Simultaneous Speech Translation (SimulST) requires balancing translation quality and latency. While Large Language Models (LLMs) excel in offline translation, current LLM-based SimulST systems predominantly rely on prefix-incremental generation. This paradigm suffers from redundant Key-Value cache recomputation and necessitates external Voice Activity Detection to process unbounded streams. To overcome these bottlenecks, we propose an end-to-end interleaved read-write framework built upon an omni-modal LLM. By interleaving speech chunks and text tokens, our architecture achieves full KV cache reuse, natively supporting segmentation-free, infinite-length inference. Furthermore, to learn optimal streaming policies without rigid offline alignments, we introduce a novel Actor-Critic self-enhancement pipeline. An RNN-T Actor dynamically samples read-write trajectories, while an LLM-based Critic evaluates these paths via intrinsic semantic and latency rewards, distilling the optimal policy back to the Actor. Extensive experiments on sentence-level (FLEURS, CoVoST2) and document-level (MuST-C, ACL 60/60) benchmarks demonstrate that our model establishes new state-of-the-art quality-latency Pareto frontiers, substantially outperforming existing cascaded and static-alignment baselines.
https://arxiv.org/abs/2611.06501
Myoelectric Control Systems (MCSs) enable voluntary control of wearable robots through muscle activity. However, intention decoding, assistance shaping, and low-level actuator control are often not explicitly distinguished, making their contributions difficult to evaluate and compare. This review introduces a functional decoder-shaper-controller framework for continuous myoelectric control of upper-limb exoskeletons. The decoder estimates an intention-related variable from surface electromyography (sEMG), the shaper maps it to a control reference according to an assistance policy, and the controller realizes that reference through actuator control. This decomposition separates intention estimation from assistance-policy design and enables comparison of heterogeneous architectures. Representative approaches are critically examined in terms of module design, calibration, and evaluation. The analysis highlights that the shaper, despite determining the magnitude and shape of assistance, lacks established design and tuning methodologies and is often embedded within the decoder or controller. Key open issues include inconsistent reporting of assistance levels, limited use of interaction-aware stability and passivity tools, and insufficient validation across degrees of freedom, users, and tasks. Building on these findings, this review provides design guidelines for systematic module-wise tuning and identifies future research priorities to bridge the gap between accurate intention decoding and safe, effective, and generalizable assistance under real-world operating conditions.
https://arxiv.org/abs/2611.03418
Improvement in enzyme engineering is usually pursued by optimising which candidates to assay within a fixed model and workflow; when the bottleneck arises from a mismatched method or a failing workflow, that route is difficult to escape. We present EnzymeRSI, a dual-loop system for recursive self-improvement (RSI). The outer loop evolves harness assets without changing model weights, the inner loop develops prediction and selection algorithms under controlled conditions, and a cloud laboratory system is specified to close the physical loop with quality-controlled feedback. By updating its prediction strategy through iterative comparison, the outer loop raised the mean development-set Spearman correlation on ProteinGym by 0.044 across five assays, reaching 0.335 on CD19 and 0.683 on OPSD (rhodopsin); of the two first places, only CD19 was produced by the outer loop itself. In the self-improvement of the ThermoMPNN algorithm the inner loop reached a PCC of 0.849, and on TadA-Bench it reached a Spearman correlation of 0.307 in 1.13 h. In three prospective wet-lab tests of the system's experimental decision-making, 10 of the 32 candidates that had not been pre-specified for the luciferase RLuc showed at least twice the wild-type activity; a recommended variant of the cytidine deaminase A3A raised 5mC conversion to 90.2%; and path selection in evolution raised the catalytic efficiency of the DNA polymerase KOD-E on a modified substrate to 31.1 times that of the parent. By treating the organisation of the research workflow and the development of algorithms as a single falsifiable dry-to-wet loop, this work offers an evolutionary paradigm for moving beyond the blind spots of a fixed method and for autonomous enzyme engineering.
