder the graph is negligible compared to the time required to construct the index. Benjamin Coleman, Santiago Segarra, Alexander J. Smola, Anshumali Shrivastava |
NeurIPS | 1 |
| 2022 | Retaining Knowledge for Learning with Dynamic DefinitionabstractMachine learning models are often deployed in settings where they must be constantly updated in response to the changes in class definitions while retaining high accuracy on previously learned definitions. A classical use case is fraud detection, where new fraud schemes come one after another. While such an update can be accomplished by re-training on the complete data, the process is inefficient and prevents real-time and on-device learning. On the other hand, efficient methods that incrementally learn from new data often result in the forgetting of previously-learned knowledge. We define this problem as Learning with Dynamic Definition (LDD) and demonstrate that popular models, such as the Vision Transformer and Roberta, exhibit substantial forgetting of past definitions. We present the first practical and provable solution to LDD. Our proposal is a hash-based sparsity model \textit{RIDDLE} that solves evolving definitions by associating samples only to relevant parameters. We prove that our model is a universal function approximator and theoretically bounds the knowledge lost during the update process. On practical tasks with evolving class definition in vision and natural language processing, \textit{RIDDLE} outperforms baselines by up to 30\% on the original dataset while providing competitive accuracy on the update dataset. Zichang Liu, Benjamin Coleman, Tianyi Zhang 0011, Anshumali Shrivastava |
NeurIPS | 2 |
| 2021 | Revisiting Consistent Hashing with Bounded LoadsabstractDynamic load balancing lies at the heart of distributed caching. Here, the goal is to assign objects (load) to servers (computing nodes) in a way that provides load balancing while at the same time dynamically adjusts to the addition or removal of servers. Load balancing is a critical topic in many areas including cloud systems, distributed databases, and distributed and data-parallel machine learning. A popular and widely adopted solution to dynamic load balancing is the two-decade-old Consistent Hashing (CH). Recently, an elegant extension was provided to account for server bounds. In this paper, we identify that existing methodologies for CH and its variants suffer from cascaded overflow, leading to poor load balancing. This cascading effect leads to decreasing performance of the hashing procedure with increasing load. To overcome the cascading effect, we propose a simple solution to CH based on recent advances in fast minwise hashing. We show, both theoretically and empirically, that our proposed solution is significantly superior for load balancing and is optimal in many senses. On the AOL search dataset and Indiana University Clicks dataset with real user activity, our proposed solution reduces cache misses by several magnitudes. John Chen 0002, Benjamin Coleman, Anshumali Shrivastava |
AAAI | 2 |
| 2021 | A One-Pass Distributed and Private Sketch for Kernel Sums with Applications to Machine Learning at ScaleabstractDifferential privacy is a compelling privacy definition that explains the privacy-utility tradeoff via formal, provable guarantees. In machine learning, we often wish to release a function over a dataset while preserving differential privacy. Although there are general algorithms to solve this problem for any function, such methods can require hours to days to run on moderately sized datasets. As a result, most private algorithms address task-dependent functions for specific applications. In this work, we propose a general purpose private sketch, or small summary of the dataset, that supports machine learning tasks such as regression, classification, density estimation, and more. Our sketch is ideal for large-scale distributed settings because it is simple to implement, mergeable, and can be created with a one-pass streaming algorithm. At the heart of our proposal is the reduction of many machine learning objectives to kernel sums. Our sketch estimates these sums using randomized contingency tables that are indexed with locality-sensitive hashing. Existing alternatives for kernel sum estimation scale poorly, often exponentially slower with an increase in dimensions. In contrast, our sketch can quickly run on large high-dimensional datasets, such as the 65 million node Friendster graph, in a single pass that takes less than 20 minutes, which is otherwise infeasible with any known alternative. Exhaustive experiments show that the privacy-utility tradeoff of our method is competitive with existing algorithms, but at an order-of-magnitude smaller computational cost. We expect that our sketch will be practically useful for differential privacy in distributed, large-scale machine learning settings. Benjamin Coleman, Anshumali Shrivastava |
CCS | 1 |
| 2021 | Practical Near Neighbor Search via Group TestingabstractWe present a new algorithm for the approximate near neighbor problem that combines classical ideas from group testing with locality-sensitive hashing (LSH). We reduce the near neighbor search problem to a group testing problem by designating neighbors as "positives," non-neighbors as "negatives," and approximate membership queries as group tests. We instantiate this framework using distance-sensitive Bloom Filters to Identify Near-Neighbor Groups (FLINNG). We prove that FLINNG has sub-linear query time and show that our algorithm comes with a variety of practical advantages. For example, FLINNG can be constructed in a single pass through the data, consists entirely of efficient integer operations, and does not require any distance computations. We conduct large-scale experiments on high-dimensional search tasks such as genome search, URL similarity search, and embedding search over the massive YFCC100M dataset. In our comparison with leading algorithms such as HNSW and FAISS, we find that FLINNG can provide up to a 10x query speedup with substantially smaller indexing time and memory. Joshua Engels, Benjamin Coleman, Anshumali Shrivastava |
NeurIPS | 2 |
