Automatic Image-Level Morphological Trait Annotation for Organismal Images

Morphological traits are physical characteristics of biological organisms that provide vital clues on how organisms interact with their environment. Yet extracting these traits remains a slow, expert-driven process, limiting their use in large-scale ecological studies. A major bottleneck is the absence of high-quality datasets linking biological images to trait-level annotations. In this work, we demonstrate that sparse autoencoders trained on foundation-model features yield monosemantic, spatially grounded neurons that consistently activate on meaningful morphological parts. Leveraging this property, we introduce a trait annotation pipeline that localizes salient regions and uses vision-language prompting to generate interpretable trait descriptions. Using this approach, we construct Bioscan-Traits, a dataset of 80K trait annotations spanning 19K insect images from BIOSCAN-5M. Human evaluation confirms the biological plausibility of the generated morphological descriptions. We assess design sensitivity through a comprehensive ablation study, systematically varying key design choices and measuring their impact on the quality of the resulting trait descriptions. By annotating traits with a modular pipeline rather than prohibitively expensive manual efforts, we offer a scalable way to inject biologically meaningful supervision into foundation models, enable large-scale morphological analyses, and bridge the gap between ecological relevance and machine-learning practicality.

Polysemanticity or Polysemy? Lexical Identity Confounds Superposition Metrics

If the same neuron activates for both "lender" and "riverside," standard metrics attribute the overlap to superposition--the neuron must be compressing two unrelated concepts. This work explores how much of the overlap is due a lexical confound: neurons fire for a shared word form (such as "bank") rather than for two compressed concepts. A 2x2 factorial decomposition reveals that the lexical-only condition (same word, different meaning) consistently exceeds the semantic-only condition (different word, same meaning) across models spanning 110M-70B parameters. The confound carries into sparse autoencoders (18-36% of features blend senses), sits in <=1% of activation dimensions, and hurts downstream tasks: filtering it out improves word sense disambiguation and makes knowledge edits more selective (p = 0.002).

Stop Probing, Start Coding: Why Linear Probes and Sparse Autoencoders Fail at Compositional Generalisation

The linear representation hypothesis states that neural network activations encode high-level concepts as linear mixtures. However, under superposition, this encoding is a projection from a higher-dimensional concept space into a lower-dimensional activation space, and a linear decision boundary in the concept space need not remain linear after projection. In this setting, classical sparse coding methods with per-sample iterative inference leverage compressed sensing guarantees to recover latent factors. Sparse autoencoders (SAEs), on the other hand, amortise sparse inference into a fixed encoder, introducing a systematic gap. We show this amortisation gap persists across training set sizes, latent dimensions, and sparsity levels, causing SAEs to fail under out-of-distribution (OOD) compositional shifts. Through controlled experiments that decompose the failure, we identify dictionary learning -- not the inference procedure -- as the binding constraint: SAE-learned dictionaries point in substantially wrong directions, and replacing the encoder with per-sample FISTA on the same dictionary does not close the gap. An oracle baseline proves the problem is solvable with a good dictionary at all scales tested. Our results reframe the SAE failure as a dictionary learning challenge, not an amortisation problem, and point to scalable dictionary learning as the key open problem for sparse inference under superposition.

Ghost-FWL: A Large-Scale Full-Waveform LiDAR Dataset for Ghost Detection and Removal

LiDAR has become an essential sensing modality in autonomous driving, robotics, and smart-city applications. However, ghost points (or ghosts), which are false reflections caused by multi-path laser returns from glass and reflective surfaces, severely degrade 3D mapping and localization accuracy. Prior ghost removal relies on geometric consistency in dense point clouds, failing on mobile LiDAR's sparse, dynamic data. We address this by exploiting full-waveform LiDAR (FWL), which captures complete temporal intensity profiles rather than just peak distances, providing crucial cues for distinguishing ghosts from genuine reflections in mobile scenarios. As this is a new task, we present Ghost-FWL, the first and largest annotated mobile FWL dataset for ghost detection and removal. Ghost-FWL comprises 24K frames across 10 diverse scenes with 7.5 billion peak-level annotations, which is 100x larger than existing annotated FWL datasets. Benefiting from this large-scale dataset, we establish a FWL-based baseline model for ghost detection and propose FWL-MAE, a masked autoencoder for efficient self-supervised representation learning on FWL data. Experiments show that our baseline outperforms existing methods in ghost removal accuracy, and our ghost removal further enhances downstream tasks such as LiDAR-based SLAM (66% trajectory error reduction) and 3D object detection (50x false positive reduction). The dataset and code is publicly available and can be accessed via the project page: https://keio-csg.github.io/Ghost-FWL

From Human Cognition to Neural Activations: Probing the Computational Primitives of Spatial Reasoning in LLMs