https://arxiv.org/abs/2611.06321
Ambient sensors offer a privacy-preserving solution for activity recognition in smart homes, yet they face a critical challenge in multi-resident environments known as Data Association, which aims to identify the resident triggering a specific anonymous sensor event. Existing approaches fundamentally fail to maintain global consistency by often yielding conflicting associations for silent residents. Additionally, these methods frequently suffer from severe trajectory fragmentation caused by the ontological mismatch of applying continuous physical motion models to discrete logical behaviors. To address these limitations, we propose a novel framework that reformulates data association as a sequential decision-making task within a Markov Decision Process (MDP). We solve the defined MDP via Behavior Cloning (BC) to avoid complex reward engineering by directly learning from expert demonstrations. We instantiate the policy using two complementary architectures, including a lightweight Transformer that treats association as a multi-label classification task over linearized event histories, and a fine-tuned Large Language Model (LLM) that reformulates the problem as conditional text generation to leverage pre-trained semantic knowledge. Extensive evaluations on three diverse datasets demonstrate that our approach significantly outperforms state-of-the-art baselines, particularly in resolving concurrent multi-resident events. Furthermore, the LLM-based policy shows preliminary cross-environment transfer potential under benchmark settings, while its robustness in real deployments still requires further validation.
https://arxiv.org/abs/2611.06296
A central challenge in AI is specifying objectives that align with human preferences. While existing theoretical results elucidate how misspecification impacts performance, they typically do not distinguish between merely suboptimal and catastrophic outcomes. To enable rigorous analysis of catastrophic risk from AI misalignment, we introduce a formal definition of catastrophic performance. Our definition is based on two reference values. The first, baseline value, captures the value attained if no agent is deployed. The second, orthogonal value, captures the value of a trajectory that is unrelated to human preferences, in a sense we describe. Orthogonal value is typically far worse than baseline value. We interpret these reference values through examples in which past human activity has altered the state of the environment to human benefit. Starting at the resulting state, an AI agent is deployed with the goal of accelerating further progress. Catastrophic performance represents this agent's undoing of benefits afforded by human activity.
https://arxiv.org/abs/2611.06219
Electroencephalography (EEG) measures brain activity through recording electrical potentials of the scalp. EEG recordings capture two distinct sets of characteristics in the signal: (1) \emph{Traits} -- information that remains relatively constant over the course of a recording session, such as subject identity, age, and sex; (2) \emph{States} -- signatures that encode responses to external stimuli, including visual, auditory, and motor information. There is limited understanding of how different EEG modeling features (signal processing and foundation models) encode state and trait characteristics. In this work, we quantify state- and trait-level features captured by EEG embeddings using a hierarchy metric and kNN purity on Brain-Computer Interface dataset trials, and find that a majority of EEG features form a macro-trait hierarchy (embeddings form trait-level clusters with micro-states within). Our linear probe results indicate that this hierarchy structure leads to suboptimal state distinguishability, negatively impacting BCI performance of EEG foundation models. To mitigate this, we explore normalization techniques that reduce trait-specific information in embeddings and provide a $\sim$ 10\% improvement in balanced accuracy for state classification. Additionally, we observe that when fine-tuning models for downstream state decoding, embedding spaces transform from macro-trait to macro-state hierarchies, which in turn lead to better state decoding.
https://arxiv.org/abs/2611.05652
Relevance propagation, which redistributes a network's prediction backward through the layers, is usually treated as a heuristic. We show that it is the solution of a single variational problem: Layer-wise Relevance Propagation (LRP) is the divergence-free flow on the active computational graph of zero relative entropy to the backward transition law of the forward activation flow; for a non-negative reference, this is a relative entropy between Markov measures on backward paths. The rules LRP$_0$, LRP$_{z^+}$ and LRP$_{\alpha,\beta}$ follow from this principle by the choice of a reference, and are instances of one rule, LRPN$_{\alpha,\beta}$, whose weights may vary from node to node, for instance with the node's activity, in the spirit of Hebb's principle. The principle rests on a measure-theoretic formalization of feed-forward networks as directed acyclic graphs of Filippov operators, which covers piecewise-smooth and discontinuous architectures (e.g. hard-routed Mixture-of-Experts) with a Clarke-Filippov generalized-gradient calculus; it also characterizes backpropagation as the adjoint equation of a Lagrangian relaxation. On networks of ReLU and max-pooling nodes, LRP$_0$ is Gradient$\times$Input, with an explicit jump across a kink where LRP$_{z^+}$ stays continuous. Taking the entropy edge by edge yields a new rule, Sinkhorn Relevance Propagation. Aggregated over an input region, the flow of a non-negative reference tells, with exact accounting, which hidden units carry its evidence, the conditioned flow being a Schrödinger bridge. On VGG-16, the conservation identities hold to round-off, and the rules are told apart by the sign of their maps, the share of the output left to the bias nodes, faithfulness, localization and class dependence; on ConvNeXt-Tiny, LRPN$_{\alpha,\beta}$ conserves the output and its Hebbian weights give the highest ABPC of the rules tested.
