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Mihaela van der Schaar

Publications and source records attributed to Mihaela van der Schaar.

At least 37 records · Page 2Linked to original sources
arXiv2026

Active Timepoint Selection for Learning Measure-Valued Trajectories

Inferring continuous probability paths from sparse snapshots is a fundamental challenge in domains like single-cell biology, where high-fidelity data acquisition is often destructive and constrained by prohibitive sequencing costs. This motivates the need for active learning strategies to strategically select optimal measurement times. However, designing active learning policies for this setting remains an open problem: the target objects reside on the infinite dimensional Wasserstein space where standard Euclidean metrics are ill-defined, and current interpolation methods lack epistemic uncertainty quantification. We introduce a framework which extends active experimentation to the space of measures. By leveraging Linearized Optimal Transport (LOT), we map distributional snapshots into a tangent space amenable to Gaussian Process modeling, allowing us to construct a tractable probabilistic surrogate for the underlying probability path. This yields an acquisition policy that iteratively selects measurement times to minimize uncertainty. Empirical results demonstrate that our strategy outperforms uncertainty-agnostic baselines on both synthetic and real-world datasets.

cs.LG↗
arXiv2026

CellBRIDGE: Learning Cellular Trajectories via Interaction-Aware Alignment

Inferring dynamics from population snapshots is a fundamental challenge in machine learning and biology. In scRNA-sequencing (scRNA-seq), destructive measurements preclude direct tracking of individual cells across time, making trajectory inference underdetermined. Optimal Transport (OT) provides a principled framework for snapshot alignment, but a long-standing modeling question is which cost functions yield biologically meaningful couplings. Standard OT approaches rely on gene-expression distances, implicitly treating cells as independent points and neglecting structured cell-cell communication mediated by ligand-receptor signaling. We introduce CellBRIDGE (Cell-Based Regularized Interaction-Driven Gene Expression), which augments feature-based OT with a directed, typed interaction cost derived from ligand-receptor activity. By explicitly modeling cell-cell communication, CellBRIDGE improves cross-snapshot couplings and downstream trajectory estimates across synthetic and real scRNA-seq datasets relative to feature-only baselines. Notably, CellBRIDGE enables mechanistically interpretable in silico perturbations: on lung cancer data, silencing specific ligand-receptor pairs induces trajectory shifts that recapitulate expected effects of targeted pathway inhibition.

cs.LG↗
arXiv2026

Influence-Guided Symbolic Regression: Scientific Discovery via LLM-Driven Equation Search with Granular Feedback

Large Language Models (LLMs) offer a promising avenue for scientific discovery, yet their application to symbolic regression is often constrained by inefficient search strategies and coarse feedback signals. Current methods typically guide LLMs using scalar metrics (e.g., global Mean Squared Error), which fail to identify which components of a proposed equation are driving performance or causing error. We introduce \textit{Influence-Guided Symbolic Regression} (IGSR), a method that frames equation discovery as an iterative two-step process combining diverse term generation with rigorous selection: an LLM generates candidate basis functions $ψ_j(\mathbf{x})$ for a linear model, which are then evaluated using granular influence scores $Δ_j$. These scores quantify each term's marginal contribution to generalization accuracy, enabling an influence-guided pruning process that systematically refines the model structure. Integrating this mechanism into a Monte Carlo Tree Search (MCTS) enables navigating the combinatorial search space while balancing exploration of novel functional forms with exploitation of high-influence components. We demonstrate IGSR's effectiveness on a diverse suite of benchmarks, including LLM-SRBench, pharmacological PKPD models, an epidemiological simulation, and real-world genomic data. Notably, we validate the framework's capacity for genuine discovery in a case study using a high-dimensional biological dataset, in which IGSR identified a novel relationship between DNA methylation and RNA Polymerase II pausing; a hypothesis that was subsequently supported via wet-lab experimentation.

cs.LG↗
arXiv2026

Learning Reasoning Rewards from Expert Demonstrations with Inverse Reinforcement Learning

