The prediction of learning curves for Natural Language Processing (NLP) models enables informed decision-making to meet specific performance objectives, while reducing computational overhead and lowering the costs associated with dataset acquisition and curation. In this work, we formulate the prediction task as a multitask learning problem, where each task's data is modelled as being organized within a two-layer hierarchy. To model the shared information and dependencies across tasks and hierarchical levels, we employ latent variable multi-output Gaussian Processes, enabling to account for task correlations and supporting zero-shot prediction of learning curves (LCs). We demonstrate that this approach facilitates the development of probabilistic scaling laws at lower costs. Applying an active learning strategy, LCs can be queried to reduce predictive uncertainty and provide predictions close to ground truth scaling laws.

Recent text-based causal methods attempt to mitigate confounding bias by estimating proxies of confounding variables that are partially or imperfectly measured from unstructured text data. These approaches, however, assume analysts have supervised labels of the confounders given text for a subset of instances, a constraint that is sometimes infeasible due to data privacy or annotation costs. In this work, we address settings in which an important confounding variable is completely unobserved. We propose a new causal inference method that uses two instances of pre-treatment text data, infers two proxies using two zero-shot models on the separate instances, and applies these proxies in the proximal g-formula. We prove, under certain assumptions about the instances of text and accuracy of the zero-shot predictions, that our method of inferring text-based proxies satisfies identification conditions of the proximal g-formula while other seemingly reasonable proposals do not. To address untestable assumptions associated with our method and the proximal g-formula, we further propose an odds ratio falsification heuristic that flags when to proceed with downstream effect estimation using the inferred proxies. We evaluate our method in synthetic and semi-synthetic settings---the latter with real-world clinical notes from MIMIC-III and open large language models for zero-shot prediction---and find that our method produces estimates with low bias. We believe that this text-based design of proxies allows for the use of proximal causal inference in a wider range of scenarios, particularly those for which obtaining suitable proxies from structured data is difficult.

Continual learning (CL) empowers pre-trained vision-language (VL) models to efficiently adapt to a sequence of downstream tasks.

Accurately predicting protein fitness with minimal experimental data is a persistent challenge in protein engineering. We introduce PRIMO (PRotein In-context Mutation Oracle), a transformer-based framework that leverages in-context learning and test-time training to adapt rapidly to new proteins and assays without large task-specific datasets. By encoding sequence information, auxiliary zero-shot predictions, and sparse experimental labels from many assays as a unified token set in a pre-training masked-language modeling paradigm, PRIMO learns to prioritize promising variants through a preference-based loss function. Across diverse protein families and properties-including both substitution and indel mutations-PRIMO outperforms zero-shot and fully supervised baselines. This work underscores the power of combining large-scale pre-training with efficient test-time adaptation to tackle challenging protein design tasks where data collection is expensive and label availability is limited.

The prediction of learning curves for Natural Language Processing (NLP) models enables informed decision-making to meet specific performance objectives, while reducing computational overhead and lowering the costs associated with dataset acquisition and curation. In this work, we formulate the prediction task as a multitask learning problem, where each task's data is modelled as being organized within a two-layer hierarchy. To model the shared information and dependencies across tasks and hierarchical levels, we employ latent variable multi-output Gaussian Processes, enabling to account for task correlations and supporting zero-shot prediction of learning curves (LCs). We demonstrate that this approach facilitates the development of probabilistic scaling laws at lower costs. Applying an active learning strategy, LCs can be queried to reduce predictive uncertainty and provide predictions close to ground truth scaling laws. We validate our framework on three small-scale NLP datasets with up to $30$ LCs. These are obtained from nanoGPT models, from bilingual translation using mBART and Transformer models, and from multilingual translation using M2M100 models of varying sizes.