https://arxiv.org/abs/2611.05594
Acoustic indices are widely used as rapid proxies for biodiversity, but they summarise the distribution of sound energy rather than the species producing it and often track richness poorly. We revise and test an Acoustic Biodiversity Index (ABI) built from species-level detections. Its primary form, ABI_E, is Shannon diversity of detections normalised by the regional species pool expected at the site and season (H / ln S_ref); temporal stability T is reported as a separate component. We first benchmarked four classifiers on a strongly labelled tropical dataset (1,216 calls, 24 classes) with recording-grouped cross-validation. BirdNET embeddings + logistic regression performed best (macro-F1 0.750 +/- 0.029), and random frame-level splits inflated accuracy from 0.41 to 0.70. We then applied BirdNET v2.4 with a location and season filter to recordings from a riverine savanna in the Zambezi Valley, Zimbabwe, and from three habitats at Emirates Park Zoo and Resort, Abu Dhabi, United Arab Emirates. A stricter post-hoc location filter removed 517 high-confidence detections of 9 implausible species, all at the zoo. After diel-matched rarefaction to equal effort (6 h), the savanna site held 21 species (Hill number 1D = 9.83; ABI_E = 0.38) against 1.3-13 species (ABI_E = 0.03-0.21) at the zoo sites. Across 149 recorded hours, ABI_E correlated strongly with richness (Spearman rho = 0.93), whereas six standard indices did not (best: ACI, rho = 0.48). The stability term was lower at the savanna site (0.39) than at the zoo (0.65-0.67), showing that it penalises the natural diel cycle of bird activity. Species-level indices with explicit false-positive control, a declared regional reference pool and effort standardisation provide a more interpretable biodiversity indicator than energy-based acoustic indices.
https://arxiv.org/abs/2610.42042
Wearable force-augmentation technologies, including exoskeletons and soft exosuits, are being developed for occupational and rehabilitation settings to enhance performance by reducing the muscular demands of movements. Yet enhanced performance also requires users to perceive the environment accurately, adapt to changing conditions, and decide whether actions are worth their physical cost. We used an elbow-assisting exosuit to investigate the physiological, perceptual and cognitive consequences of force augmentation during lifting. We assessed weight perception, adaptation in a volatile environment, and effort-based decision-making with and without assistance. While assistance reduced muscle activity, its behavioural outcomes did not simply reflect this biomechanical change. Assistance reduced perceived weight, but this effect was strongly shaped by participants' initial experience. Assistance also selectively reduced adaptation to changing environmental contingencies. Finally, reducing the muscular demands of lifting did not translate straightforwardly into how demanding the action felt or whether participants chose to perform it: differences in effort-based decisions were shaped by initial experience rather than simply tracking reductions in muscle activity or perceived fatigue. Together, we show that the perceptual and cognitive consequences of force augmentation cannot be inferred from its biomechanical benefits alone. Effective augmentation therefore requires perceptual and cognitive outcomes to be evaluated alongside physical performance.
https://arxiv.org/abs/2610.41679
In continuous spiking keyword spotting, temporally correlated acoustic frames can repeatedly trigger memory access and neural computation at a dense input interface, even when hidden activity is sparse. Predictive processing and sensory adaptation suggest retaining predictable input locally and responding selectively to deviations. Inspired by this mechanism, we propose Predictive Signed-Dyadic Coding (PG). PG maintains a local prediction for each input channel and transmits an event only when the residual exceeds a learned threshold. Each event carries a sign and a finite power-of-two magnitude, and the receiver reconstructs it with fixed-point shifts and additions. In Mandarin keyword spotting, INPUT-PG reaches 90.00% accuracy while reducing mean SRAM reads by 33.87% and inference cycles by 32.77%. PG provides a hardware interface for research on low-power continuous speech processing and event-based sensory systems.