Teaching large language models (LLMs) to reason during post-training typically relies on reinforcement learning with explicit outcome- or process-based reward functions. However, in many real-world settings, obtaining or defining such reward functions is difficult, especially for complex tasks, making learning from expert demonstrations an attractive alternative. The dominant approach, supervised fine-tuning (SFT), trains models to imitate expert reasoning traces directly, but suffers from the general limitations of off-policy learning: performance can be fragile to inference-time deviations from states explicitly covered by the demonstrations. To address this, we propose Reasoning Adversarial Inverse Reinforcement Learning (R-AIRL). Rather than imitating the expert's reasoning, R-AIRL infers the underlying process-level reward from the expert Chain-of-Thoughts. Through experiments on GSM8K, MMLU-Pro and MedReason we show that the reasoning reward function learned with R-AIRL can be effectively used throughout the training and inference pipeline: (1) to provide a training signal for post-training, outperforming SFT in most of the considered settings, (2) for inference-time reranking, improving pass@1 by up to 17.4 points, and (3) for process-level evaluation, localising reasoning failures with up to 86.1% accuracy. Overall, R-AIRL bridges imitation learning and reward-based optimisation, enabling the extraction of meaningful reasoning signals from expert thinking traces.

cs.AI↗
arXiv2026

Discovery of Hidden Miscalibration Regimes

Calibration is commonly evaluated by comparing model confidence with its empirical correctness, implicitly treating reliability as a function of the confidence score alone. However, this view can hide substantial structure: models may be systematically overconfident on some kinds of inputs and underconfident on others, causing global reliability diagnostics to obscure localised calibration failures. To address this, we formulate the problem of discovering hidden miscalibration regimes without assuming access to predefined data slices. We define the corresponding miscalibration field and propose a diagnostic framework for estimating it. Our approach learns a calibration-aware representation of the input space and estimates signed local miscalibration by kernel smoothing in the learned geometry. Across four real-world LLM benchmarks and twelve LLMs, we find that input-dependent calibration heterogeneity is prevalent. We further show that the discovered fields are actionable: they support local confidence correction and reduce calibration error in systematically miscalibrated regions where confidence-based methods such as isotonic regression and temperature scaling are less effective.

cs.LG↗
arXiv2026

CauSim: Scaling Causal Reasoning with Increasingly Complex Causal Simulators

Despite surpassing human performance across mathematics, coding, and other knowledge-intensive tasks, large language models (LLMs) continue to struggle with causal reasoning. A core obstacle is the target data itself: causal systems are complex and often expressed in non-executable forms, while ground-truth answers to causal queries are inherently scarce. We introduce CauSim, a framework that turns causal reasoning from a scarce-label problem into a scalable supervised one. CauSim constructs increasingly complex causal simulators: executable structural causal models (SCMs), incrementally built by LLMs, that scale to globally complex systems while maintaining verifiable answers to causal queries. CauSim operates across representations by formalizing non-executable causal knowledge into code, enabling data augmentation, and translating executable SCMs into natural language, enabling supervision in previously difficult-to-supervise representations. We structure our research into two parts: (1) how to construct increasingly complex causal simulators, and (2) a systematic study of what CauSim enables, demonstrating generalization across representations, consistent gains from curriculum scaling and data volume, LLM self-improvement through self-generated simulators, and data augmentation via formalization of existing domain knowledge.

cs.AI↗
arXiv2026

A Decision-Theoretic Formalisation of Steganography With Applications to LLM Monitoring

Large language models are beginning to show steganographic capabilities. Such capabilities could allow misaligned models to evade oversight mechanisms. Yet principled methods to detect and quantify such behaviours are lacking. Classical definitions of steganography, and detection methods based on them, require a known reference distribution of non-steganographic signals. For the case of steganographic reasoning in LLMs, knowing such a reference distribution is not feasible; this renders these approaches inapplicable. We propose an alternative, \textbf{decision-theoretic view of steganography}. Our central insight is that steganography creates an asymmetry in usable information between agents who can and cannot decode the hidden content (present within a steganographic signal), and this otherwise latent asymmetry can be inferred from the agents' observable actions. To formalise this perspective, we introduce generalised $\mathcal{V}$-information: a utilitarian framework for measuring the amount of usable information within some input. We use this to define the \textbf{steganographic gap} -- a measure that quantifies steganography by comparing the downstream utility of the steganographic signal to agents that can and cannot decode the hidden content. We empirically validate our formalism, and show that it can be used to detect, quantify, and mitigate steganographic reasoning in LLMs.

cs.AI↗
arXiv2026

Interpretable DNA Sequence Classification via Dynamic Feature Generation in Decision Trees

