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An experimental study of the behavior of a high efficiency residential heat pump in cooling mode with common installation faults imposed

Faults are believed to be common in split system air-conditioner and heat pump systems, due to operating degradation or installation problems. Common faults include improper refrigerant charge, reduced evaporator airflow, liquid line restrictions, and the presence of non-condensable gas. Laboratory tests were used to quantify fault impacts on performance of a heat pump system, and impacts on indicator variables such as refrigerant temperatures and pressures. This paper describes a large set of laboratory tests implemented on a high efficiency heat pump operating in cooling mode. This system uses R-410A refrigerant and has a rotary compressor, TXV, two accumulators, and a compensator. A small number of previous experimental studies have been done previously to study the effects of some operating faults, but none has examined a modern system with these components. The tests were conducted with a range of fault intensities and driving conditions. The results are compared to previous researchers’ experimental results. The system’s performance was found to be quite robust in the presence of faults. The TXV, accumulators, and compensator significantly reduce sensitivity to refrigerant charge and liquid line restriction faults, and other faults to a lesser extent.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

ComStock Measure Documentation: Heat Pump Rooftop Units with Standard Performance

This documentation focuses on a single end-use savings shape measure - heat pump rooftop units (HP-RTUs) with standard efficiencies that are prevalent in the current market. Today, these products are claimed as standard efficiency by the manufacturers and are most commonly installed. This document will primarily discuss the additional changes of performance and configuration of the standard efficiency HP-RTUs while a comprehensive overview of the fundamental modeling methodology and background of the HP-RTU measure, including applicability, sizing scheme, and other key assumptions can be found in the original documentation: Heat Pump RTU. The definition of "standard efficiency" can be a bit vague when considering detailed specifics other than efficiency metrics of a heat pump. Thus, we have focused on reflecting products where manufacturers claim as standard efficiency and products that are not top-of-the-line in their model lineup. Based on gathering information from eight products from four major manufacturers, there are some common (or relatively prevalent) characteristics and we have defined standard efficiency product as follows: direct drive outdoor unit fan, two stages of heat pump cooling, single stage heat pump heating (i.e., all compressors running at the same time), heat pump minimum lockout temperature of 0°F (-17.8°C), backup electric resistance heating, backup heating runs at the same time as heat pump heating , heat pump heating locking out below minimum operating temperature, IEER in between 11-13, and HSPF in between 8-8.9. There are cases where some of these products have other variations: a variable frequency drive fan, dual fuel (i.e., gas backup heating) option, three or more cooling stages, two stages of heat pump heating, no backup heating as default , etc. However, this work tried to reflect the most common and prevalent options for a standard efficiency product.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

NFD Methodology Report

The NetFlow Dynamics (NFD) model was developed for estimating the availability of a commodity supplied by a national- or regional-scale infrastructure following unexpected disruption of one or more of its components. The large scope of the disruptions of interest produce changes in availability lasting days to weeks. Consequently, the model does not resolve daily variations in system state and does not include the long-term processes that cause infrastructures to evolve as assets are added and removed according to owners ’planning decisions. NFD simulates fluid flow, including petroleum and other incompressible fluids, as well as natural gas and other compressible fluids, through pipeline networks characterized by limits on transmission capacity and storage. It was designed to enable efficient exploration of possible transmission system responses to large-scale disruptions lasting for days or longer. The model formulation reflects constraints on transmission and storage capacity imposed by the physical system assets. Those capacity limits are input parameters and are not derived from more basic system properties such as pipeline diameters and compressor power. A system’s response to a large disruption is controlled by operational decisions as well as damage to physical assets. The NFD model formulation allows users to efficiently consider alternative scenarios about the way remaining capacity might be used so that the analysis result appropriately reflects uncertainties about operator response.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Operation of helium sub-atmospheric multistage cryogenic centrifugal compressor trains: Part 2 – Transient modeling and pump-down path selection

