#01Nov 5, 2026
cs.LG
Synthesis of Ovarian Cancer Multi-Omics Datasets: A Biology-Informed Evaluation Framework
Déborah Boyenval, Alina Malyutina, Jaana Oikkonen and 2 more
Paired multi-omic cancer cohorts are costly to assemble and difficult to share, motivating synthetic cohorts as a complementary resource. As generative model development accelerates, we shift the focus from proposing yet another architecture to defining evaluation criteria that determine whether synthetic data preserve biologically relevant structure. We introduce a biology-informed and patient-disjoint framework for evaluating the generation of paired RNA expression and copy-number variation (CNV) profiles, and apply it to the longitudinal DECIDER high-grade serous ovarian cancer cohort. The framework assesses modality-specific fidelity and coherence between RNA and CNV pairs using agreement between real training and held-out data as a reference, alongside complementary training-data proximity diagnostics. We adapt three multi-omic integration architectures based on variational autoencoders to generate paired profiles. The model leading several fidelity and coherence measures also shows the strongest training-data proximity. The protocol and case study offer the community a reference for comparing future multi-omic generators.
#02Nov 5, 2026
cs.AI
Scientist World: Grow a Research World for AI-Scientists
Taiming Lu, Sachin Konan, Zhuang Liu
AI-Scientists arrived, but a world for them to grow in did not. Human scientists take theirs for granted $-$ centuries of open problems and shared ideas, waiting in the scientific literature. To AI-Scientists, that world is readable but not runnable, so we build Scientist World for them: every research paper becomes an executable environment. Our autonomous pipeline extracts each paper's open-ended research question and reproduces its proposed method as the baseline; an AI-Scientist entering the environment is evaluated against what the human authors achieved. We release the first 1,000 verified environments. With the world as an evaluation, we found that frontier AI-Scientists can already surpass the human researchers 74% of the time. As a record of how AI does science, it contains 6,400 hours of research traces, with every idea, experiment, failure, and success. As a training ground, we are able to raise (+158%) a small model to match frontier models in research ideation. At last, AI-Scientists' own world has arrived, grown from and growing with science itself.
#03Nov 5, 2026
cs.AI
Learning a patient world model for health system simulation in intensive care
Yingtai Li, Ruoyan Wang, Yu Li and 1 more
Designing healthcare strategies requires anticipating their clinical and operational consequences before implementation, a task that often relies on health system simulation. Such a simulation necessitates modeling how patient states evolve and generate care demands. However, conventional approaches typically tailor compact state transitions to a single policy question and omit history-dependent dynamics, thus requiring the redefinition of states and transitions when there is a new question that entails different clinical information. We propose to learn a patient world model from longitudinal EHRs using a neural network to provide a shared clinical representation of patient trajectories that can serve simulation questions across scenarios. Taking ICU operations as an example, we train the model on MIMIC-IV, freeze it, and couple its time-queryable predictions to shared ICU calendars, resources, and queues via scenario-specific mappings, so that one model renders admission demand, care tasks, and discharge proposals across simulations evaluating ICU bed capacity, care dispatch, and post-ICU transfer capacity. Experiments show that our model matches Markov and semi-Markov comparators in aggregate occupancy and directional responses to capacity and dispatch policies. It also reproduces policy gains from replayed observed trajectories. For patients entering the same support state from different prior trajectories, the learned representation captures a 24-h recovery difference (-6.4 predicted versus -6.7 observed percentage points), a contrast missed by compact state models, which propagates into distinct simulated care demand, queue burden, and bed use. These results indicate that a learned world model of patient dynamics has the potential to replace question-specific state models, allowing new care policies to be evaluated by reconfiguring the scenario without model rebuilding.
#04Nov 5, 2026
cs.LG
Same Behavior, Different Mechanism: What Finite Experiments Can Certify About Integrated Information
Linqian Wu, Diaoxuan He
Interpretability, AI auditing and assessments of machine consciousness increasingly rest on mechanism-level quantities: functionals of a system's causal transition law that describe how it computes, not what it outputs. Experiments see that law only through finite, partial and noisy interventions. We ask when such a quantity is identifiable from an experiment's access, continuous in the mechanism and certifiable from finite data, and answer exactly for a deliberately demanding case - the integrated information $\varphi$ of integrated information theory - in stochastic networks of four and five units with known ground truth. Behavior can be silent: a recurrent and a feed-forward network with identical input-output laws at their response delay carry 0.28 and 0 bits, yet internal recordings separate them within 4-53 trials. Partial access can be just as blind: in our examples, units left out of a one-step recording impose precision floors of 0.30-1.02 bits that no sample size lowers, and in all-but-self parity networks, recordings of any length see several hidden units only through the product of their fidelities - a symmetry that one intervention broke in exact checks. The measure has sharp edges: because $\varphi$ selects a partition, and the cause and effect it specifies, by one criterion and reports another, infinitesimal changes of mechanism that cross an edge change it by 25-100% at 99% of the edges we found in random networks, and about 1% of surrogate models that fit interventional data almost perfectly misreport it by more than 20%. One-sided claims survive: the same data certify a lower bound on both sides of an edge, and we prove $\varphi>1.004$ bits throughout a 64-dimensional region of mechanisms and certify it from about $10^7$ controlled transitions with false-certificate probability at most $α$. Measurability is thus a design question with computable answers.
#05Nov 5, 2026
cs.LG
A Hidden Markov Preference Model for Online Prediction of Adversary Actions
Angel Daruna, Michael Cogswell, Tixiao Shan and 3 more
A defender anticipating an attacker needs a probability distribution over the attacker's next action from information available before that action occurs. Two structures complicate this: the attacker's behavioral regime persists and can switch within an episode, and each action combines an operation with state-dependent arguments whose feasible values change over time. We capture both with a hidden Markov model whose latent state is the active regime and whose regime-conditioned action law is defined on a feasibility-masked tree of executable actions. The same likelihood forms the next-action distribution and updates the regime belief once the action is seen, and a partially observed prefix contributes its resolved local factors. Estimation separates into convex logistic fits that Baum-Welch reuses when regimes are unlabeled. We derive a reach-weighted nodewise KL expression for regime information, a sequence-wise log-loss bound for switching regime paths, and a uniform fallback guarantee. On the CAGE 2 cyber defense benchmark the filtered latent state is worth 0.8 nats per step, and after a controller switch the loss begins to fall in three steps against ten for a recurrent baseline.