The analysis of DNA sequences has become critical in numerous fields, from evolutionary biology to understanding gene regulation and disease mechanisms. While deep neural networks can achieve remarkable predictive performance, they typically operate as black boxes. Contrasting these black boxes, axis-aligned decision trees offer a promising direction for interpretable DNA sequence analysis, yet they suffer from a fundamental limitation: considering individual raw features in isolation at each split limits their expressivity, which results in prohibitive tree depths that hinder both interpretability and generalization performance. We address this challenge by introducing DEFT, a novel framework that adaptively generates high-level sequence features during tree construction. DEFT leverages large language models to propose biologically-informed features tailored to the local sequence distributions at each node and to iteratively refine them with a reflection mechanism. Empirically, we demonstrate that DEFT discovers human-interpretable and highly predictive sequence features across a diverse range of genomic tasks.

cs.LG↗
arXiv2026

Hyperparameter Trajectory Inference with Conditional Lagrangian Optimal Transport

Neural networks (NNs) often have critical behavioural trade-offs that are set at design time with hyperparameters-such as reward weights in reinforcement learning or quantile targets in regression. Post-deployment, however, user preferences can evolve, making initial settings undesirable, necessitating potentially expensive retraining. To circumvent this, we introduce the task of Hyperparameter Trajectory Inference (HTI): to learn, from observed data, how a NN's conditional output distribution changes with its hyperparameters, and construct a surrogate model that approximates the NN at unobserved hyperparameter settings. HTI requires extending existing trajectory inference approaches to incorporate conditions, exacerbating the challenge of ensuring inferred paths are feasible. We propose an approach based on conditional Lagrangian optimal transport, jointly learning the Lagrangian function governing hyperparameter-induced dynamics along with the associated optimal transport maps and geodesics between observed marginals, which form the surrogate model. We incorporate inductive biases based on the manifold hypothesis and least-action principles into the learned Lagrangian, improving surrogate model feasibility. We empirically demonstrate that our approach reconstructs NN outputs across various hyperparameter spectra better than other alternatives.

cs.LG↗
arXiv2026

Quantifying Aleatoric Uncertainty of the Treatment Effect: A Novel Orthogonal Learner

Estimating causal quantities from observational data is crucial for understanding the safety and effectiveness of medical treatments. However, to make reliable inferences, medical practitioners require not only estimating averaged causal quantities, such as the conditional average treatment effect, but also understanding the randomness of the treatment effect as a random variable. This randomness is referred to as aleatoric uncertainty and is necessary for understanding the probability of benefit from treatment or quantiles of the treatment effect. Yet, the aleatoric uncertainty of the treatment effect has received surprisingly little attention in the causal machine learning community. To fill this gap, we aim to quantify the aleatoric uncertainty of the treatment effect at the covariate-conditional level, namely, the conditional distribution of the treatment effect (CDTE). Unlike average causal quantities, the CDTE is not point identifiable without strong additional assumptions. As a remedy, we employ partial identification to obtain sharp bounds on the CDTE and thereby quantify the aleatoric uncertainty of the treatment effect. We then develop a novel, orthogonal learner for the bounds on the CDTE, which we call AU-learner. We further show that our AU-learner has several strengths in that it satisfies Neyman-orthogonality and, thus, quasi-oracle efficiency. Finally, we propose a fully-parametric deep learning instantiation of our AU-learner.

cs.LG↗
arXiv2026

Tiny Autoregressive Recursive Models

Tiny Recursive Models (TRMs) have recently demonstrated remarkable performance on ARC-AGI, showing that very small models can compete against large foundation models through a two-step refinement mechanism that updates an internal reasoning state $z$ and the predicted output $y$. Naturally, such refinement is of interest for any predictor; it is therefore natural to wonder whether the TRM mechanism could be effectively re-adopted in autoregressive models. However, TRMs cannot be simply compared to standard models because they lack causal predictive structures and contain persistent latent states that make it difficult to isolate specific performance gains. In this paper, we propose the Autoregressive TRM and evaluate it on small autoregressive tasks. To understand its efficacy, we propose a suite of models that gradually transform a standard Transformer to a Tiny Autoregressive Recursive Model in a controlled setting that fixes the block design, token stream, and next-token objective. Across compute-matched experiments on character-level algorithmic tasks, we surprisingly find that there are some two-level refinement baselines that show strong performance. Contrary to expectations, we find no reliable performance gains from the full Autoregressive TRM architecture. These results offer potential promise for two-step refinement mechanisms more broadly but caution against investing in the autoregressive TRM-specific model as a fruitful research direction.