Low-pressure conditions required for operation of helium cryogenic systems below the normal boiling point (i.e. 4.2 K) are established through a transient process, commonly referred to as ‘pump-down’. This process is defined as the transition from pressures above atmospheric conditions to the saturation pressure which corresponds to a specified operational temperature. The FRIB 2 K system consists of five cryogenic centrifugal compressors which are operated in series. Historically, the pump-down process path has been established through empirical methods and system operator experience. Investigation into the pump-down process at FRIB aimed to develop a pump-down methodology which relies on theoretical model predictions rather than empirically developed process paths. Ensuring stable operation during the pump-down process involved application of a centrifugal compressor performance prediction model, which is described in Part 1 of this paper. Compressor performance maps can be directly used to evaluate the stability of a selected pump-down path and anticipate the overall reliability of the selected path. In conjunction with the compressor performance maps, a system pressure model was developed to estimate the transient pressure response during the pump-down process. Lastly, an explicit equation was developed to establish a mass flow rate profile for the pump-down process. Implementation of the presented methodology (including the developed models) allows for the system operator to determine a continuous pump-down path which maintains compressor stability while conforming to overall system capabilities. Altogether, the methodology presented has resulted in simplification of transient pump-down operations and increased the reliability, stability and efficiency of the pump-down process.

Compressor train control↗

Efficient turbine engine using integrated ammonia fuel processing

A gas turbine engine includes a core engine that includes a core flow path where air is compressed in a compressor section, communicated to a combustor section, mixed with an ammonia based fuel and ignited to generate a high energy combusted gas flow that is expanded through a turbine section. The turbine section is mechanically coupled to drive the compressor section. An ammonia flow path communicates an ammonia flow to the combustor section. A cracking device is disposed in the ammonia flow path. The cracking device is configured to decompose the ammonia flow into a fuel flow containing hydrogen (H2). At least one heat exchanger is upstream of the cracking device that provides thermal communication between the ammonia flow and a working fluid flow such that the ammonia fluid flow accepts thermal energy from the working fluid flow.

Smith, Lance L.↗

U.S. Industrial and Commercial Motor System Market Assessment Report Volume 1: Characteristics of the Installed Base

