Abstract Genetic Programming (GP) often uses large training sets and requires all individuals to be evaluated on all training cases during selection. Random down-sampled lexicase selection evaluates individuals on only a random subset of the training cases, allowing for more individuals to be explored with the same number of program executions. However, sampling randomly can exclude important cases from the down-sample for a number of generations, while cases that measure the same behavior (synonymous cases) may be overused. In this work, we introduce Informed Down-Sampled Lexicase Selection. This method leverages population statistics to build down-samples that contain more distinct and therefore informative training cases. Through an empirical investigation across two different GP systems (PushGP and Grammar-Guided GP), we find that informed down-sampling significantly outperforms random down-sampling on a set of contemporary program synthesis benchmark problems. Through an analysis of the created down-samples, we find that important training cases are included in the down-sample consistently across independent evolutionary runs and systems. We hypothesize that this improvement can be attributed to the ability of Informed Down-Sampled Lexicase Selection to maintain more specialist individuals over the course of evolution, while still benefiting from reduced per-evaluation costs.
more »
« less
On the Feasibility and Benefits of Extensive Evaluation
Benchmark and system parameters often have a significant impact on performance evaluation, which raises a long-lasting question about which settings we should use. This paper studies the feasibility and benefits of extensive evaluation. A full extensive evaluation, which tests all possible settings, is usually too expensive. This work investigates whether it is possible to sample a subset of the settings and, upon them, generate observations that match those from a full extensive evaluation. Towards this goal, we have explored the incremental sampling approach, which starts by measuring a small subset of random settings, builds a prediction model on these samples using the popular ANOVA approach, adds more samples if the model is not accurate enough, and terminates otherwise. To summarize our findings: 1) Enhancing a research prototype to support extensive evaluation mostly involves changing hard-coded configurations, which does not take much effort. 2) Some systems are highly predictable, which means that they can achieve accurate predictions with a low sampling rate, but some systems are less predictable. 3) We have not found a method that can consistently outperform random sampling + ANOVA. Based on these findings, we provide recommendations to improve artifact predictability and strategies for selecting parameter values during evaluation.
more »
« less
- PAR ID:
- 10611855
- Publisher / Repository:
- ACM
- Date Published:
- Journal Name:
- Proceedings of the ACM on Management of Data
- Volume:
- 2
- Issue:
- 4
- ISSN:
- 2836-6573
- Page Range / eLocation ID:
- 1 to 24
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Motivation Despite numerous RNA-seq samples available at large databases, most RNA-seq analysis tools are evaluated on a limited number of RNA-seq samples. This drives a need for methods to select a representative subset from all available RNA-seq samples to facilitate comprehensive, unbiased evaluation of bioinformatics tools. In sequence-based approaches for representative set selection (e.g. a k-mer counting approach that selects a subset based on k-mer similarities between RNA-seq samples), because of the large numbers of available RNA-seq samples and of k-mers/sequences in each sample, computing the full similarity matrix using k-mers/sequences for the entire set of RNA-seq samples in a large database (e.g. the SRA) has memory and runtime challenges; this makes direct representative set selection infeasible with limited computing resources. Results We developed a novel computational method called ‘hierarchical representative set selection’ to handle this challenge. Hierarchical representative set selection is a divide-and-conquer-like algorithm that breaks representative set selection into sub-selections and hierarchically selects representative samples through multiple levels. We demonstrate that hierarchical representative set selection can achieve summarization quality close to that of direct representative set selection, while largely reducing runtime and memory requirements of computing the full similarity matrix (up to 8.4× runtime reduction and 5.35× memory reduction for 10 000 and 12 000 samples respectively that could be practically run with direct subset selection). We show that hierarchical representative set selection substantially outperforms random sampling on the entire SRA set of RNA-seq samples, making it a practical solution to representative set selection on large databases like the SRA. Availability and implementation The code is available at https://github.com/Kingsford-Group/hierrepsetselection and https://github.com/Kingsford-Group/jellyfishsim. Supplementary information Supplementary data are available at Bioinformatics online.more » « less
-
Offline reinforcement learning (offline RL) considers problems where learning is performed using only previously collected samples and is helpful for the settings in which collecting new data is costly or risky. In model-based offline RL, the learner performs estimation (or optimization) using a model constructed according to the empirical transition frequencies. We analyze the sample complexity of vanilla model-based offline RL with dependent samples in the infinite-horizon discounted-reward setting. In our setting, the samples obey the dynamics of the Markov decision process and, consequently, may have interdependencies. Under no assumption of independent samples, we provide a high-probability, polynomial sample complexity bound for vanilla model-based off-policy evaluation that requires partial or uniform coverage. We extend this result to the off-policy optimization under uniform coverage. As a comparison to the model-based approach, we analyze the sample complexity of off-policy evaluation with vanilla importance sampling in the infinite-horizon setting. Finally, we provide an estimator that outperforms the sample-mean estimator for almost deterministic dynamics that are prevalent in reinforcement learning.more » « less
-
Chakrabarti, Amit; Swamy, Chaitanya (Ed.)We consider the problem of sampling from the ferromagnetic Potts and random-cluster models on a general family of random graphs via the Glauber dynamics for the random-cluster model. The random-cluster model is parametrized by an edge probability p ∈ (0,1) and a cluster weight q > 0. We establish that for every q ≥ 1, the random-cluster Glauber dynamics mixes in optimal Θ(nlog n) steps on n-vertex random graphs having a prescribed degree sequence with bounded average branching γ throughout the full high-temperature uniqueness regime p < p_u(q,γ). The family of random graph models we consider includes the Erdős-Rényi random graph G(n,γ/n), and so we provide the first polynomial-time sampling algorithm for the ferromagnetic Potts model on Erdős-Rényi random graphs for the full tree uniqueness regime. We accompany our results with mixing time lower bounds (exponential in the largest degree) for the Potts Glauber dynamics, in the same settings where our Θ(n log n) bounds for the random-cluster Glauber dynamics apply. This reveals a novel and significant computational advantage of random-cluster based algorithms for sampling from the Potts model at high temperatures.more » « less
-
Abstract Although ecosystems respond to global change at regional to continental scales (i.e., macroscales), model predictions of ecosystem responses often rely on data from targeted monitoring of a small proportion of sampled ecosystems within a particular geographic area. In this study, we examined how the sampling strategy used to collect data for such models influences predictive performance. We subsampled a large and spatially extensive data set to investigate how macroscale sampling strategy affects prediction of ecosystem characteristics in 6,784 lakes across a 1.8‐million‐km2area. We estimated model predictive performance for different subsets of the data set to mimic three common sampling strategies for collecting observations of ecosystem characteristics: random sampling design, stratified random sampling design, and targeted sampling. We found that sampling strategy influenced model predictive performance such that (1) stratified random sampling designs did not improve predictive performance compared to simple random sampling designs and (2) although one of the scenarios that mimicked targeted (non‐random) sampling had the poorest performing predictive models, the other targeted sampling scenarios resulted in models with similar predictive performance to that of the random sampling scenarios. Our results suggest that although potential biases in data sets from some forms of targeted sampling may limit predictive performance, compiling existing spatially extensive data sets can result in models with good predictive performance that may inform a wide range of science questions and policy goals related to global change.more » « less
An official website of the United States government

