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Record W4283740504 · doi:10.1088/2399-1984/ac7d81

Roadmap for network-based biocomputation

2022· article· en· W4283740504 on OpenAlex

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

fundA Canadian funder is recorded on the work.
no affNo Canadian affiliation: this work is invisible to an affiliation-only frame.
No Canadian affiliation. An affiliation-only frame, the usual design, would never have seen this work. It is one of the works that make the case for inverting the frame.

Bibliographic record

VenueNano Futures · 2022
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicAdvanced biosensing and bioanalysis techniques
Canadian institutionsnot available
FundersQueensland University of TechnologyVolkswagen FoundationEuropean CommissionBar-Ilan UniversityMcGill University
KeywordsScalabilityComputer scienceMassively parallelScale (ratio)Distributed computingEnergy consumptionKey (lock)Parallel computingEngineering

Abstract

fetched live from OpenAlex

Abstract Network-based biocomputation (NBC) is an alternative, parallel computation approach that can potentially solve technologically important, combinatorial problems with much lower energy consumption than electronic processors. In NBC, a combinatorial problem is encoded into a physical, nanofabricated network. The problem is solved by biological agents (such as cytoskeletal filaments driven by molecular motors) that explore all possible pathways through the network in a massively parallel and highly energy-efficient manner. Whereas there is currently a rapid development in the size and types of problems that can be solved by NBC in proof-of-principle experiments, significant challenges still need to be overcome before NBC can be scaled up to fill a technological niche and reach an industrial level of manufacturing. Here, we provide a roadmap that identifies key scientific and technological needs. Specifically, we identify technology benchmarks that need to be reached or overcome, as well as possible solutions for how to achieve this. These include methods for large-scale production of nanoscale physical networks, for dynamically changing pathways in these networks, for encoding information onto biological agents, for single-molecule readout technology, as well as the integration of each of these approaches in large-scale production. We also introduce figures of merit that help analyze the scalability of various types of NBC networks and we use these to evaluate scenarios for major technological impact of NBC. A major milestone for NBC will be to increase parallelization to a point where the technology is able to outperform the current run time of electronic processors. If this can be achieved, NBC would offer a drastic advantage in terms of orders of magnitude lower energy consumption. In addition, the fundamentally different architecture of NBC compared to conventional electronic computers may make it more advantageous to use NBC to solve certain types of problems and instances that are easy to parallelize. To achieve these objectives, the purpose of this roadmap is to identify pre-competitive research domains, enabling cooperation between industry, institutes, and universities for sharing research and development efforts and reducing development cost and time.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.343
Threshold uncertainty score0.340

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.008
GPT teacher head0.268
Teacher spread0.260 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it