Motor systems are an integral part of our industrial and commercial facilities. They provide the motive force behind the fans, pumps, compressors, chillers, and conveyors in these facilities. Given their centrality to any facility’s operations, they are a critical energy end use to understand, particularly when developing technologies and policies to meet sustainability goals, improve productivity, and enhance resilience. In the late 1990s, the U.S. Department of Energy (DOE) conducted two seminal studies to better understand the installed stock and energy savings opportunities of industrial and commercial motor systems. In the industrial sector, The United States Industrial Electric Motor Systems Market Opportunities Assessment used primary data collected through onsite assessments and led to a greater understanding of the installed base of motor systems, their characteristics, and the opportunities for energy savings (U.S. Department of Energy, 2002). Notable findings included the following: Industrial motor systems consumed 679 billion kilowatt-hours (kWh) in 1994, representing 23 percent of U.S. electricity consumption. Cost-effective energy efficiency measures could result in 62-104 billion kWh of energy savings annually. Sixty-two percent of the energy savings potential was from fan, pump, and compressor end use equipment. Nearly half of motor system electricity consumption was attributable to approximately 3,500 facilities, or 1.5 percent of U.S. manufacturing facilities. Opportunities for Energy Savings in the Residential and Commercial Sectors with High Efficiency Electric Motors provided an evaluation of the installed stock of motor driven equipment in U.S. commercial and residential buildings and opportunities for utilization of high efficiency motors and variable speed technologies (Arthur D. Little, 1999). Notable findings included the following: Commercial motor systems consumed 343 billion kWh in 1995, with refrigeration and space conditioning constituting 93 percent of the total. Cost-effective energy efficiency measures could result in 51 billion kWh of energy savings annually. Due in no small part to these seminal studies, motor system technologies and usage characteristics have changed drastically since the late 1990s. Greater awareness of cost-effective strategies for reducing motor system electricity consumption have been developed and deployed. This includes several software tools, literature, and utility and government programs promoting energy efficiency improvements in motor driven systems. Additionally, several rounds of energy efficiency standards have been enacted, resulting in improved installed motor efficiency. The cost of variable speed drives has dropped substantially, and combined with utility rebate programs, has led to their greater adoption. Further, since these results were published, the U.S. manufacturing sector has undergone a massive transformation. Due to global competition, some sectors have relocated operations overseas. Others have brought operations onshore to avail low cost and abundant natural gas. Additionally, automation and robotics have pervaded the entire sector. Consequently, these two reports likely do not represent the current state of motor driven systems in U.S. industrial and commercial facilities. As cited in recent studies, the lack of current information on motor system electricity consumption and use characteristics limits the ability to conduct analysis on energy savings potential, develop technologies to address energy and productivity gaps, and develop programs to promote energy efficiency practices and technologies for motor systems (International Energy Agency, 2007; UNIDO, 2010; McKane and Hasanbeigi, 2011; Waide and Brunner, 2011). Specifically, the lack of information affects a range of stakeholders: Governments must rely on outdated information when setting research agendas, developing policies, and designing energy efficiency programs and offerings. Utilities and energy efficiency programs cannot identify the current market needs or potential impact when designing rebate and energy efficiency programs. Electric grid planners cannot identify motor system usage characteristics when developing plans to support the resilience of the electric grid. Manufacturers of motors, motor driven equipment, and drives are hampered when developing technologies to meet the needs of their market. Motor system end users are limited in their ability to identify energy saving opportunities within their own facilities because they do not have reliable benchmark information. In response to the lack of current information and analysis on industrial and commercial motor systems, the DOE initiated an update to these two studies. Launched in 2016 and led by Lawrence Berkeley National Laboratory (LBNL), the Motor System Market Assessment (MSMA) provides an updated, more comprehensive assessment of the installed stock of motor systems in both the industrial and commercial sectors, a review of the supply chains supporting motor and drives in the U.S., and the performance improvement opportunity available from using best available technologies and maintenance and operation practices. The outcomes of the MSMA are documented in three U.S. Industrial and Commercial Motor System Market Assessment reports, with this report being the first listed: 1. Volume 1: Characteristics of the Installed Base (this report) documents the findings on the installed base of motor systems in the U.S. industrial and commercial sectors. Quantification of energy savings potential is not documented in this report but in Volume 3. 2. Volume 2: Motors and Drives Supply Chain Review reviews the state of supply chains for motors and drives installed in U.S. industrial and commercial facilities, focusing on advanced motor and drive technologies and their constituent materials. 3. Volume 3: Energy Savings Opportunity analyzes the energy performance improvement opportunity for the installed base of U.S. industrial and commercial motor systems. This report has been prepared as a reference for motor system stakeholders. It provides factual information as could be best determined by the assessment results and avoids speculating on any findings.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

waveSZ: A Hardware-Algorithm Co-Design of Efficient Lossy Compression for Scientific Data

Error-bounded lossy compression is critical to the success of extreme-scale scientific research because of ever-increasing volumes of data produced by today's high-performance computing (HPC) applications. Not only can error-controlled lossy compressors significantly reduce the I/O and storage burden but they can retain high data fidelity for post analysis. Existing state-of-the-art lossy compressors, however, generally suffer from relatively low compression and decompression throughput (up to hundreds of megabytes per second on a single CPU core), which considerably restrict the adoption of lossy compression by many HPC applications especially those with a fairly high data production rate. In this paper, we propose a highly efficient lossy compression approach based on field programmable gate arrays (FPGAs) under the state-of-the-art lossy compression model SZ. Our contributions are fourfold. (1) We adopt a wavefront memory layout to alleviate the data dependency during the prediction for higher-dimensional predictors, such as the Lorenzo predictor. (2) We propose a co-design framework named WAVESZ based on the wavefront memory layout and the characteristics of SZ algorithm and carefully implement it by using high-level synthesis. (3) We propose a hardware-algorithm co-optimization method to improve the performance. (4) We evaluate our proposed WAVESZ on three real-world HPC simulation datasets from the Scientific Data Reduction Benchmarks and compare it with other state-of-the-art methods on both CPUs and FPGAs. Experiments show that our WAVESZ can improve SZ's compression throughput by 6.9x similar to 8.7x over the production version running on a state-of-the-art CPU and improve the compression ratio and throughput by 2.1x and 5.8x on average, respectively, respectively, compared with the state-of-the-art FPGA design.

