The Inference Report

Robust and accurate neural decoders are integral to neurotechnologies such as brain-computer interfaces and closed-loop experiments. Recent work has shown that tokenizing neural data at the spike level facilitates multi-session pretraining and delivers state-of-the-art decoding performance. However, current spike-based models are restricted to supervised learning (SL), limiting training to datasets with paired behavioural labels. To address this limitation, we introduce MOJO (Masked autOencoder-based JOint training), a training framework for spike-tokenizing models that jointly leverages self-supervised learning (SSL) via masked autoencoding and SL objectives. We evaluate MOJO on three spiking datasets spanning monkey motor cortex during reaching tasks and multi-regional mouse recordings during vision and decision making tasks, demonstrating superior performance over purely SL-trained models. This improvement is especially pronounced when training with limited labelled data, particularly in few-shot finetuning, where only a small amount of labelled data from a new session is available. Incorporating SSL also yields more interpretable neuronal representations, improving performance on brain region classification and spike-statistics prediction without explicit optimization for these tasks. We further show that MOJO generalizes beyond spiking data to human electrocorticography during speech, where it continues to outperform purely SL-trained models and achieves performance comparable to neuro-foundation models (NFMs) designed specifically for continuous signals. Overall, augmenting spike-tokenizing models with SSL improves performance in label-impoverished settings and enables the use of unlabelled data across various tasks and species, while generalizing to other neural modalities. These results suggest a path towards more flexible and scalable data usage when training NFMs.

Linear Independent Component Analysis (ICA) recovers jointly independent source signals from their linear mixtures. To achieve this, classical ICA algorithms attempt to maximize non-Gaussianity, measured by negentropy, which is linked to independence by information theory. Because exact negentropy optimization is intractable, they rely on proxy contrast functions, such as fourth-order cumulants, and parametric log-likelihoods. We propose instead to measure non-Gaussianity using the squared Wasserstein distance $W_2^2$ to a standard Gaussian. We prove that the Wasserstein distance between a standard normal distribution and linear projections of the data is maximized when the projection recovers an independent component. Based on this observation, we propose the OT-ICA algorithm which finds this projection by gradient-based optimization. Empirical evaluation on simulated data shows that OT-ICA outperforms proxy-based methods for different distributions of the latent variables. Application to EEG artifact removal and econometric price discovery confirm OT-ICA can be used for applied ICA tasks without distributional assumptions.

Automated Program Repair (APR) has witnessed significant progress with the advent of Large Language Models (LLMs). However, as modern software systems increasingly expose rich graphical user interfaces, effectively leveraging visual information from bug screenshots has become essential for understanding bugs and generating accurate fixes in multimodal scenarios. Real-world issue reports frequently contain heterogeneous visual attachments including UI screenshots, IDE snapshots, GIFs, and text-centric images, each with distinct visual patterns and domain-specific semantics that impose substantial perceptual demands on MLLMs. Furthermore, bug screenshots often contain large expanses of uninformative and bug-irrelevant regions, distracting the model's attention and limiting patch diversity. To address these challenges, we propose VisualRepair, an MLLM-based framework for visual software issue repair comprising two core modules: Image Type-aware Tool Calling (ITTC), which classifies input images and dynamically invokes a tailored tool-calling chain for robust visual interpretation, and Dynamic Test-time Region Focusing (DTRF), which grounds multiple bug-related region candidates and refines them via an adaptive zoom-in and zoom-out strategy to improve fault localization and promote diverse patch generation. Extensive experiments on the SWE-bench Multimodal benchmark demonstrate that VisualRepair consistently outperforms state-of-the-art approaches. VisualRepair resolves 196 and 25 instances on the test and dev sets, respectively, surpassing the best baseline by 10 and 11 instances. These results highlight the effectiveness of type-aware visual understanding and region-focused localization for automated visual software issue repair.

Bioacoustic foundation models rely on large-scale citizen science platforms like Xeno-Canto for geographically and ecologically diverse data. Recent work has shown that supervision alone can produce SotA species detection models when trained on this large-scale data -- however, there remains unutilized potential in the form of recording metadata readily available within these community-driven data hubs. In this work, we explore the use of metadata -- such as location and time -- as auxiliary supervision signals, allowing the model to leverage species-metadata correlations in its learned representation. Auxiliary metadata losses provide additional information beyond vocalizations alone that can encourage a richer, more robust representation that generalizes better to species distribution and acoustic domain shifts -- important challenges for deployment in real-world passive acoustic monitoring (PAM) settings. We introduce MetaPerch, a new foundation model that achieves strong species identification performance across multiple challenging domains and present an extensive empirical study of the effects of 9 diverse metadata sources on 17 bioacoustic datasets.

Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored. We ask how much biosecurity-relevant signal is linearly accessible in these representations by training minimal linear and attention probes on frozen Evo 2 layer-26 activations, without fine-tuning the underlying model. Across held-out metagenomic test sets, the probes detect antimicrobial resistance (AMR) with strong discrimination: a linear probe reaches a region-level ROC-AUC of 0.888 (mean-pool), rising to 0.977 with a single-head attention probe. The probes resolve finer-grained AMR drug-class subcategories and separate them from unrelated functional genes, providing additional evidence that the learned signal is not explained solely by generic functional-gene status. Bacterial virulence is also decodable, though more weakly (region-level ROC-AUC 0.833). The AMR probe retains comparable ranking performance on simulated short reads without retraining, enabling evaluation before assembly in settings where assembly is computationally costly or unreliable. It achieves a read-level ROC-AUC of 0.898 (mean-pool), comparable to the mean-pooled full-region result. Within SynGenome, AMR-associated prompt labels are only weakly recoverable from Evo 1.5-generated sequences; these prompt-derived labels do not establish the function of the generated response sequences. A complementary sparse-autoencoder analysis recovers interpretable resistance-associated features but proves less consistent than the supervised probes. Together, these results position lightweight embedding-based probes as a fast, inexpensive first-pass detection layer for metagenomic biosurveillance and map both strengths and current limits of the approach. This work was conducted as part of the AIxBio Hackathon 2026 hosted by BlueDot Impact, Apart Research, and Cambridge Biosecurity Hub.

Forecasters are evaluated by backtesting, which replays resolved questions and grades the probability the system would have assigned before the outcome was known. For LLMs, two channels leak the answer into this test. A model that retrieves can surface reports written after the event, turning forecasting into a lookup, and each new model is trained on data closer to the event, so a question that lay in the future for last year's models sits inside this year's training data. Either way, the test grades recall while claiming to grade foresight. We introduce Hindcast, which closes both leaks by grading a model as if it stood at a chosen past date $t_0$, before the outcome existed in either channel. Hindcast replays resolved Polymarket prediction markets against a frozen snapshot of public Reddit, lets the model read only posts written before $t_0$, and scores each forecast against both what happened and the market's own price at $t_0$, itself a human forecast made from the same past information. Because the cutoff is set per market and the snapshot never changes, the evaluation re-runs on new markets as models improve, without going stale. Once the leak is closed, retrieval still helps most models, but only where Reddit discussed the event beforehand. Where the archive carried only speculation, retrieval hurts.