Receiver-Surface Hit Patterns via Legendre Approximation for Molecular Signal Detection

Molecular communication (MC) suffers from severe diffusion memory because molecules released for one symbol may arrive during later symbols. Neural sequence detectors, especially sliding bidirectional recurrent neural networks (SBRNNs), can substantially outperform threshold detectors in such channels. This raises a central question for MC channel coding: does a code whose advantage was established under threshold detection retain it when both coded and uncoded transmission are evaluated with neural detection? This letter answers this question for run-length-limited ISI-mitigation (RLIM) codes, a class of constrained codes previously shown to provide large BER gains in MC. Across the tested operating points, the best RLIM-SBRNN receiver beats the best uncoded receiver, chosen between threshold and SBRNN detection, in $46$ of $59$ cases, with a mean gain of $10.36\times$ over those wins. We also propose an RLIM-tailored training mask for compact SBRNN detectors, improving the unmasked RLIM-SBRNN in $227$ of $236$ comparisons with $3.267\times$ mean gain when masking is beneficial. Finally, the compact masked RLIM-SBRNN is competitive with channel-state-aware MLSE despite using no channel knowledge.

In wireless communications, recovering the optimal solution to the multiple-input multiple-output (MIMO) detection problem is NP-hard. Obtaining high-quality suboptimal solutions with a favorable performance-complexity trade-off is particularly challenging in under-determined systems with $N_t$ transmit antennas and $N_r < N_t$ receive antennas. Recent diffusion-based MIMO detectors have shown promise, but they require extensive sampling iterations at inference time, and their performance degrades in under-determined scenarios. We propose GD4, a graph-based discrete denoising diffusion method for MIMO detection. Unlike existing diffusion-based detectors that operate in a continuous relaxed space, GD4 performs denoising directly in the discrete symbol space and enables fast inference with one or a few denoising evaluations. Numerical results show that, under a similar inference-time compute budget, GD4 produces higher-quality suboptimal solutions than existing diffusion-based detectors and some widely used classical baseline including box-constrained Babai point and the $K$-best box-constrained randomized Klein-Babai point in both under-determined and overdetermined settings.

Predicting tandem mass spectra (MS/MS) from molecular structures represents a central task in analytical chemistry with direct relevance to clinical metabolomics, systems biology, and adjacent disciplines. In this work, we revisit the problem through the lens of object detection on molecular graphs. Molecular fragmentation, a central step in MS/MS prediction, can be approximated as detecting a set of subgraphs (i.e., fragments) and their associated spectral contributions. Existing fragment-based models follow a two-stage paradigm -- first generating candidate fragments and then scoring them -- analogous to two-stage R-CNNs in computer vision. Towards higher accuracy and faster inference, we introduce GLACIER, a single-stage transformer-based fragment detection neural network for molecular graphs. This unified formulation eliminates the need for candidate enumeration, enabling scalable and globally consistent modeling of molecular fragmentation. GLACIER is faster and more accurate than existing state-of-the-art by a significant margin, achieving 70.0% and 69.7% Top-1 retrieval accuracy with and without contrastive finetuning on the MassSpecGym dataset (from the previous SOTA of 64.0%) and 52.5% and 38.5% respectively on the NIST'20 dataset (from 33.2%). Furthermore, GLACIER provides nearly 8-fold inference speedup over our prior two-stage model. Code is available at https://github.com/coleygroup/ms-pred