Current non-invasive neuroimaging techniques trade off between spatial resolution and temporal resolution. While magnetoencephalography (MEG) can capture rapid neural dynamics and functional magnetic resonance imaging (fMRI) can spatially localize brain activity, a unified picture that preserves both high resolutions remains an unsolved challenge with existing source localization or MEG-fMRI fusion methods, especially for single-trial naturalistic data. We collected whole-head MEG when subjects listened passively to more than seven hours of narrative stories, using the same stimuli in an open fMRI dataset (LeBel et al., 2023). We developed a transformer-based encoding model that combines the MEG and fMRI from these two naturalistic speech comprehension experiments to estimate latent cortical source responses with high spatiotemporal resolution. Our model is trained to predict MEG and fMRI from multiple subjects simultaneously, with a latent layer that represents our estimates of reconstructed cortical sources. Our model predicts MEG better than the common standard of single-modality encoding models, and it also yields source estimates with higher spatial and temporal fidelity than classic minimum-norm solutions in simulation experiments. We validated the estimated latent sources by showing its strong generalizability across unseen subjects and modalities. Estimated activity in our source space predict electrocorticography (ECoG) better than an ECoG-trained encoding model in an entirely new dataset. By integrating the power of large naturalistic experiments, MEG, fMRI, and encoding models, we propose a practical route towards millisecond-and-millimeter brain mapping.

Electronic Health Records (EHRs) provide a rich, longitudinal view of patient health and hold significant potential for advancing clinical decision support, risk prediction, and data-driven healthcare research. However, most artificial intelligence (AI) models for EHRs are designed for narrow, single-purpose tasks, limiting their generalizability and utility in real-world settings. Here, we present CEHR-XGPT, a general-purpose foundation model for EHR data that unifies three essential capabilities - feature representation, zero-shot prediction, and synthetic data generation - within a single architecture. To support temporal reasoning over clinical sequences, CEHR-XGPT incorporates a novel time-token-based learning framework that explicitly encodes patients' dynamic timelines into the model structure. CEHR-XGPT demonstrates strong performance across all three tasks and generalizes effectively to external datasets through vocabulary expansion and fine-tuning. Its versatility enables rapid model development, cohort discovery, and patient outcome forecasting without the need for task-specific retraining.

The emergence of long-context large language models (LLMs) has enabled the use of hundreds, or even thousands, of demonstrations for in-context learning (ICL) - a previously impractical regime. This paper investigates whether traditional ICL selection strategies, which balance the similarity of ICL examples to the test input (using a text retriever) with diversity within the ICL set, remain effective when utilizing a large number of demonstrations. Our experiments demonstrate that, while longer contexts can accommodate more examples, simply increasing the number of demonstrations does not guarantee improved performance. Smart ICL selection remains crucial, even with thousands of demonstrations. To further enhance ICL in this setting, we introduce Refract ICL, a novel ICL selection algorithm specifically designed to focus LLM attention on challenging examples by strategically repeating them within the context and incorporating zero-shot predictions as error signals. Our results show that Refract ICL significantly improves the performance of extremely long-context models such as Gemini 1.5 Pro, particularly on tasks with a smaller number of output classes.

Recent text-based causal methods attempt to mitigate confounding bias by estimating proxies of confounding variables that are partially or imperfectly measured from unstructured text data. These approaches, however, assume analysts have supervised labels of the confounders given text for a subset of instances, a constraint that is sometimes infeasible due to data privacy or annotation costs. In this work, we address settings in which an important confounding variable is completely unobserved. We propose a new causal inference method that uses two instances of pre-treatment text data, infers two proxies using two zero-shot models on the separate instances, and applies these proxies in the proximal g-formula. We prove, under certain assumptions about the instances of text and accuracy of the zero-shot predictions, that our method of inferring text-based proxies satisfies identification conditions of the proximal g-formula while other seemingly reasonable proposals do not.

Continual learning (CL) empowers pre-trained vision-language (VL) models to efficiently adapt to a sequence of downstream tasks. However, these models often encounter challenges in retaining previously acquired skills due to parameter shifts and limited access to historical data. In response, recent efforts focus on devising specific frameworks and various replay strategies, striving for a typical learning-forgetting trade-off. Surprisingly, both our empirical research and theoretical analysis demonstrate that the stability of the model in consecutive zero-shot predictions serves as a reliable indicator of its anti-forgetting capabilities for previously learned tasks. Motivated by these insights, we develop a novel replay-free CL method named ZAF (Zero-shot Antidote to Forgetting), which preserves acquired knowledge through a zero-shot stability regularization applied to wild data in a plug-and-play manner.