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Researcher profile

Benjamin Coleman

Benjamin Coleman contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningData Structures and AlgorithmsInformation RetrievalComputational GeometryCryptography and Securityeess.SPGenomicsInformation Theorymath.ITMethodologyNeural and Evolutionary Computing

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Published work

9 published item(s)

preprint2026arXiv

PACEvolve: Enabling Long-Horizon Progress-Aware Consistent Evolution

Large Language Models (LLMs) have emerged as powerful operators for evolutionary search, yet the design of efficient search scaffolds remains ad hoc. While promising, current LLM-in-the-loop systems lack a systematic approach to managing the evolutionary process. We identify three distinct failure modes: Context Pollution, where experiment history biases future candidate generation; Mode Collapse, where agents stagnate in local minima due to poor exploration-exploitation balance; and Weak Collaboration, where rigid crossover strategies fail to leverage parallel search trajectories effectively. We introduce Progress-Aware Consistent Evolution (PACEvolve), a framework designed to robustly govern the agent's context and search dynamics, to address these challenges. PACEvolve combines hierarchical context management (HCM) with pruning to address context pollution; momentum-based backtracking (MBB) to escape local minima; and a self-adaptive sampling policy that unifies backtracking and crossover for dynamic search coordination (CE), allowing agents to balance internal refinement with cross-trajectory collaboration. We demonstrate that PACEvolve provides a systematic path to consistent, long-horizon self-improvement, achieving state-of-the-art results on LLM-SR and KernelBench, while discovering solutions surpassing the record on Modded NanoGPT.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

PACEvolve++: Improving Test-time Learning for Evolutionary Search Agents

Large language models have become drivers of evolutionary search, but most systems rely on a fixed, prompt-elicited policy to sample next candidates. This limits adaptation in practical engineering and research tasks, where evaluations are expensive, and progress depends on learning task-specific search dynamics. We introduce PACEvolve++, an advisor-model reinforcement learning framework for test-time policy adaptation in evolutionary search agents. PACEvolve++ decouples strategic search decisions from implementation: a trainable advisor generates, assesses, and selects hypotheses, while a stronger frontier model translates selected hypotheses into executable candidates. To train the advisor under non-stationary feedback, we propose a phase-adaptive approach that adapts its optimization strategy to different phases of the evolutionary process. Early in evolution, it uses group-relative feedback to learn broad search preferences; later, as reward gaps compress, it emphasizes best-of-$k$ frontier contribution to support stable refinement. Across expert-parallel load balancing, sequential recommendation, and protein fitness extrapolation, PACEvolve++ outperforms the state-of-the-art evolutionary search framework with frontier models, achieving faster convergence and stabilizing test-time training during evolutionary search.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO)

DNA 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.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Density Sketches for Sampling and Estimation

We introduce Density sketches (DS): a succinct online summary of the data distribution. DS can accurately estimate point wise probability density. Interestingly, DS also provides a capability to sample unseen novel data from the underlying data distribution. Thus, analogous to popular generative models, DS allows us to succinctly replace the real-data in almost all machine learning pipelines with synthetic examples drawn from the same distribution as the original data. However, unlike generative models, which do not have any statistical guarantees, DS leads to theoretically sound asymptotically converging consistent estimators of the underlying density function. Density sketches also have many appealing properties making them ideal for large-scale distributed applications. DS construction is an online algorithm. The sketches are additive, i.e., the sum of two sketches is the sketch of the combined data. These properties allow data to be collected from distributed sources, compressed into a density sketch, efficiently transmitted in the sketch form to a central server, merged, and re-sampled into a synthetic database for modeling applications. Thus, density sketches can potentially revolutionize how we store, communicate, and distribute data.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