https://arxiv.org/abs/2610.41381
Financial AI workflows that reuse investor knowledge need persistent memory that integrates observations across sources and periods without losing identity or provenance. In a knowledge graph, recurring observations may use different surface forms, fragmenting relationship histories and preventing evidence from accumulating. We introduce Fusion and Identity Registry for Memory Evolution (FIRME), a registry-anchored memory graph that reconciles incoming observations to persistent canonical relationships and retains their source, time, and context. Within periods, rule-based fusion links investor-call discussions to portfolio cash-flow signals, directly or through a fixed product-topic ontology. Across periods, canonical identities and persistent aliases direct recurring observations to the same relationship history; deterministic updates summarize reinforcement, inactivity, and reactivation. We evaluate FIRME on proprietary investor-call and cash-flow records and on S&P 500 earnings-call transcripts. Compared with a historical registry that retains canonical identities and semantic fallback but omits alias memory, FIRME increases final-period Correct Match Rate by 7.8-12.1 percentage points across four dataset-backend settings under a fixed-judge and fallback-review protocol. A blinded human audit of 200 incoming observations per setting finds Correct Match Rate gains of 9.0-16.5 points and reattachment-recall gains of 22.5-29.0 points, with higher observed merge precision in all four samples. A separate audit finds valid evidence paths for 293 of 300 outputs from full within-period fusion in the investor-call setting. Extraction-faithfulness and round-trip diagnostics assess source grounding and preservation of extractor-derived graph content.
https://arxiv.org/abs/2610.40482
Humans and animals have a unique capacity to generalize and learn in novel circumstances, including "0-shot" inference (ZI) and continual learning (CL) -- two powerful cognitive abilities. Despite this importance, efforts to model ZI and CL are seriously limited in several ways. First, existing models typically lack components critical to ZI and CL in the brain, namely, strong inductive biases (for ZI) and autonomous control of learning (for CL). Second, models can be less tractable to analysis if model components are overly complex (lacking simplicity), or too task-restricted if model components are overly bespoke (lacking expressivity). Here we introduce autonomous Hebbian networks ("AutoHebb"), a class of online learning feedforward neural networks that realize strong inductive biases and autonomously controlled learning, and are both simple and expressive. Unlike standard models that learn via externally controlled optimization (e.g. gradient descent), AutoHebb networks combine external feedback with internally generated activity to produce a global learning signal ('neuromodulator') fed back to the network. The neuromodulator in turn gates a biologically grounded local learning rule (3-factor Hebbian rule) that updates networks' plastic weights. Using meta-learning to search for fixed (non-plastic) weights, we find that AutoHebb networks (1) succeed on ZI tasks, (2) show emergent (untrained) ZI/CL abilities, (3) admit reverse-engineering into explicit algorithms, and (4) outperform modern learning models on ZI/CL tasks. Lastly, performance comparisons to related models implied an essential role for three model components: meta-learning, Hebbian plasticity, and autonomous control of learning. These findings indicate that AutoHebb may be useful in hypothesis generation, analysis, and discovery of biologically grounded forms of learning and generalization.
https://arxiv.org/abs/2610.40757
This work develops a physics-informed multimodal deep learning framework for 10- to 110-minute-ahead probabilistic photovoltaic power forecasting. The forecasting model is built on a four-branch architecture that separately encodes plant-level temporal history and inverter-level spatial cloud dynamics through a graph attention encoder with a learned adjacency, known-future solar geometry, and the current meteorological state, fused through gated cross-attention. The geometry branch adds two forward-looking physical signals, spatial cloud heterogeneity and inverter ramp-down activity, each empirically weighted toward the horizon where it is most predictive. The decoder anchors its prediction to a smart persistence baseline, learning a horizon-conditioned correction, and the resulting quantile forecasts are calibrated online through a kernel-weighted adaptive conformal calibration step. The proposed model outperforms all 14 baselines, achieving a forecast skill score (FSS) of 0.2950, 0.099 above the next-best model. A branch-composition ablation shows that every branch contributes positively and the model retains substantial skill in challenging overcast and variable sky conditions (FSS 0.198 and 0.255).
https://arxiv.org/abs/2610.40418
Clients observing different parts of a prediction task may learn locally equivalent models with incompatible behavior outside their observed support. We study whether redundant models permit local low-loss paths toward a compatible shared model. CovFedAvg retains local models and curve controls on clients, fits a common endpoint through aggregated gradient contributions, and selects an actual candidate model using distributed training losses. No centralized calibration examples or client-to-client sample exchange are required. Exact selection guarantees no higher evaluated training loss than the previous model and the current-round FedAvg candidate; this is not a global-optimality, stationarity, generalization, or differential-privacy guarantee. We state conditional client-compatibility and approximate-selection bounds and retain corrected transformation identities and a separate full-gradient safeguard theorem for reference algorithms. A complementary input-support example recovers the shared absolute-value regression, while matched direct fine-tuning also solves it. Across a synthetic support task, recorded activity-recognition subjects, and participating and future gas-sensor batches, we evaluate five methods, five seeds, two network widths, and 20 rounds without calibration data. At width 16, CovFedAvg raises participating-Gas macro balanced accuracy from FedAvg's 88.88% to 89.84%; matched distributed fine-tuning reaches 91.65%. Results support feasibility and modest gains over FedAvg, but do not establish a curve-specific advantage over equally costly optimization. Exact-sum numerical experiments establish data flow; end-to-end privacy requires additional mechanisms and analysis.