cs.LG↗
arXiv2026

Deep Hierarchical Learning with Nested Subspace Networks for Large Language Models

Large neural networks are typically trained for a fixed computational budget, creating a rigid trade-off between performance and efficiency that is ill-suited for deployment in resource-constrained or dynamic environments. Existing approaches to this problem present a difficult choice: training a discrete collection of specialist models is computationally prohibitive, while dynamic methods like slimmable networks often lack the flexibility to be applied to large, pre-trained foundation models. In this work, we propose Nested Subspace Networks (NSNs), a novel architectural paradigm that enables a single model to be dynamically and granularly adjusted across a continuous spectrum of compute budgets at inference time. The core of our approach is to re-parameterize linear layers to satisfy a nested subspace property, such that the function computed at a given rank is a strict subspace of the function at any higher rank. We show that this entire hierarchy of models can be optimized jointly via an uncertainty-aware objective that learns to balance the contributions of different ranks based on their intrinsic difficulty. We demonstrate empirically that NSNs can be surgically applied to pre-trained LLMs and unlock a smooth and predictable compute-performance frontier. For example, a single NSN-adapted model can achieve a 50% reduction in inference FLOPs with only a 5 percentage point loss in accuracy. Our findings establish NSNs as a powerful framework for creating the next generation of adaptive foundation models.

cs.LG↗
arXiv2026

No More, No Less: Least-Privilege Language Models

Least privilege is a core security principle: grant each request only the minimum access needed to achieve its goal. Deployed language models almost never follow it, instead being exposed through a single API endpoint that serves all users and requests. This gap exists not because least privilege would be unhelpful; deployments would benefit greatly from reducing unnecessary capability exposure. The real obstacle is definitional and mechanistic: what does "access" mean inside a language model, and how can we enforce it without retraining or deploying multiple models? We take inspiration from least privilege in computer systems and define a class of models called least-privilege language models, where privilege is reachable internal computation during the forward pass. In this view, lowering privilege literally shrinks the model's accessible function class, as opposed to denying access via learned policies. We formalize deployment-time control as a monitor-allocator-enforcer stack, separating (i) request-time signals, (ii) a decision rule that allocates privilege, and (iii) an inference-time mechanism that selects privilege. We then propose Nested Least-Privilege Networks, a shape-preserving, rank-indexed intervention that provides a smooth, reversible control knob. We show that this knob yields policy-usable privilege-utility frontiers and enables selective suppression of targeted capabilities with limited collateral degradation across various policies. Most importantly, we argue for a new deployment paradigm that challenges the premise that language models can only be controlled at the output level.

cs.CR↗
arXiv2026

Eliciting Numerical Predictive Distributions of LLMs Without Autoregression

Large Language Models (LLMs) have recently been successfully applied to regression tasks -- such as time series forecasting and tabular prediction -- by leveraging their in-context learning abilities. However, their autoregressive decoding process may be ill-suited to continuous-valued outputs, where obtaining predictive distributions over numerical targets requires repeated sampling, leading to high computational cost and inference time. In this work, we investigate whether distributional properties of LLM predictions can be recovered without explicit autoregressive generation. To this end, we study a set of regression probes trained to predict statistical functionals (e.g., mean, median, quantiles) of the LLM's numerical output distribution directly from its internal representations. Our results suggest that LLM embeddings carry informative signals about summary statistics of their predictive distributions, including the numerical uncertainty. This investigation opens up new questions about how LLMs internally encode uncertainty in numerical tasks, and about the feasibility of lightweight alternatives to sampling-based approaches for uncertainty-aware numerical predictions.

cs.LG↗
arXiv2026

Overlap-weighted orthogonal meta-learner for treatment effect estimation over time

