#01Nov 10, 2026
cs.LG
Causal Concept Explanations for Deep Neural Models
Josh Rountree, Pulkit Verma, Oswin So and 2 more
Concept-based explanations in neural models are important for the development, certification, and adoption of autonomous systems. Yet, interpretability remains correlational. Without methods to guide and quantify causal relationships between explanations, a concept explanation can be provided without being necessary or sufficient for the observed output thereby appearing correct while misleading. We introduce Causal Concept Wrapper Network (CCW-Net), the first use of interventional mediation analysis from fields such as economics, medicine, and epidemiology as a training objective to align causal effects of concept-based explanations with a model's output. We further apply mediation analysis as an evaluation tool to quantify, per concept label combination, how much of any model's output is causally attributable to each concept explanation. As a training objective, CCW-Net shapes a model's concept representations such that they are both necessary and sufficient for the outputs they are credited with and independent of other concepts' contributions. Counterfactual concept representations anchor a set of causal alignment criteria: necessity, sufficiency, and independence. Necessity drives irrelevant concept effects toward zero, sufficiency ensures relevant concept representations fully reconstruct a model's output, and independence enforces the total effect decomposes linearly across concepts. We evaluate CCW-Net across aircraft control, driving, and image classification. CCW-Net provides a step toward concept-based explanations that are not merely interpretable, but quantifiably causal, supporting safer evaluation, certification, and deployment of transparent and trustworthy neural models.
#02Nov 10, 2026
cs.LG
Emergent Biological Capabilities in a Foundation Model for Molecular Interactions
Adi Mashiach
Foundation models trained on large unlabeled corpora develop emergent capabilities, tasks that go beyond the training objective. We extend this paradigm to multimodal biology with Bonbon, a foundation model for molecular interactions trained on approximately 3.2 trillion tokens of paired protein-ligand sequences. From a single representation space, Bonbon exhibits three zero-shot emergent capabilities at hierarchical levels of resolution: functional (mechanism of action), residue (binding site localization, including orthosteric/allosteric discrimination), and bond (covalent versus non-covalent engagement). All three capabilities generalize to out-of-distribution complexes. Bonbon was trained on protein-ligand sequences alone, without any task-specific supervision and without structural coordinates. We conducted controlled scaling experiments across six model scales from 42M to 1.6B parameters; every capability evaluated shows a sharp jump at the largest scale on continuous metrics, even as pretraining loss decreases smoothly. This demonstrates that loss-based scaling laws alone are insufficient to predict when zero-shot emergent capabilities become available. The capabilities reported here emerge after training at a 1:2,000 parameter-to-token ratio to accommodate the sparsity of paired biological interaction data. The same frozen representations achieve state-of-the-art binding and affinity prediction at five orders of magnitude greater speed than co-folding methods. In prospective wet-lab validation across nine disease targets spanning seven protein families, Bonbon achieves a 61.5% dose-response hit rate on de novo compounds, yielding structurally novel molecules not previously reported to inhibit these proteins, including for out-of-distribution targets.
#03Nov 10, 2026
cs.SD
Exploring Post-Hoc Disentanglement of Audio Foundation Models for Music Similarity
Lucas de Souza Brandão, Gabriel da Costa Merlin, Diego Furtado Silva
Audio foundation models like CLAP, MuQ, and MERT excel at capturing general musical similarity. On the other hand, their entangled latent spaces limit interpretability and fine-grained attribute control. Conditional Similarity Networks (CSN) address this by pairing a backbone representation model with learned masks that gate the embedding space into attribute-specific subspaces. However, existing methods train the backbone from scratch, rather than leveraging pretrained foundation models. We instead present a systematic study of post-hoc disentanglement, adapting CSN to gate frozen pretrained embeddings. We evaluate adding trainable parameters to adapt the embedding under different masking and pooling regimes across two datasets. Our findings show that minimal adaptation capacity is sufficient for post-hoc gating to improve both attribute-specific disentanglement and overall retrieval performance, while pooling, masking, and depth choices yield limited additional gains.
#04Nov 10, 2026
cs.LG
Forward-Value Discretization: Faster Stochastic Diffusion Sampling Without High-Order Approximation
Yuchen Jiao, Na Li, Changxiao Cai and 2 more
Stochastic diffusion samplers often require substantially more neural function evaluations (NFEs) than deterministic samplers to achieve comparable sample quality. Although higher-order discretization accelerates deterministic sampling, its benefits for stochastic sampling remains unclear. We establish matching upper and worst-case lower bounds showing that stochastic samplers with higher-order approximations remain first-order convergent, even with exact score functions. Thus, increasing the approximation order does not generally improve the convergence order. Motivated by this limitation, we introduce forward-value discretization, a training-free framework that evaluates the data/noise prediction model at a lookahead estimate constructed from previous predictions. For deterministic sampling, the resulting Forward DPMSolver (F-DPMSolver), improves sample quality at low NFE budgets through its DDIM-based variant, despite remaining first-order convergent. For stochastic sampling, we develop Forward DDPM (F-DDPM), which evaluates the model at a cleaner lookahead point adjusted for subsequent noise injection. This estimate reuses both the previous model prediction and the previously injected noise. Both variants admit first-order convergence guarantees with one model evaluation per iteration. Across CIFAR-10, ImageNet, FFHQ, and LSUN, F-DDPM consistently achieves lower FID than the evaluated stochastic baselines at matched NFE budgets. With 1.5 times as many NFEs as deterministic baselines, it achieves competitive sample quality, narrowing the practical efficiency gap between stochastic and deterministic sampling. Code is available at https://github.com/Na-Li66/F-DDPM.
#05Nov 10, 2026
cs.CV
UGG: Unified Generative Geometry Model
Amani Kiruga, Zhiyi Li, Ruojin Cai and 4 more
Understanding 4D scenes is a core challenge in visual intelligence, requiring models to jointly capture scene geometry, appearance, and dynamics from partial observations. However, existing approaches are subdivided into feedforward models for direct geometric prediction, and generative models for visual synthesis. We introduce UGG, a unified framework for 4D scene understanding that jointly models RGB video and geometric representations such as depth and camera pose. By assigning different noise levels across modalities and time, UGG formulates visual generation and geometric prediction as conditional completion within a single generative model. This flexible formulation enables the model to learn from diverse, heterogeneous datasets with different subsets of geometric and visual annotations. Furthermore, our generative formulation enables inference-time search over multiple plausible scene hypotheses, using geometric evidence extracted from observed RGB frames to improve geometric prediction without ground truth geometry. We demonstrate UGG's effectiveness over non-unified baselines across camera-controlled video generation, depth estimation, and camera pose prediction, including in challenging sparse observation settings. Code and visualizations are available at https://ugg-model.github.io/