https://arxiv.org/abs/2610.39902
The ability to predict farrowing time in pigs is crucial for optimal farm management and ensuring piglet survival. This study investigates the potential of explainable artificial intelligence for precision livestock farming, focusing on acceleration sensor data from sows around the time of farrowing. Accurately predicting farrowing allows farmers to balance both, piglet safety by avoiding piglet crushing events and the mother sow's welfare, by avoiding early crating. Traditional machine learning models often lack interpretability (``closed-box'' problem). Explainable artificial intelligence offers a solution by revealing the decision-making processes within the models. This work is split into two stages. First the detection of nest building behaviour and second the prediction of the remaining time to farrowing. The nest building detection was possible for 166 out of 180 sows and successful within 48 hours before farrowing for 149 sows. The nest building detection is purely based on the change of a sow's activity level and uses no machine learning techniques. Further, this study utilizes symbolic regression, an open-box modelling technique that generates interpretable mathematical formulas, to predict the remaining time until the onset of farrowing. The results are compared with closed-box models, like support vector regression and artificial neural networks, for both explainability and performance. Notably, symbolic regression achieved a mean absolute error of 9.28 hours for the time-to-farrowing prediction, outperforming the closed-box models in terms of performance and interpretability. This research demonstrates that explainable artificial intelligence, specifically symbolic regression, can offer both interpretable results and competitive performance in precision livestock farming.
https://arxiv.org/abs/2610.39839
Modeling human-object interaction (HOI) in real environments requires jointly representing whole-body motion, manipulated objects, and scene geometry, yet existing datasets trade off scalable capture against structured, scene-aligned supervision. We introduce SituHOI, a large-scale RGB-D dataset containing 18,429 annotated clips across 16 indoor rooms and approximately 86 hours of quality-screened activity. It pairs recordings from a single moving RGB-D camera with static scene scans, object geometry, language descriptions, and estimated human and object trajectories. Using the scans as persistent references, our pipeline combines camera localization and depth-based metric alignment with human mesh recovery, object tracking, and temporal refinement to register all geometric annotations in a shared floor-aligned frame. These data support FlexHOI-Bench, a goal-conditioned joint motion prediction benchmark with variable observation and prediction durations. Given observed histories, scene and object geometry, and a terminal object pose, models predict future human and object motion. We provide SharedHOI as a reference predictor and evaluate world-space accuracy and human-object coordination. On a MoCap subset, our pipeline reduces human G-MPJPE from 195.4 to 68.3 mm and object translation error from 43.0 to 28.7 mm. SharedHOI leads four adapted baselines on all three aggregate FlexHOI-Bench metrics. Data will be released upon acceptance. An anonymized code repository is available at this https URL.
https://arxiv.org/abs/2610.23980
Molecular discovery requires navigating vast combinatorial search spaces while balancing competing biological objectives. AI agents can automate expert-defined molecular design protocols, but automation alone does not address how to optimize workflows for new tasks or improve their development through experience. Here we introduce MoLRSI, an AI agent that combines systematic optimization of workflows and model architectures with persistent cross-task memory to recursively improve its search policy for molecular discovery. Workflow performance, refinement outcomes, and execution feedback guide subsequent searches, allowing the agent to improve both its workflows and its strategy for developing them. We evaluate MoLRSI in two challenging molecular discovery settings that require balancing competing properties. In antibiotic discovery, MoLRSI developed a screening workflow balancing antibacterial activity, cytotoxicity and structural novelty, achieving an experimental hit rate of 15.9%, compared with 8.7% for a previous expert-led workflow using the same training data and screening library. In de novo peptide-MHC binder design, MoLRSI developed workflows that jointly consider target binding and specificity, producing eight experimentally validated hits against MART-1 and SARS-CoV-1 pMHCs with preferential binding over tested off-targets while Claude Science completely failed. These findings demonstrate how experience-guided workflow optimization can address competing discovery objectives while improving the search strategies used in subsequent campaigns.
