#01Oct 29, 2026
q-bio.QM
Learning developmental dynamics from lineage context
Gokul Gowri, Nic Fishman, William N. Colgan and 10 more
A central goal of biology is to predict the dynamics of multicellular systems. Lineage context (the states of a cell's sisters, cousins, etc.) could inform these predictions, but how best to leverage it remains unclear. Here we introduce lineage inpainting, a generative modeling approach that uses lineage context with tree-structured transformers and stochastic interpolants to model cell state dynamics across lineage trees. Applied to a lineage-traced transcriptional atlas of mouse embryogenesis, it recovers dynamics not resolved by gene expression alone, including multiple transcriptional convergence events where distinct lineages are drawn to a common state. Despite being fit on unperturbed development, lineage inpainting can generate hypotheses about perturbation responses by simulating counterfactuals. These simulations agree in many cases with observed developmental phenotypes, including a single-cell measurement of the Tbx5 knockout response. Our results show that lineage information provides a rich source of context for learning multicellular dynamics.
#02Oct 29, 2026
eess.AS
Discovering Interpretable Acoustic Features in Autoregressive Voice-Cloning TTS Models
Anuj Diwan, David Harwath, Eunsol Choi
Voice-cloning TTS models synthesize an unseen speaker's voice from brief speech prompts, but it remains unclear which acoustic properties they represent and use. We introduce a feature-based interpretability framework for autoregressive voice-cloning TTS models, analyzing features from sparse autoencoders (SAEs), PCA, and random directions via sparse probing, steering, and quantitative auto-interpretability. We focus on Qwen3-TTS and extend probing and steering to $5$ additional models to test generalization across architectures. These models encode concepts like pitch, energy, noise, and accent, but sparse prediction and steering are effective only for some concepts. Strong probing does not always translate to steering or vice-versa. SAEs are useful for sparse probing of human-labelled concepts and novel-concept discovery, while PCA is competitive for dense probing and steering. Auto-interpretability finds $684$ automatically validated SAE features in Qwen3-TTS covering speaker clusters, speaking style, and recording conditions beyond known concepts. Overall, we perform a comprehensive interpretability study of autoregressive voice-cloning TTS models.
#03Oct 29, 2026
cs.LG
The Precision Wall: An Optimizer-Dependent Boundary for Optimization under Power-Law Measurement Spectra
Lngel Kyo
In low-rank matrix sensing of a rank-$D$ factor $U^\ast \in \mathbb{R}^{V \times D}$, replacing isotropic Gaussian designs with power-law measurement covariance $Σ= \mathrm{diag}(j^{-s})_{j=1}^V$ leaves the Burer--Monteiro landscape free of spurious local minima, yet division-normalised first-order optimizers stall above a critical exponent $s^\ast$. We trace this failure to a numerical precision wall. At the ground truth, the smallest non-gauge expected Hessian eigenvalue scales at leading order as $V^{-(s+1)}D^{-s}$. When this curvature drops below the effective denominator floor $ε_O$ of optimizer $O$, normalisation noise overwhelms rare-direction gradients, yielding the leading-order boundary $s^\ast_O(V, D) = [\log(1/ε_O) - \log V]/\log(VD) + δ_O$, where $δ_O$ is a metric-dependent detection lag. With $δ_{\mathrm{Adam}}$ calibrated on four configurations and frozen, this formula predicts Adam's onset within $0.45$ across all 16 cells of a held-out grid ($V \in \{64,128,256,512\} \times D \in \{4,8,16,32\}$), separates fixed-$VD$ pairs, and distinguishes denominator-precision walls from conditioning and sign-quantisation walls. The approximation fails at $D = 2$, reflects a finite-$D$ spectral crossover, and saturates below $\varepsilon_0 = 10^{-8}$ at a dynamical floor.
#04Oct 29, 2026
cs.LG
A Pretrained Model for Bayesian Filtering in Heterogeneous Dynamical Systems
Ke Fan, Wen Wu, Haitao Su and 3 more
Filtering has not yet had its foundation-model moment: state estimation is still dominated either by online Bayesian filtering algorithms that require known dy- namics as inputs, or by learning-based neural filters trained from scratch for a single system or parametric family. The core challenge is structural heterogene- ity: dynamical systems differ in their governing dynamics, physical scales, and noise levels, precluding a shared representation space for a reusable filter. To bridge this gap, we introduce FilterFM, the first pretrained model for Bayesian filtering that estimates latent states across heterogeneous dynamical systems with a single checkpoint. FilterFM employs a hierarchical two-level observation se- quence encoder and a prior-to-posterior state-reconstruction module that together handle varying observation and state dimensions across heterogeneous systems, while modeling state uncertainty via quantile prediction. Trained on a mixture of heterogeneous filtering tasks, FilterFM exhibits superior in-domain performance, delivering significant gains in estimation accuracy, runtime efficiency, and noise robustness compared to existing baselines. Beyond in-domain performance, it marks the first model to successfully enable zero-shot filtering on unseen dynamics, bridging the generalization gap in state estimation. Furthermore, we uncover clear scaling behaviors in foundation-model-based Bayesian filtering, which combined with comprehensive component ablation studies, validate the structural optimality of our design and broaden the generalization scope for this research field.
#05Oct 29, 2026
eess.SY
Adaptive Scenario Generation for KL-DRO Around a Learned Density Model
Aron Brenner, Saurabh Amin
Distributionally robust optimization (DRO) hedges data-driven two-stage stochastic programs against error in the distribution estimated from a finite record, and standard ambiguity sets differ in how they treat realizations absent from that record. A divergence ball around the empirical distribution contains only reweightings of the record, whereas a transport ball also contains distributions supported off the record, including on realizations the data-generating process cannot produce, against which the decision is then hedged as well. We instead propose a Kullback-Leibler (KL) ball centered at a density model fitted to the record, the learned nominal, which lets the adversary up-weight costly unobserved realizations in proportion to the probability the model assigns them. Solving the resulting problem poses a second difficulty, because it can accommodate only a few scenarios, and an independent sample of that size is likely to omit the rare realizations on which the worst case concentrates. We therefore build the scenario set adaptively, alternating between solving the finite problem and drawing new realizations from the learned nominal, steered toward the worst case at the current decision, with importance weights that correct the draws back to the model. On a multi-item newsvendor problem and a capacity expansion problem on realistic grid data, centering the ball at the learned nominal rather than at the record lowers cost under distribution shift, at comparable in-distribution cost, when the record is scarce and the model class captures structure that lets it extrapolate beyond the record. The advantage fades as the record grows or as the shift departs from the structure the model has learned.