#01Nov 10, 2026
cs.LG
When Does the Real Wiring Win? Testing connectome structure-function claims against unmeasured physiology
Yeyuan Liu
Connectome-constrained models are often used to argue that a measured wiring diagram outperforms shuffled or rewired wiring, and hence that structure shapes function. Such comparisons can confound wiring with how the models are tuned: a connectome fixes who connects to whom, not the excitability, gains or plasticity rates the model also needs, and modellers often tune these until the real-wiring model works. We separate three estimands: physiology tuned on the real wiring and transferred to nulls (P1), each wiring tuned on its own (P2), and P2 restricted to physiology consistent with independent data (P3). The biases involved are known in machine learning (under-tuned baselines, inherited weights, winner's curse); we measure what they do to biological conclusions, using synthetic ground truth, placebo nulls and three Drosophila circuit models. Some claims survive every protocol we test: segregated reward and punishment dopamine improves learning, and head-direction topography is required for a persistent bump. Others do not. In the mushroom body, the real Kenyon-cell output wiring beats a cross-subtype identity shuffle by 0.09 under P1 and P2 but loses to it by 0.09 under P3 (95% CIs exclude zero; held-out runs confirm). The verdict is set by the share of alpha'beta' cells among active Kenyon cells, which P1 selects low; at the share implied by imaging (about 44%) the real-wiring model fails to learn, exposing a model inadequacy rather than a deficit of the fly's wiring. In flyvis, P1 penalises a mirrored connectome, which has a constructed solution within 0.07 (median) of the real error, more than a spatially shuffled one in 50 of 50 members; the ranking survives ten-fold longer retraining but depends on the checkpoint at fifty-fold. A credible structural claim needs matched optimisation, data-constrained physiology and a model that still works there.
#02Nov 10, 2026
cs.LG
Emergent Biological Capabilities in a Foundation Model for Molecular Interactions
Adi Mashiach
Foundation models trained on large unlabeled corpora develop emergent capabilities, tasks that go beyond the training objective. We extend this paradigm to multimodal biology with Bonbon, a foundation model for molecular interactions trained on approximately 3.2 trillion tokens of paired protein-ligand sequences. From a single representation space, Bonbon exhibits three zero-shot emergent capabilities at hierarchical levels of resolution: functional (mechanism of action), residue (binding site localization, including orthosteric/allosteric discrimination), and bond (covalent versus non-covalent engagement). All three capabilities generalize to out-of-distribution complexes. Bonbon was trained on protein-ligand sequences alone, without any task-specific supervision and without structural coordinates. We conducted controlled scaling experiments across six model scales from 42M to 1.6B parameters; every capability evaluated shows a sharp jump at the largest scale on continuous metrics, even as pretraining loss decreases smoothly. This demonstrates that loss-based scaling laws alone are insufficient to predict when zero-shot emergent capabilities become available. The capabilities reported here emerge after training at a 1:2,000 parameter-to-token ratio to accommodate the sparsity of paired biological interaction data. The same frozen representations achieve state-of-the-art binding and affinity prediction at five orders of magnitude greater speed than co-folding methods. In prospective wet-lab validation across nine disease targets spanning seven protein families, Bonbon achieves a 61.5% dose-response hit rate on de novo compounds, yielding structurally novel molecules not previously reported to inhibit these proteins, including for out-of-distribution targets.
#03Nov 10, 2026
cs.CL
Pterodactyl: Pushing the Limits of Efficient Automated Translation Evaluation
Evelyn Y. Garland, Carola F. Berger
In this paper, we present 1020 Group's submission to the WMT26 shared task on automated quality evaluation. Our system, Pterodactyl, was engineered specifically for subtasks 2 and 3, that is, segment-level quality score prediction and the detection of error-free segments. Pterodactyl is a highly customizable, ultra-low cost system optimized for binary classification in translation triage and data curation. It is based on an LLM-as-a-judge approach, with prompt engineering and model selection guided by ROC analysis. We also developed several variants of Pterodactyl that were specifically adapted for subtasks 3.
#04Nov 10, 2026
cs.RO
TanCRAFT: Context-Reasoned Anticipatory Feedback for Assembly Tasks
Sassan Mokhtar, Lars Doorenbos, Marius Bock and 4 more
Preventing human error in physical assembly tasks requires assistance systems that can intervene before mistakes are made. This is especially challenging in settings where users are free to choose the construction order and correctness depends on the evolving assembly rather than a fixed next step. We present TanCRAFT, a four-stage real-time predictive assistance system that tracks the scene state, reasons about the current partial assembly, forecasts the near-future motion of manipulated pieces, and intervenes when the predicted placement is incompatible with the target. We instantiate our framework and confirm its effectiveness in a controlled tangram assembly task through offline benchmarks and a within-subject user study. Our findings show that the predictive feedback significantly reduces mistakes relative to unguided and reactive sessions, while yielding the lowest mean perceived workload and shortest mean completion time. Overall, these results demonstrate the value of predictive feedback for error prevention and provide a step toward cost-aware assistance for automation and human-robot workcells.
#05Nov 10, 2026
cs.CV
RS-JEPA: Remote Sensing Joint-Embedding Predictive Architecture with Scan-Path Views for Cross-Sensor Image Retrieval
Tanishq Rachamalla, Srishti Kaushik, Muhammad Attique Khan and 2 more
Cross-sensor remote sensing image retrieval aims to find scenes with the same content across heterogeneous sensors, such as SAR and optical or panchromatic (PAN) and multispectral (MS) imagery, without manual labels. Existing self-supervised methods either reconstruct sensor-specific pixel detail, align each image only with its co-registered twin, or rely on large transformers with 118-173M parameters (and up to 398M). We introduce RS-JEPA, a compact joint-embedding predictive framework built on a Vision Mamba encoder shared by both sensors. Since a state-space encoder reads an image as an ordered sequence of patches, we propose scan-path views, which treat two reading orders of the same image as two views with identical pixels and predict the hidden patches in one order from the visible patches in the other.To keep this prediction challenging, we propose Adversarial View Coupling (AVC), which learns the hardest split of the visible patches, and a neighbourhood consensus loss that aligns the scene similarities of both sensors. Extensive experiments on SAR-optical (BEN-14K, CBRSIR-VS) and PAN-MS (DSRSID) benchmarks demonstrate that RS-JEPA achieves the highest F1@5 among twelve re-implemented methods (72.92, 80.35 and 94.43) with a retrieval network of only 3.88M parameters (14.57M in training, 8-16times fewer than prior JEPA retrievers). Like prior methods, RS-JEPA trains on co-registered pairs. Our results highlight reading order as a source of self-supervised views. code: https://github.com/Tanishq251/RSJEPA.