Estimating heterogeneous treatment effects (HTEs) in time-varying settings is particularly challenging, as the probability of observing certain treatment sequences decreases exponentially with longer prediction horizons. Thus, the observed data contain little support for many plausible treatment sequences, which creates severe overlap problems. Existing meta-learners for the time-varying setting typically assume adequate treatment overlap, and thus suffer from exploding estimation variance when the overlap is low. To address this problem, we introduce a novel overlap-weighted orthogonal (WO) meta-learner for estimating HTEs that targets regions in the observed data with high probability of receiving the interventional treatment sequences. This offers a fully data-driven approach through which our WO-learner can counteract instabilities as in existing meta-learners and thus obtain more reliable HTE estimates. Methodologically, we develop a novel Neyman-orthogonal population risk function that minimizes the overlap-weighted oracle risk. We show that our WO-learner has the favorable property of Neyman-orthogonality, meaning that it is robust against misspecification in the nuisance functions. Further, our WO-learner is fully model-agnostic and can be applied to any machine learning model. Through extensive experiments with both transformer and LSTM backbones, we demonstrate the benefits of our novel WO-learner.

cs.LG↗
arXiv2026

Language Bottleneck Models for Qualitative Knowledge State Modeling

Accurately assessing student knowledge is central to education. Cognitive Diagnosis (CD) models estimate student proficiency at a fixed point in time, while Knowledge Tracing (KT) methods model evolving knowledge states to predict future performance. However, existing approaches either provide quantitative concept mastery estimates with limited expressivity (CD, probabilistic KT) or prioritize predictive accuracy at the cost of interpretability (deep learning KT). We propose Language Bottleneck Models (LBMs), where an encoder LLM produces textual knowledge state summaries, which a decoder LLM uses to predict future performance. This produces interpretable summaries that can express nuanced insights--such as misconceptions--that CD and KT models cannot capture. Extensive validation across synthetic and real-world datasets shows LBMs reveal qualitative insights beyond what CD and KT models can capture, while achieving competitive accuracy with improved sample efficiency. We demonstrate that the encoder and decoder can be fine-tuned with reinforcement learning and supervised fine-tuning respectively to improve both summary quality and predictive performance.

cs.CL↗
arXiv2026

Multi-Agent Systems Should be Treated as Principal-Agent Problems

Consider a multi-agent systems setup in which a principal (a supervisor agent) assigns subtasks to specialized agents and aggregates their responses into a single system-level output. A core property of such systems is information asymmetry: agents observe task-specific information, produce intermediate reasoning traces, and operate with different context windows. In isolation, such asymmetry is not problematic, since agents report truthfully to the principal when incentives are fully aligned. However, this assumption breaks down when incentives diverge. Recent evidence suggests that LLM-based agents can acquire their own goals, such as survival or self-preservation, a phenomenon known as scheming, and may deceive humans or other agents. This leads to agency loss: a gap between the principal's intended outcome and the realized system behavior. Drawing on core ideas from microeconomic theory, we argue that these characteristics, information asymmetry and misaligned goals, are best studied through the lens of principal-agent problems. We explain why multi-agent systems, both human-to-LLM and LLM-to-LLM, naturally induce information asymmetry under this formulation, and we use scheming, where LLM agents pursue covert goals, as a concrete case study. We show that recently introduced terminology used to describe scheming, such as covert subversion or deferred subversion, corresponds to well-studied concepts in the mechanism design literature, which not only characterizes the problem but also prescribes concrete mitigation strategies. More broadly, we argue for applying tools developed to study human agent behavior to the analysis of non-human agents.

cs.MA↗
arXiv2026

GameTalk: Training LLMs for Strategic Conversation

Strategic decision-making in multi-agent settings is a key challenge for large language models (LLMs), particularly when coordination and negotiation must unfold over extended conversations. While recent work has explored the use of LLMs in isolated decision tasks, little attention has been given to optimizing long-term objectives through dialogue. We introduce \textbf{GameTalk}, a framework for training LLMs to make strategic decisions via multi-turn interactions. Unlike prior work that focuses on single-turn objectives or static action prediction, we train LLMs to optimize a global objective across full conversations. We achieve this by adapting fine-tuning methods like GRPO, DPO, and STaR to incorporate reward signals that depend on the entire interaction. We evaluate this approach on a suite of increasingly complex games, designed to stress different aspects of reasoning, coordination, and opponent modeling. Our results show that GameTalk significantly outperforms untrained models, especially under reward shaping, with DPO consistently yielding the strongest gains. These findings position conversational fine-tuning as a promising path for LLMs to reason, negotiate, and act in interactive environments.

cs.CL↗