A One-Pass Private Sketch for Most Machine Learning Tasks

Differential privacy (DP) is a compelling privacy definition that explains the privacy-utility tradeoff via formal, provable guarantees. Inspired by recent progress toward general-purpose data release algorithms, we propose a private sketch, or small summary of the dataset, that supports a multitude of machine learning tasks including regression, classification, density estimation, near-neighbor search, and more. Our sketch consists of randomized contingency tables that are indexed with locality-sensitive hashing and constructed with an efficient one-pass algorithm. We prove competitive error bounds for DP kernel density estimation. Existing methods for DP kernel density estimation scale poorly, often exponentially slower with an increase in dimensions. In contrast, our sketch can quickly run on large, high-dimensional datasets in a single pass. Exhaustive experiments show that our generic sketch delivers a similar privacy-utility tradeoff when compared to existing DP methods at a fraction of the computation cost. We expect that our sketch will enable differential privacy in distributed, large-scale machine learning settings.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Bloom Origami Assays: Practical Group Testing

We study the problem usually referred to as group testing in the context of COVID-19. Given n samples collected from patients, how should we select and test mixtures of samples to maximize information and minimize the number of tests? Group testing is a well-studied problem with several appealing solutions, but recent biological studies impose practical constraints for COVID-19 that are incompatible with traditional methods. Furthermore, existing methods use unnecessarily restrictive solutions, which were devised for settings with more memory and compute constraints than the problem at hand. This results in poor utility. In the new setting, we obtain strong solutions for small values of n using evolutionary strategies. We then develop a new method combining Bloom filters with belief propagation to scale to larger values of n (more than 100) with good empirical results. We also present a more accurate decoding algorithm that is tailored for specific COVID-19 settings. This work demonstrates the practical gap between dedicated algorithms and well-known generic solutions. Our efforts results in a new and practical multiplex method yielding strong empirical performance without mixing more than a chosen number of patients into the same probe. Finally, we briefly discuss adaptive methods, casting them into the framework of adaptive sub-modularity.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

RAMBO: Repeated And Merged BloOm Filter for Ultra-fast Multiple Set Membership Testing (MSMT) on Large-Scale Data

Multiple Set Membership Testing (MSMT) is a well-known problem in a variety of search and query applications. Given a dataset of K different sets and a query q, it aims to find all of the sets containing the query. Trivially, an MSMT instance can be reduced to K membership testing instances, each with the same q, leading to O(K) query time with a simple array of Bloom Filters. We propose a data-structure called RAMBO (Repeated And Merged BloOm Filter) that achieves O(\sqrt{K} log K) query time in expectation with an additional worst-case memory cost factor of O(log K) beyond the array of Bloom Filters. Due to this, RAMBO is a very fast and accurate data-structure. Apart from being embarrassingly parallel, supporting cheap updates for streaming inputs, zero false-negative rate, and low false-positive rate, RAMBO beats the state-of-the-art approaches for genome indexing methods: COBS (Compact bit-sliced signature index), Sequence Bloom Trees (a Bloofi based implementation), HowDeSBT, SSBT, and document indexing methods like BitFunnel. The proposed data-structure is simply a count-min sketch type arrangement of a membership testing utility (Bloom Filter in our case). It indexes k-grams and provides an approximate membership testing based search utility. The simplicity of the algorithm and embarrassingly parallel architecture allows us to index a 170 TB genome dataset in a mere 14 hours on a cluster of 100 nodes while competing methods require weeks.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

STORM: Foundations of End-to-End Empirical Risk Minimization on the Edge

Empirical risk minimization is perhaps the most influential idea in statistical learning, with applications to nearly all scientific and technical domains in the form of regression and classification models. To analyze massive streaming datasets in distributed computing environments, practitioners increasingly prefer to deploy regression models on edge rather than in the cloud. By keeping data on edge devices, we minimize the energy, communication, and data security risk associated with the model. Although it is equally advantageous to train models at the edge, a common assumption is that the model was originally trained in the cloud, since training typically requires substantial computation and memory. To this end, we propose STORM, an online sketch for empirical risk minimization. STORM compresses a data stream into a tiny array of integer counters. This sketch is sufficient to estimate a variety of surrogate losses over the original dataset. We provide rigorous theoretical analysis and show that STORM can estimate a carefully chosen surrogate loss for the least-squares objective. In an exhaustive experimental comparison for linear regression models on real-world datasets, we find that STORM allows accurate regression models to be trained.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Sub-linear Memory Sketches for Near Neighbor Search on Streaming Data

We 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.

0 citations0 reviewsNo code linkedOpen access