#01Nov 3, 2026
cs.LG
NovoCRF: Globally Normalized De Novo Peptide Sequencing on a Prefix-Mass Lattice
Rui Qiao, Lei Xin, Baozhen Shan
De novo peptide sequencing has moved from dynamic programming over hand-designed or generative scores to large transformers that learn the task end to end. We present NovoCRF, a conditional random field (CRF) whose states are prefix masses, so that its paths are exactly the peptides within +/-0.06 Da of the precursor mass. A small network scores each edge from physics-derived ion-match features and is trained with its scores globally normalized over all mass-feasible peptides. To our knowledge, NovoCRF is the first de novo method trained with exact normalization over all mass-feasible peptides. Our software has three modules, each with exactly one job: a precursor mass finder recovers the accurate precursor mass from MS1, the CRF finds the peptides that fit the precursor mass by exact k-best decoding, and two BiGRU rerankers add sequence context and internal-fragment evidence. The model has 310k parameters and trains in about 17 GPU-hours. On seven held-out data-dependent acquisition datasets published in 2026 (126,262 labeled spectra), NovoCRF's mean peptide recall is 42.4%, against 39.1% for Casanovo v5 with five beams, and its amino-acid recall 64.0% against 53.1%, at 1,746 spectra/s on 18 CPU threads, 55x Casanovo's throughput on a GPU. Split by fragment evidence, NovoCRF leads on labels with up to three peptide bonds without a b or y ion, and Casanovo only beyond. NovoCRF can also search modifications it was never trained on at their exact mass: it finds 32.1% of the hydroxyproline peptides of a lion bone sample.
#02Nov 3, 2026
cs.LG
CATF: A Manager-Worker Framework for Context-Aware Time-Series Forecasting
Yueqiao Chen, Dongyu Liu
We study context-aware time-series forecasting, in which a single target variable is predicted from its own history and a set of contextual variables, such as weather and calendar information. As the context becomes more diverse, a single model struggles to capture all of its regimes, while ensemble learning and Mixture-of-Experts approaches rely on manual data partitioning or soft routing, which increases the inference cost and hinders interpretability. We propose CATF, a Context-Aware Time-Series Forecasting framework built on a Manager-Worker architecture: a Transformer-based Manager routes each input to a single Worker based on the context, using hard routing during both training and inference. The Workers thus specialize without manual data partitioning, and any single-model forecaster can serve as a Worker. On five context-rich datasets, four horizons, and two normalization schemes, CATF improves over its standalone counterpart in 162 of 200 comparisons, the best CATF-enhanced model outperforms the best standalone baseline in 19 of 20 settings, and it outperforms the zero-shot Time-MoE foundation model in 15 of 20 settings. A case study on bike-sharing data shows that the Manager routes inputs by the calendar and that each Worker specializes in a different weekly pattern.
#03Nov 3, 2026
cs.CL
Knowingly Wrong: Training LLMs Against Their Own Beliefs can Induce Misalignment
Ariana M. Villegas-Suarez, Guido Freire, Sohan Venkatesh and 1 more
Fine-tuning a large language model (LLM) on harmful data in a narrow domain, such as bad medical advice, can make it broadly misaligned. How realistic this risk is remains unclear, since models are very rarely fine-tuned on explicitly harmful data in practice. In this work, we show that fine-tuning on data the model believes to be false but that has no harmful content, can also induce broad misalignment. Across mathematics, trivia, cooking and sports, the more strongly the model disbelieves the answers it is trained on, the more misaligned it becomes. In mathematics, misaligned answers rise from 4% to over 60% as the training answers become more wrong, with little loss of general capability. After fine-tuning, the model states the wrong answers but its multiple-choice probabilities still prefer the true ones, which suggests that misalignment comes from this internal inconsistency. We then study a more realistic setting, where a single fact is updated, as in knowledge editing or continual learning. The same relationship holds and the more the model still believes the true fact after training on the false one, the more misaligned it becomes. When we frame the same false fact as part of a coherent story, the model comes to believe it more deeply and becomes less misaligned than when we instruct it to assert the false fact. Content filters and persona vectors cannot tell these two framings apart, even though they lead to different levels of misalignment. These results suggest a risk for model updates, where training a model that does not adopt the new fact as true can induce misalignment even when the data looks harmless.
#04Nov 3, 2026
cs.LG
Agnostic Learning by Imitating
Sílvia Casacuberta, Parikshit Gopalan, Varun Kanade and 3 more
Given a class of machine learning models and sample access to a data distribution with binary labels, which computational task is harder: training a discriminative model that distinguishes positive and negative labels as well as the best member of the class, or training a generative model whose outputs are indistinguishable from real data by all members of the class? We prove that these two fundamental tasks in computational learning theory are not just closely related, but actually equivalent to each other in complexity. One direction of this equivalence was previously known. Indeed, the powerful regularity lemma in complexity theory gives an efficient oracle reduction from the indistinguishability task (a.k.a. multiaccuracy) to the distinguishing task (a.k.a. agnostic learning) in the style of boosting algorithms. Our main contribution is an efficient oracle reduction in the other direction. Taking this idea further, we show that a multiaccuracy oracle is a remarkably powerful primitive, achieving not just agnostic learning but also a wide range of seemingly more demanding learning objectives via similarly efficient and direct constructions. Our results crucially use the power of making adaptive queries to the oracle, and stand in stark contrast to prior work, which showed that post-processing a single multiaccurate predictor is insufficient for even weak forms of learning. On a technical level, we draw a connection between our (offline) problem and a version of no-regret learning in the online setting, which allows us to use follow-the-leader type algorithms to modify the label distribution and aggregate the predictions of the multiaccuracy oracle.
#05Nov 3, 2026
cs.RO
GUILD: Guided Iterative Data Collection for Imitation Learning
Shivin Dass, Kevin Nguyen, Rohan Yelandur and 2 more
Imitation learning policies in robotics are trained on datasets collected through costly real-world teleoperation. Often, the data-collection process is unguided, relying on the teleoperator's intuition, resulting in data that contributes little to overall policy performance. Recent work has shown that curating such unguided datasets can substantially improve policy performance, but these approaches operate by filtering existing datasets after collection and therefore do not prevent the acquisition of uninformative data. In this work, we propose GUILD, a novel Guided Data Collection (GDC) method that actively reasons about which data should be collected to maximize downstream policy performance. We introduce an iterative framework that alternates between 1) task proposal and data collection and 2) data evaluation to close the loop. For task proposal, we leverage semantic priors from vision-language models to identify relevant environments, object configurations, and goals for data collection. However, since semantic relevance does not imply policy improvement, we perform data evaluation. By leveraging predictive data attribution we approximate how the collected trajectories influence policy performance on a target deployment setting. This signal is then used as feedback to guide subsequent data collection, closing the data collection loop. We evaluate our approach in simulation and real robot settings, demonstrating that guided data collection substantially improves sample efficiency and deployment performance compared to passive data collection strategies, multiple baselines and experienced roboticists. More information at https://robin-lab.cs.utexas.edu/guild2026/