https://arxiv.org/abs/2610.39714
Computer-use agents plan on a screenshot for several seconds and then click at a position on the screen; if the page has changed in the meantime, the click lands on an unintended element. Prior work treats the planning interval as the source of this risk. Measuring planned clicks on 31 public web pages, we find that the risk lies in page loading: 0.4% of clicks planned on fully loaded pages became stale within 30 seconds, against 17% of clicks planned in the first second after a page opened. On these pages, waiting about one second for network activity to stop removes most of this risk, yet the wait rules of eight of ten widely used open-source agents leave more than 1% of clicks stale. Commercial pages keep loading for longer: in the HTTP Archive's public crawl, 15% of 65 desktop booking and buying home pages went 500 ms without network requests within 3 seconds of their HTML being parsed, against 63% of 3,028 .gov pages, and 52% shifted their layout within 6.5 seconds of a network-idle wait capped at 3 seconds, against 8% (61% against 26% among pages recorded in full). Where a check before the click is needed, as before irreversible actions and on pages that are still loading, a pixel comparison verifies the target's position as accurately as a frontier vision-language model at one eighth of the latency, and a 4B model matches the frontier model in verifying whether the previous action succeeded. We release a benchmark generator, a break-even formula for when a check pays, and three rules for agent developers: this https URL
https://arxiv.org/abs/2610.39282
Time-series forecasters are ranked almost entirely by accuracy metrics, but a forecast's decision value, its effect on the downstream decision, need not track accuracy and is rarely measured. This problem compounds as large language model (LLM) agents increasingly consume forecasters as tools, mediating them through stochastic, opaque policies. We present Vendster, an evaluation arena measuring how a forecaster's bias and prediction-interval width change the outcome of a buyer--vendor discount negotiation between two LLM agents. In the reference instance Vendster-M5, sampling base demand patterns from the M5 dataset, we evaluate two frontier-closed LLM families (Claude Opus 4.6 and GPT-5.6 Sol) and two open ones (DeepSeek-V3.2 and Qwen3-235B-A22B). Model-generated forecasts raise sales target attainment by up to +17 percentage points (p<0.001), yet standard forecast evaluation metrics such as relWQL and MASE do not predict negotiation outcomes at a statistically significant level. To isolate the causal structure, we substitute in synthetic forecasts with controlled bias and interval width. Under-prediction bias significantly improves outcomes for agents that react more to the forecasts---dose-response slopes -0.387 and -0.416 (p<0.001). Interval width has no statistically significant effect at zero bias. These findings indicate that the direction of forecast bias and agent forecast-reactivity are more strongly associated with downstream outcomes than forecast accuracy. Vendster is fully customizable and released under CC BY-NC 4.0 at this https URL.
https://arxiv.org/abs/2610.38292
Designing microbial strains for growth-coupled production, in which cellular growth is linked to the synthesis of a target compound through genetic interventions, is a fundamental goal in metabolic engineering. Constraint-based methods can identify growth-coupled deletion strategies, but design for each target typically requires a separate search across a large number of possible gene-deletion combinations. This motivates a reusable approach that learns from previously evaluated strain designs to prioritize candidate interventions before downstream constraint-based evaluation. We present a reproducible protocol for growth-coupled gene deletion design that learns and ranks gene-deletion priorities for each target metabolite. Using computationally curated deletion strategies as learning resources, the protocol generates continuous deletion-priority rankings, constructs candidate strategies at adjustable search-space budgets, and evaluates these candidates through constraint-based metabolic analysis. Its learning component, HGPRGDel, explicitly represents gene-protein-reaction (GPR) logic, capturing how multiple genes can jointly support a reaction or alternative genes can maintain its activity, while integrating molecular and reaction-level information. Across e_coli_core, iMM904, and iML1515, the protocol achieves the highest macro-F1 and AUC among the evaluated learning configurations. HGPRGDel's rankings recovered an average of 90% of the reference deletion genes from MetNetComp by examining fewer genes than the evaluated baseline methods. By separating learned intervention prioritization from downstream constraint-based assessment, the protocol provides a reproducible framework for reusing strain-design knowledge while controlling the size of the candidate space and retaining mechanistic evaluation of growth-coupled production.
https://arxiv.org/abs/2610.37478