Researcher profile

Ken Duffy

Ken Duffy contributes to research discovery and scholarly infrastructure.

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Published work

3 published item(s)

preprint2026arXiv

NOVA: Fundamental Limits of Knowledge Discovery Through AI

Can AI systems discover genuinely new knowledge through iterative self improvement, and if so, at what cost? We introduce the NOVA framework, which models the common ``generate, verify, accumulate, retrain'' loop as an adaptive sampling process over a knowledge space. We identify sufficient conditions under which accumulated genuine knowledge eventually covers a finite domain, and show how their violations produce distinct failure modes: contamination, forgetting, exploration failure, and acceptance failure. We then analyze imperfect verification and identify a contamination trap: as easy-to-find knowledge is exhausted, the model mass assigned to new valid artifacts shrinks, so even small false-positive rates can cause invalid artifacts to enter the knowledge base faster than genuine discoveries. We clarify that Good--Turing estimation is a local batch-diversity diagnostic, not an estimator of the historically undiscovered valid mass that governs long-term discovery. Under a separate tail-equivalence assumption relating the model's effective discovery distribution to a Zipf law with exponent $α>1$, we prove that the cumulative generation cost required to obtain $D$ distinct genuine discoveries satisfies $R_{\mathrm{cum}}(D)=Θ(c_{\mathrm{gen}}D^α)$, where $c_{\mathrm{gen}}$ is the per-candidate generation cost. This scaling law quantifies asymptotic diminishing returns as the discovery frontier advances. Finally, we formalize human amplification through guidance, generation, and verification, explaining why expert input is most valuable near autonomous exploration barriers.

preprint2021arXiv

5G NR CA-Polar Maximum Likelihood Decoding by GRAND

CA-Polar codes have been selected for all control channel communications in 5G NR, but accurate, computationally feasible decoders are still subject to development. Here we report the performance of a recently proposed class of optimally precise Maximum Likelihood (ML) decoders, GRAND, that can be used with any block-code. As published theoretical results indicate that GRAND is computationally efficient for short-length, high-rate codes and 5G CA-Polar codes are in that class, here we consider GRAND's utility for decoding them. Simulation results indicate that decoding of 5G CA-Polar codes by GRAND, and a simple soft detection variant, is a practical possibility.

preprint2021arXiv

A Coding Theory Perspective on Multiplexed Molecular Profiling of Biological Tissues

High-throughput and quantitative experimental technologies are experiencing rapid advances in the biological sciences. One important recent technique is multiplexed fluorescence in situ hybridization (mFISH), which enables the identification and localization of large numbers of individual strands of RNA within single cells. Core to that technology is a coding problem: with each RNA sequence of interest being a codeword, how to design a codebook of probes, and how to decode the resulting noisy measurements? Published work has relied on assumptions of uniformly distributed codewords and binary symmetric channels for decoding and to a lesser degree for code construction. Here we establish that both of these assumptions are inappropriate in the context of mFISH experiments and substantial decoding performance gains can be obtained by using more appropriate, less classical, assumptions. We propose a more appropriate asymmetric channel model that can be readily parameterized from data and use it to develop a maximum a posteriori (MAP) decoders. We show that false discovery rate for rare RNAs, which is the key experimental metric, is vastly improved with MAP decoders even when employed with the existing sub-optimal codebook. Using an evolutionary optimization methodology, we further show that by permuting the codebook to better align with the prior, which is an experimentally straightforward procedure, significant further improvements are possible.