arXiv subjects

Hongbin Ni

Publications and source records attributed to Hongbin Ni.

4 recordsLinked to original sources

arXiv2026

Reliability Limits and Decoding for Partial Nanopore Protein Rereads With Persistent State

Repeated observations of one physical object need not constitute independent channel uses. We model partial nanopore protein rereads as a finite-alphabet channel with canonical content, persistent readout, and pass-local coverage and synchronization. For exact compound-pass data, matched inference approaches the equivalence-class canonical posterior, and sitewise excess Bayes risk admits an action-aware achievable exponent. In an aligned specialization, observation-local redraw can cause linear-in-$K$ growth in true-label negative log-likelihood (NLL). We derive order-$b$ projection-stability bounds and an exact passwise-fusion diagnostic. On a PASTOR-informed semi-synthetic hard-symbol channel, label-blind deterministic-mixture importance sampling (LB-IS) agrees with exact enumeration at $L=7$. At $L=24, K=10$, LB-IS meets every prespecified aggregate absolute marginal-posterior and score-agreement criterion against a fixed high-allocation reference in three selected conditions. Joint agreement holds for the representative and high-NLL conditions, while the near-zero condition remains inconclusive. Exact $L \leq 6$ benchmarks identify order 4 as the smallest tested common cap. At target scale, the reference supports selected unprojected functionals, while neither order 4 nor 5 attains joint agreement, defining a tested finite-memory boundary. Across 16 cells, the order-4 shared branch lowers NLL by 0.033-0.224 nats per residue relative to pass-local.

cs.IT↗

arXiv2026

MC-BRIDGE: A Modular Receiver-Chain Simulation Framework for OECT-Based Molecular Communication

Organic electrochemical transistor (OECT)-based molecular communication (MC) receivers connect transport and binding to device current, noise, calibration, and detection. We present MC-BRIDGE (Molecular Communication Bioelectronic Receiver-chain Integrated Design and Guided Evaluation), a modular framework linking release, extracellular diffusion, finite-area observation, stochastic binding, and OECT transduction to charge-domain detection. On an independent electrical time grid, it generates sequence-wide multichannel colored noise, performs control-channel referencing and charge integration, and supports molecule-shift-keying (MoSK), concentration-shift-keying (CSK), and Hybrid decisions. Through common module interfaces, it estimates symbol error rate (SER) and decoded-symbol mutual information and analyzes inter-symbol interference (ISI). At nominal separation, the passive finite-area observer retains 27.5 percent of the center-point decision-charge magnitude, while correlation between the selective and control channels determines whether control referencing helps. After adaptive search, held-out records with seeds disjoint from search and calibration test the selected and next-lower budgets, yielding a tested-grid upper bound on the minimum budget meeting the SER target. This passive-field test resets receptor occupancy, excludes ISI, and calibrates thresholds on separate records at each operating point. Retaining transport and receptor memory instead produces high SER. Thus, geometry, covariance, calibration, and memory can change receiver conclusions.

cs.IT↗

arXiv2026

A Control-Referenced Tri-Channel OECT Receiver for Hybrid Molecular Communication Toward Brain Organoid Interfaces

Brain organoid interfaces that seek neuromodulator readout benefit from chemical receivers with molecular specificity and tolerance to drift. This paper presents a receiver-centric theoretical study of a control-referenced tri-channel organic electrochemical transistor (OECT) receiver with dopamine- and serotonin-selective pixels alongside a hydrogel-matched control pixel. The Ag/AgCl electrode provides the electrochemical gate reference, whereas the control pixel is used only as a matched reference for common-mode drift and other low-frequency baseline fluctuations during amplitude decisions. We couple finite-duration release, restricted diffusion with clearance, aptamer binding, OECT transduction, and correlated thermal, flicker, and drift noise, and we evaluate MoSK, CSK-4, and a 2-bit Hybrid detector on the same front-end by Monte Carlo simulation. At $r=45$ micrometers, control referencing mainly benefits the Hybrid amplitude branch, reducing Hybrid SER from $3.71\times 10^{-2}$ to $1.09\times 10^{-2}$ at $N_m=1.40\times 10^4$ molecules/symbol while barely changing the MoSK component. In calibrated no-ISI front-end benchmarks, Hybrid+CTRL reaches an LoD of 11866 molecules/symbol at 45 micrometers and remains below CSK-4+CTRL over much of the medium-to-long-distance range studied. The reported SER and LoD values are scenario-based receiver forecasts, whereas the more transferable result is the regime-dependent rule for when matched control referencing benefits Hybrid amplitude decoding.

eess.SY↗

arXiv2024

ART-Rx: A Proportional-Integral-Derivative (PID) Controlled Adaptive Real-Time Threshold Receiver for Molecular Communication

Molecular communication (MC) in microfluidic channels faces significant challenges in signal detection due to the stochastic nature of molecule propagation and dynamic, noisy environments. Conventional detection methods often struggle under varying channel conditions, leading to high bit error rates (BER) and reduced communication efficiency. This paper introduces ART-Rx, a novel Adaptive Real-Time Threshold Receiver for MC that addresses these challenges. Implemented within a conceptual system-on-chip (SoC), ART-Rx employs a Proportional-Integral-Derivative (PID) controller to dynamically adjust the detection threshold based on observed errors in real time. Comprehensive simulations using MATLAB and Smoldyn compare ART-Rx's performance against a statistically optimal detection threshold across various scenarios, including different levels of interference, concentration shift keying (CSK) levels, flow velocities, transmitter-receiver distances, diffusion coefficients, and binding rates. The results demonstrate that ART-Rx significantly outperforms conventional methods, maintaining consistently low BER and bit error probabilities (BEP) even in high-noise conditions and extreme channel environments. The system exhibits exceptional robustness to interference and shows the potential to enable higher data rates in CSK modulation. Furthermore, because ART-Rx is effectively adaptable to varying environmental conditions in microfluidic channels, it offers a computationally efficient and straightforward approach to enhance signal detection in nanoscale communication systems. This approach presents a promising control theory-based solution to improve the reliability of data transmission in practical MC systems, with potential applications in healthcare, brain-machine interfaces (BMI), and the Internet of Bio-Nano Things (IoBNT).

cs.ET↗