Physics-Informed Machine Learning (PIML) has successfully integrated mechanistic understanding into machine learning, particularly in domains governed by well-known physical laws. This success has motivated efforts to apply PIML to biology, a field rich in dynamical systems but shaped by different constraints. Biological modeling, however, presents unique challenges: multi-faceted and uncertain prior knowledge, heterogeneous and noisy data, partial observability, and complex, high-dimensional networks. In this position paper, we argue that these challenges should not be seen as obstacles to PIML, but as catalysts for its evolution. We propose Biology-Informed Machine Learning (BIML): a principled extension of PIML that retains its structural grounding while adapting to the practical realities of biology. Rather than replacing PIML, BIML retools its methods to operate under softer, probabilistic forms of prior knowledge. We outline four foundational pillars as a roadmap for this transition: uncertainty quantification, contextualization, constrained latent structure inference, and scalability. Foundation Models and Large Language Models will be key enablers, bridging human expertise with computational modeling. We conclude with concrete recommendations to build the BIML ecosystem and channel PIML-inspired innovation toward challenges of high scientific and societal relevance.

Learning rules--prescriptions for updating model parameters to improve performance--are typically assumed rather than derived. Why do some learning rules work better than others, and under what assumptions can a given rule be considered optimal? We propose a theoretical framework that casts learning rules as policies for navigating (partially observable) loss landscapes, and identifies optimal rules as solutions to an associated optimal control problem. A range of well-known rules emerge naturally within this framework under different assumptions: gradient descent from short-horizon optimization, momentum from longer-horizon planning, natural gradients from accounting for parameter space geometry, non-gradient rules from partial controllability, and adaptive optimizers like Adam from online Bayesian inference of loss landscape shape. We further show that continual learning strategies like weight resetting can be understood as optimal responses to task uncertainty. By unifying these phenomena under a single objective, our framework clarifies the computational structure of learning and offers a principled foundation for designing adaptive algorithms.

Advanced reasoning models with agentic capabilities (AI agents) are deployed to interact with humans and to solve sequential decision-making problems under (approximate) utility functions and internal models. When such problems have resource or failure constraints where action sequences may be forcibly terminated once resources are exhausted, agents face implicit trade-offs that reshape their utility-driven (rational) behaviour. Additionally, since these agents are typically commissioned by a human principal to act on their behalf, asymmetries in constraint exposure can give rise to previously unanticipated misalignment between human objectives and agent incentives. We formalise this setting through a survival bandit framework, provide theoretical and empirical results that quantify the impact of survival-driven preference shifts, identify conditions under which misalignment emerges and propose mechanisms to mitigate the emergence of risk-seeking or risk-averse behaviours. As a result, this work aims to increase understanding and interpretability of emergent behaviours of AI agents operating under such survival pressure, and offer guidelines for safely deploying such AI systems in critical resource-limited environments.

Bayesian Network models are a powerful tool to collaboratively optimize production processes in various manufacturing industries. When interacting, collaborating parties must preserve their business secrets by maintaining the confidentiality of their model structures and parameters. While most realistic industry scenarios involve hybrid settings, handling both discrete and continuous data, current state-ofthe-art methods for collaborative and confidential inference only support discrete data and have high communication costs. In a centralized setting, Junction Trees enable efficient inference even in hybrid scenarios without discretizing continuous variables, but no extension for collaborative and confidential scenarios exists. To address this research gap, we introduce Hybrid CCJT, the first framework for confidential multiparty inference in hybrid domains with semi-honest, non-colluding adversaries, comprising: (i) a method to construct a strongly-rooted Junction Tree across collaborating parties through a novel construct of interface cliques; and, (ii) a protocol for confidential inference built upon multiparty computation primitives comprising a one-time alignment phase and a belief propagation system for combining the inference results across the Junction Tree cliques. Extensive evaluation on nine datasets shows that Hybrid CCJT improves the predictive accuracy of continuous target variables by 32% on average compared to the state-of-the-art, while reducing communication costs by a median 10.4 under purely discrete scenarios.

Recent work analyzing in-context learning (ICL) has identified a broad set of strategies that describe model behavior in different experimental conditions. We aim to unify these findings by asking why a model learns these disparate strategies in the first place. Specifically, we start with the observation that when trained to learn a mixture of tasks, as is popular in the literature, the strategies learned by a model for performing ICL can be captured by a family of Bayesian predictors: a memorizing predictor, which assumes a discrete prior on the set of seen tasks, and a generalizing predictor, where the prior matches the underlying task distribution. Adopting the normative lens of rational analysis, where a learner's behavior is explained as an optimal adaptation to data given computational constraints, we develop a hierarchical Bayesian framework that almost perfectly predicts Transformer nexttoken predictions throughout training--without assuming access to its weights. Under this framework, pretraining is viewed as a process of updating the posterior probability of different strategies, and inference-time behavior as a posteriorweighted average over these strategies' predictions. Our framework draws on common assumptions about neural network learning dynamics, which make explicit a tradeoff between loss and complexity among candidate strategies: beyond how well it explains the data, a model's preference towards implementing a strategy is dictated by its complexity. This helps explain well-known ICL phenomena, while offering novel predictions: e.g., we show a superlinear trend in the timescale for transitioning from generalization to memorization as task diversity increases. Overall, our work advances an explanatory and predictive account of ICL grounded in tradeoffs between strategy loss and complexity.

Label shift adaptation aims to recover target class priors when the labelled source distribution P and the unlabelled target distribution Qshare P(X | Y) = Q(X | Y) but P(Y) = Q(Y). Classical black-box shift estimators invert an empirical confusion matrix of a frozen classifier, producing a brittle point estimate that ignores sampling noise and similarity among classes.

Retinal vessel segmentation is critical for medical diagnosis, yet existing models often struggle to generalize across domains due to appearance variability, limited annotations, and complex vascular morphology. We propose GraphSeg, a variational Bayesian framework that integrates anatomical graph priors with structure-aware image decomposition to enhance cross-domain segmentation.

Uncertainty quantification (UQ) for adaptively collected data, such as that coming from adaptive experiments, bandits, or reinforcement learning, is necessary for critical elements of data collection such as ensuring safety and conducting afterstudy inference. The data's adaptivity creates significant challenges for frequentist UQ, yet Bayesian UQ remains the same as if the data were independent and identically distributed (i.i.d.), making it an appealing and commonly used approach. Bayesian UQ requires the (correct) specification of a prior distribution while frequentist UQ does not, but for i.i.d.

Density estimation is essential for generative modeling, particularly with the rise of modern neural networks. While existing methods capture complex data distributions, they often lack interpretability and uncertainty quantification.

We propose Energy-based generator matching (EGM), a modality-agnostic approach to train generative models from energy functions in the absence of data. Extending the recently proposed generator matching, EGM enables training of arbitrary continuous-time Markov processes, e.g., diffusion, flow, and jump, and can generate data from continuous, discrete, and a mixture of two modalities. To this end, we propose estimating the generator matching loss using self-normalized importance sampling with an additional bootstrapping trick to reduce variance in the importance weight.