Compression Ratio↗

Hybrid Electrochemical Hydrogen/Metal Hydride Compressor (Final Technical Report)

Various alternatives to traditional mechanical compressor systems have been considered, including MHC and EHC. Both MHCs and EHCs are solid-state systems that have no moving parts other than valves. Both are quiet and have low maintenance requirements. However, strength and material issues as well as water and heat management issues have challenged EHCs, especially, when operated at very high pressures. Similarly, low efficiency, especially, when staging is required to attain high, pressure ratios, has challenged MHCs and has made them too complex and expensive. Material degradation, due to hydrogen impurity effects, has also created issues for MHCs. One novel alternative evaluated here is to combine EHC and MHC technologies in a way to maximize their advantages and to minimize each of their challenges to improve the overall systems performance on a path to meet or exceed current DOE targets. A hybrid EH/MH compressor takes advantage of lower maintenance and operating costs as well as increased reliability associated with both the MHC and EHC technologies over traditional mechanical compressors. Neither the MHC nor the EHC have any moving parts other than valves. The hybrid system also takes advantage of the higher efficiency and lower cost of the EHC by operating at lower delivery pressures combined with the robust and simple operation of a single-stage, MH compressor at higher pressures. Both MHC and EHC technologies are scalable and can be used for a variety of hydrogen compression and delivery applications.

08 HYDROGEN↗

Energy efficiency of blower heater non-purge compressed air dryers

This research focuses on twin tower regenerative closed loop desiccant dryers, specifically: blower heater non-purge (BHNP) with and without cooling water pumps, compressed-air heater purge (CHP), blower heater purge (BHP) and pressure swing heaterless (PSH). The research was conducted by collecting and analysing real time current draw data on air compressors and associated dryers at eight different facilities (13 air compressors) in terms of energy, power and cost. A decision tool was developed to depict the operational characteristics (power, energy and cost) of each type of dryer if used in conjunction with the selected compressor system. Finally, this research, on an equivalent normalised basis, compared and contrasted the different types of dryers in terms of performance and cost. Here, the research concluded that of the five types of desiccant dryer types observed the most energy efficient was the BHNP (with cooling water pump), subject to the operational conditions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Eureka: Enabling Fine-Grained Access and Range Queries on Compressed Scientific Data via Data-Index Co-Compression

Handling large-scale scientific data in high-performance computing (HPC) environments poses significant challenges, including excessive I/O, high storage costs, and slow query performance. Traditional approaches often require full data decompression and scans, making them impractical for real-time or interactive analysis. To address these limitations, we introduce Eureka, a unified data-index co-compression framework that enables fine-grained access and efficient range queries on compressed scientific datasets. Eureka integrates spatial domain decomposition with block-wise error-bounded lossy compression to support selective decompression. It constructs a hierarchical AVL-tree index during compression to capture block-level value ranges, enabling fast pruning during query execution. To reduce metadata overhead, the index itself is also compressed while ensuring recall-preserving results. Experiments on six diverse HPC simulation datasets show that Eureka achieves up to 25x data compression and over 300x index compression, surpassing state-of-the-art compressors such as SZ3 and ZFP in rate-distortion performance. Additionally, Eureka delivers over 30x speedup for low-selectivity range queries, making it a scalable and efficient solution for modern scientific data analysis.

