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Jul 7

Thinking in Different Spaces: Domain-Specific Latent Geometry Survives Cross-Architecture Translation

We investigate whether independently trained language models converge to geometrically compatible latent representations, and whether this compatibility can be exploited to correct model behavior at inference time without any weight updates. We learn a linear projection matrix that maps activation vectors from a large teacher model into the coordinate system of a smaller student model, then intervene on the student's residual stream during generation by substituting its internal state with the translated teacher representation. Across a fully crossed experimental matrix of 20 heterogeneous teacher-student pairings spanning mixture-of-experts, dense, code-specialized, and synthetically trained architectures, the Ridge projection consistently achieves R^2 = 0.50 on verbal reasoning and R^2 = 0.40 on mathematical reasoning, collapsing to R^2 = -0.22 under permutation control and R^2 = 0.01 under L_1 regularization. Behavioral correction rates range from 14.0% to 50.0% on TruthfulQA (mean 25.2%) and from 8.5% to 43.3% on GSM8K arithmetic reasoning (mean 25.5%), demonstrating that the method generalizes across fundamentally different reasoning domains. We report a near-zero correlation between geometric alignment quality and behavioral correction rate (r = -0.07), revealing a dissociation between representation space fidelity and output space impact. Intervention strength is architecture-specific: student models exhibit characteristic sensitivity profiles that invert across domains, with the most steerable verbal student becoming the least steerable mathematical student. Finally, a double dissociation experiment conducted across all 20 model pairings confirms without exception that projection matrices collapse catastrophically when transferred across reasoning domains (mean R^2 = -3.83 in both transfer directions), establishing domain-specific subspace geometry as a universal property of LMs.

  • 3 authors
·
Mar 19

Enhanced Sampling, Public Dataset and Generative Model for Drug-Protein Dissociation Dynamics

Drug-protein binding and dissociation dynamics are fundamental to understanding molecular interactions in biological systems. While many tools for drug-protein interaction studies have emerged, especially artificial intelligence (AI)-based generative models, predictive tools on binding/dissociation kinetics and dynamics are still limited. We propose a novel research paradigm that combines molecular dynamics (MD) simulations, enhanced sampling, and AI generative models to address this issue. We propose an enhanced sampling strategy to efficiently implement the drug-protein dissociation process in MD simulations and estimate the free energy surface (FES). We constructed a program pipeline of MD simulations based on this sampling strategy, thus generating a dataset including 26,612 drug-protein dissociation trajectories containing about 13 million frames. We named this dissociation dynamics dataset DD-13M and used it to train a deep equivariant generative model UnbindingFlow, which can generate collision-free dissociation trajectories. The DD-13M database and UnbindingFlow model represent a significant advancement in computational structural biology, and we anticipate its broad applicability in machine learning studies of drug-protein interactions. Our ongoing efforts focus on expanding this methodology to encompass a broader spectrum of drug-protein complexes and exploring novel applications in pathway prediction.

  • 9 authors
·
Apr 25, 2025