| 2021 | Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO)abstractDNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past years and has shown no sign of slowing down. Several recent attempts have been made to tame the computational burden of sequence search on these terabyte and petabyte-scale datasets, including raw reads and assembled genomes. However, no known implementation provides both fast query and construction time, keeps the low false-positive requirement, and offers cheap storage of the data structure. We propose a data structure for search called RAMBO (Repeated And Merged BloOm Filter) which is significantly faster in query time than state-of-the-art genome indexing methods- COBS (Compact bit-sliced signature index), Sequence Bloom Trees, HowDeSBT, and SSBT. Furthermore, it supports insertion and query process parallelism, cheap updates for streaming inputs, has a zero false-negative rate, a low false-positive rate, and a small index size. RAMBO converts the search problem into set membership testing among K documents. Interestingly, it is a count-min sketch type arrangement of a membership testing utility (Bloom Filter in our case). The simplicity of the algorithm and embarrassingly parallel architecture allows us to stream and index a 170TB whole-genome sequence dataset in a mere 9 hours on a cluster of 100 nodes while competing methods require weeks. Minghao Yan, Benjamin Coleman, Bryce Kille, Ryan A. Leo Elworth, Tharun Medini, Todd J. Treangen, Anshumali Shrivastava |
SIGMOD Conference | 3 |
| 2020 | Sub-linear Memory Sketches for Near Neighbor Search on Streaming DataabstractWe present the first sublinear memory sketch that can be queried to find the nearest neighbors in a dataset. Our online sketching algorithm compresses an N element dataset to a sketch of size $O(N^b \log^3 N)$ in $O(N^{(b+1)} \log^3 N)$ time, where $b < 1$. This sketch can correctly report the nearest neighbors of any query that satisfies a stability condition parameterized by $b$. We achieve sublinear memory performance on stable queries by combining recent advances in locality sensitive hash (LSH)-based estimators, online kernel density estimation, and compressed sensing. Our theoretical results shed new light on the memory-accuracy tradeoff for nearest neighbor search, and our sketch, which consists entirely of short integer arrays, has a variety of attractive features in practice. We evaluate the memory-recall tradeoff of our method on a friend recommendation task in the Google plus social media network. We obtain orders of magnitude better compression than the random projection based alternative while retaining the ability to report the nearest neighbors of practical queries. Benjamin Coleman, Richard G. Baraniuk, Anshumali Shrivastava |
ICML | 1 |
| 2020 | Sub-linear RACE Sketches for Approximate Kernel Density Estimation on Streaming DataabstractKernel density estimation is a simple and effective method that lies at the heart of many important machine learning applications. Unfortunately, kernel methods scale poorly for large, high dimensional datasets. Approximate kernel density estimation has a prohibitively high memory and computation cost, especially in the streaming setting. Recent sampling algorithms for high dimensional densities can reduce the computation cost but cannot operate online, while streaming algorithms cannot handle high dimensional datasets due to the curse of dimensionality. We propose RACE, an efficient sketching algorithm for kernel density estimation on high-dimensional streaming data. RACE compresses a set of N high dimensional vectors into tiny arrays of integer counters. These arrays are sufficient to estimate the kernel density for a large class of kernels. Our one-pass sketch is simple to implement and comes with strong theoretical guarantees. We evaluate our method on real-world high-dimensional datasets and show that our sketch achieves 10x better compression compared to existing methods.1 Benjamin Coleman, Anshumali Shrivastava |
WWW | 1 |
| 2018 | SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation dataabstractRNA-protein binding is critical to gene regulation, controlling fundamental processes including splicing, translation, localization and stability, and aberrant RNA-protein interactions are known to play a role in a wide variety of diseases. However, molecular understanding of RNA-protein interactions remains limited; in particular, identification of RNA motifs that bind proteins has long been challenging, especially when such motifs depend on both sequence and structure. Moreover, although RNA binding proteins (RBPs) often contain more than one binding domain, algorithms capable of identifying more than one binding motif simultaneously have not been developed. In this paper we present a novel pipeline to determine binding peaks in crosslinking immunoprecipitation (CLIP) data, to discover multiple possible RNA sequence/structure motifs among them, and to experimentally validate such motifs. At the core is a new semi-automatic algorithm SARNAclust, the first unsupervised method to identify and deconvolve multiple sequence/structure motifs simultaneously. SARNAclust computes similarity between sequence/structure objects using a graph kernel, providing the ability to isolate the impact of specific features through the bulge graph formalism. Application of SARNAclust to synthetic data shows its capability of clustering 5 motifs at once with a V-measure value of over 0.95, while GraphClust achieves only a V-measure of 0.083 and RNAcontext cannot detect any of the motifs. When applied to existing eCLIP sets, SARNAclust finds known motifs for SLBP and HNRNPC and novel motifs for several other RBPs such as AGGF1, AKAP8L and ILF3. We demonstrate an experimental validation protocol, a targeted Bind-n-Seq-like high-throughput sequencing approach that relies on RNA inverse folding for oligo pool design, that can validate the components within the SLBP motif. Finally, we use this protocol to experimentally interrogate the SARNAclust motif predictions for protein ILF3. Our results support a newly identified partially double-stranded UUUUUGAGA motif similar to that known for the splicing factor HNRNPC. Iván Dotú, Scott I. Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras, Jeffrey H. Chuang |
PLoS Comput. Biol. | 3 |