Yan, Ning↗

Modeling Assessment of Residential Air-to-Water Heat Pumps Coupled with Cooling Thermal Storage

This study explored the performance and operating cost viability of air-to-water heat pumps (AWHPs) coupled with thermal energy storage (TES) in efficient new residential construction. AWHPs are an emerging technology in this country, but offer promise in terms of high efficiency, fully contained and factory charged outdoor refrigeration system, and hydronic delivery capabilities, which facilitates zoning, ducts in conditioned space, and TES integration for summer load-shifting. Although this AWHP+TES strategy is not yet mainstream, the authors feel that in ten years as decarbonization efforts proceed and TOU rates become more common, strategies such as this will be more accessible. Validated EnergyPlus simulation models were developed based on detailed monitoring data collected over several years at Pacific Gas and Electric's CVRH laboratory test homes located in Stockton, California. One of the CVRH test homes (1,962 ft 2 two-story) had been testing various AWHP systems and configurations over the past six years. The validated model was then updated with high efficiency IECC ZERH envelope and component requirements for climate zones 1-5, including ducts in conditioned space thermal distribution. Simulations were completed for the 1,962 ft 2 home in each climate zone for a minimum efficiency ASHP, an AWHP coupled with a fan coil, and an AWHP coupled with TES sized to eliminate summer on-peak compressor operation. To maintain consistency in reporting energy use estimates, all cases were run with a similar indoor thermostat control strategy to pre-cool the house below the nominal 76 degrees Fahrenheit set point prior to the on-peak period and float slightly above the set point during the peak period. The AWHP+TES configuration was controlled to alternately condition the indoor space or to charge the TES tanks prior to the beginning of the on-peak. Three composite TOU rates were developed based on existing TOU rates across the U.S. to provide differing economic scenarios to evaluate customer bill impacts throughout the summer. Two of the TOU rates had short three-hour peak periods, while the third rate had a longer seven-hour duration peak period. AWHP modeling projections were based on the observed field performance of the Chiltrix CX34 variable speed unit. Other products on the market or entering the market in the near term would likely perform differently.

25 ENERGY STORAGE↗

Advanced blade-shaped thermal energy storage device: Development and application

Thermal energy storage (TES) using phase change materials (PCMs) is a promising approach for capturing and reusing excess thermal energy, yet widespread adoption is limited by low thermal conductivity, bulky configurations, and inadequate scalability. Here, this study presents a modular, blade-shaped TES prototype designed to address these challenges. The device integrates a lightweight aluminum shell, an embedded serpentine coil for active or passive heat exchange, and a cost-effective corrugated metal mesh for enhanced PCM thermal conductivity. With thickness-to-length and thickness-to-width ratios of 0.03 and 0.08, respectively, the blade-shaped TES achieves a compact, modular form factor suitable for space-constrained applications. Experimental testing demonstrated the efficient charge and discharge behavior of blade-shaped TES, capturing PCM superheating, phase-change transitions, and subcooling dynamics, with charging and discharging efficiencies of 94.9% and 94.6%, respectively. Also, the system can potentially achieve higher energy density than that of conventional TES designs. When integrated into a household refrigerator during the study, three blade-shaped TES modules successfully shifted 100% of peak-time compressor operation to off-peak hours, reducing energy consumption while maintaining more stable compartment temperatures. The blade-shaped TES's thin geometry, modularity, and enhanced thermal performance support scalable deployment across residential, commercial, and industrial applications, providing a versatile, cost-effective solution for high-efficiency, demand-flexible thermal energy management.

Blade-shaped↗

DICE-gas turbine compound reheat combined cycle

Coal-fired Direct Injection Carbon Engine – Gas Turbine (DICE-GT) Compound-Reheat Combined Cycle (CRCC), is a combined cycle power plant comprising a multiplicity of coal-fired reciprocating internal combustion engines (RICE), which is commonly referred to by the acronym DICE (Direct Injection Carbon Engine); a natural gas-fired gas turbine (turbine and combustor); a heat recovery steam generator (HRSG); a steam turbine generator; and an integrally geared and intercooled centrifugal air compressor. Finally, the concept uses coal-water slurry/fluid in the DICE and natural gas (or hydrogen) in the gas turbine for unmatched efficiency (well above 50% net LHV) and modularity (block sizes of 120, 240 and 360 MW) with easy adaptability to carbon capture and sequestration with minimal additional cost, complexity and performance hit.

42 ENGINEERING↗

Soft Matter Thermal and Mechnical Devices

The participant company, Treau, makes homes and buildings more comfortable with quiet, energy efficient, and easy to install heating and cooling systems. They entered the Cyclotron Road program with an idea for a heat exchanger and compressor and a general idea that the building heating and cooling sector was the best first target market. While at Cyclotron Road, they used the Cyclotron Road program staff and Berkeley Lab expertise to better understand the needs of the heating and cooling equipment market. This was critical to understand who the end customer was, and what features were needed in this market. They were then able to conduct product development with this target market/customer in mind. The Cyclotron Road program was also critical in building a manufacturing and scale-up plan that allowed the participant to build a credible growth and fundraising strategy. By the end of the program, the participant had a working prototype testing at Berkeley Lab’s HVAC testing facilities.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Development and field demonstration of residential air source integrated heat pump using a three-stage compressor

To promote decarbonization and all electrification at residential sectors, it is necessary to use air source heat pumps (ASHPs) to replace natural gas for space heating and water heating. ASHPs are widely utilized for residential space cooling, heating, and water heating due to their simplicity and cost-effectiveness. However, their performance can be compromised in cold climates, where they may experience reduced heating capacity. A multi-functional heat pump, using a single compressor, to meet all home space conditioning and water heating demands, is an emerging technology. To address this limitation, we have developed and demonstrated an air source integrated heat pump to fulfill comprehensive home comfort requirements. This system employs a three-stage compressor and a single set of heat exchangers and valves, optimizing functionality while minimizing costs. The performance of the developed system was rigorously evaluated in both laboratory and field settings. In laboratory conditions, the system achieved a Seasonal Energy Efficiency Ratio of 17.0 (average COP of 4.98) and a Heating Seasonal Performance Factor of 11.0 (3.22). Additionally, in its most efficient operational mode—combining space cooling and water heating—the unit attained a total energy efficiency exceeding 7.0 seasonal COP in the field and could heat a 189-liter tank of water in just 25 min. The field study corroborated the laboratory findings, validating the system’s performance in real-world conditions. Here, this integrated heat pump represents an ideal solution for decarbonizing homes in northern climates by providing efficient space heating and water heating, thereby replacing the need for natural gas.

Integrated heat pump↗

Micro-Environmental Control System (Final Report)

This project developed an innovative micro-environmental control system (µX) that enables office buildings to reduce energy used for heating and cooling by 15% or more. The µX is a compact, quiet, and ergonomic device that is designed to be installed under an office workstation; it is designed to maintain occupant comfort when room thermostat setpoints are incremented by 4°F or more (warmer in the summer and cooler in the winter) to save energy. When ambient room temperatures are outside of the usual comfort range, the µX maintains occupant comfort by delivering personalized cooling or heating locally to each office worker. The µX provides personalized cooling using a micro vapor compression system that includes a new high-performance micro-scroll compressor and a novel thermal storage unit. The vapor compression system operates at night to freeze a phase-change material (PCM). During the workday, the cooling stored in the PCM is released as a cool breeze of air to make occupants more comfortable. The micro-scroll compressor was developed specifically for this application; it is smaller than any of its type, minimizing the amount of power needed. In heating mode, the µX maintains occupant comfort using a foot heating mat with an infrared reflective box. The µX R&D project was conducted by Syracuse University in collaboration with United Technologies Research Center, Air Innovations, Bush Technical, and Cornell University. Over the course of the initial three-year project, the team developed and evaluated four versions of the unit, advancing the concept to Technology Readiness Level 6. The capabilities of individual proof-of-concept prototypes were verified in tests that were conducted with: 1) units in psychrometric chambers, 2) an instrumented manikin in a laboratory, and 3) human subjects in laboratories that simulate office environments. The tests verified that the µX prototypes met or exceeded all performance targets required to enable office buildings to reduce energy used for heating and cooling by 15% or more by maintaining occupant comfort when thermostat setpoints are incremented by 4°F or more.

25 ENERGY STORAGE↗

NUMERICAL PREDICTIONS OF MEAN PERFORMANCE AND DYNAMIC BEHAVIOR OF A 10 MWe SCO2 COMPRESSOR WITH TEST DATA VALIDATION

High-fidelity aerodynamic analysis has been demonstrated for mean performance and unsteady dynamics in a sCO2 compressor designed by Hanwha Power Systems Americas for a 10 MWe Concentrating Solar Power plant. Simulations were performed with CRUNCH CFD® software tool that was matured to accurately model near critical real fluid effects in sCO2. Pre-test predictions for mean performance were validated with test data collected later. Performance predictions were accurate and captured sensitivity of the efficiency to inlet temperature of CO2 as well as steep drop-off at high flow rates due to condensation in the inlet throat. Detailed analysis was performed to understand the source of these performance losses at near critical conditions. Unsteady dynamic effects in the compressor at off-design conditions were also identified and quantified. In particular a system wide “condensation surge” condition was detected at high flow coefficients that results in large amplitude pulsations with accompanying mass flow fluctuations at low frequencies and has potential to cause damage in closed loop systems.

hosangadi, ashvin↗

Efficient DNA sequence compression with neural networks

Abstract Background The increasing production of genomic data has led to an intensified need for models that can cope efficiently with the lossless compression of DNA sequences. Important applications include long-term storage and compression-based data analysis. In the literature, only a few recent articles propose the use of neural networks for DNA sequence compression. However, they fall short when compared with specific DNA compression tools, such as GeCo2. This limitation is due to the absence of models specifically designed for DNA sequences. In this work, we combine the power of neural networks with specific DNA models. For this purpose, we created GeCo3, a new genomic sequence compressor that uses neural networks for mixing multiple context and substitution-tolerant context models. Findings We benchmark GeCo3 as a reference-free DNA compressor in 5 datasets, including a balanced and comprehensive dataset of DNA sequences, the Y-chromosome and human mitogenome, 2 compilations of archaeal and virus genomes, 4 whole genomes, and 2 collections of FASTQ data of a human virome and ancient DNA. GeCo3 achieves a solid improvement in compression over the previous version (GeCo2) of $2.4\%$, $7.1\%$, $6.1\%$, $5.8\%$, and $6.0\%$, respectively. To test its performance as a reference-based DNA compressor, we benchmark GeCo3 in 4 datasets constituted by the pairwise compression of the chromosomes of the genomes of several primates. GeCo3 improves the compression in $12.4\%$, $11.7\%$, $10.8\%$, and $10.1\%$ over the state of the art. The cost of this compression improvement is some additional computational time (1.7–3 times slower than GeCo2). The RAM use is constant, and the tool scales efficiently, independently of the sequence size. Overall, these values outperform the state of the art. Conclusions GeCo3 is a genomic sequence compressor with a neural network mixing approach that provides additional gains over top specific genomic compressors. The proposed mixing method is portable, requiring only the probabilities of the models as inputs, providing easy adaptation to other data compressors or compression-based data analysis tools. GeCo3 is released under GPLv3 and is available for free download at https://github.com/cobilab/geco3.

Silva, Milton↗