As spatial intelligence becomes an increasingly important capability for foundation models, it remains unclear whether large language models' (LLMs) performance on spatial reasoning benchmarks reflects structured internal spatial representations or reliance on linguistic heuristics. We address this question from a mechanistic perspective by examining how spatial information is internally represented and used. Drawing on computational theories of human spatial cognition, we decompose spatial reasoning into three primitives, relational composition, representational transformation, and stateful spatial updating, and design controlled task families for each. We evaluate multilingual LLMs in English, Chinese, and Arabic under single pass inference, and analyze internal representations using linear probing, sparse autoencoder based feature analysis, and causal interventions. We find that task relevant spatial information is encoded in intermediate layers and can causally influence behavior, but these representations are transient, fragmented across task families, and weakly integrated into final predictions. Cross linguistic analysis further reveals mechanistic degeneracy, where similar behavioral performance arises from distinct internal pathways. Overall, our results suggest that current LLMs exhibit limited and context dependent spatial representations rather than robust, general purpose spatial reasoning, highlighting the need for mechanistic evaluation beyond benchmark accuracy.

A Universal Vibe? Finding and Controlling Language-Agnostic Informal Register with SAEs

While multilingual language models successfully transfer factual and syntactic knowledge across languages, it remains unclear whether they process culture-specific pragmatic registers, such as slang, as isolated language-specific memorizations or as unified, abstract concepts. We study this by probing the internal representations of Gemma-2-9B-IT using Sparse Autoencoders (SAEs) across three typologically diverse source languages: English, Hebrew, and Russian. To definitively isolate pragmatic register processing from trivial lexical sensitivity, we introduce a novel dataset in which every target term is polysemous, appearing in both literal and informal contexts. We find that while much of the informal-register signal is distributed across language-specific features, a small but highly robust cross-linguistic core consistently emerges. This shared core forms a geometrically coherent ``informal register subspace'' that sharpens in the model's deeper layers. Crucially, these shared representations are not merely correlational: activation steering with these features causally shifts output formality across all source languages and transfers zero-shot to six unseen languages spanning diverse language families and scripts. Together, these results provide the first mechanistic evidence that multilingual LLMs internalize informal register not just as surface-level heuristics, but as a portable, language-agnostic pragmatic abstraction.

How Pruning Reshapes Features: Sparse Autoencoder Analysis of Weight-Pruned Language Models

Weight pruning is a standard technique for compressing large language models, yet its effect on learned internal representations remains poorly understood. We present the first systematic study of how unstructured pruning reshapes the feature geometry of language models, using Sparse Autoencoders (SAEs) as interpretability probes. Across three model families (Gemma 3 1B, Gemma 2 2B, Llama 3.2 1B), two pruning methods (magnitude and Wanda), and six sparsity levels (0--60%), we investigate five research questions spanning seed stability, feature survival, SAE transferability, feature fragility, and causal relevance. Our most striking finding is that rare SAE features--those with low firing rates--survive pruning far better than frequent ones, with within-condition Spearman correlations of rho = -1.0 in 11 of 17 experimental conditions. This counter-intuitive result suggests that pruning acts as implicit feature selection, preferentially destroying high-frequency generic features while preserving specialized rare ones. We further show that Wanda pruning preserves feature structure up to 3.7x better than magnitude pruning, that pre-trained SAEs remain viable on Wanda-pruned models up to 50% sparsity, and that geometric feature survival does not predict causal importance--a dissociation with implications for interpretability under compression.

GaussianGPT: Towards Autoregressive 3D Gaussian Scene Generation

Most recent advances in 3D generative modeling rely on diffusion or flow-matching formulations. We instead explore a fully autoregressive alternative and introduce GaussianGPT, a transformer-based model that directly generates 3D Gaussians via next-token prediction, thus facilitating full 3D scene generation. We first compress Gaussian primitives into a discrete latent grid using a sparse 3D convolutional autoencoder with vector quantization. The resulting tokens are serialized and modeled using a causal transformer with 3D rotary positional embedding, enabling sequential generation of spatial structure and appearance. Unlike diffusion-based methods that refine scenes holistically, our formulation constructs scenes step-by-step, naturally supporting completion, outpainting, controllable sampling via temperature, and flexible generation horizons. This formulation leverages the compositional inductive biases and scalability of autoregressive modeling while operating on explicit representations compatible with modern neural rendering pipelines, positioning autoregressive transformers as a complementary paradigm for controllable and context-aware 3D generation.

Sparse Visual Thought Circuits in Vision-Language Models

Sparse autoencoders (SAEs) improve interpretability in multimodal models, but it remains unclear whether SAE features form modular, composable units for reasoning-an assumption underlying many intervention-based steering methods. We test this modularity hypothesis and find it often fails: intervening on a task-selective feature set can modestly improve reasoning accuracy, while intervening on the union of two such sets reliably induces output drift (large unintended changes in predictions) and degrades accuracy, even under norm-matched perturbations. This non modular circuit interference is consistent with shared internal pathways where feature unions amplify activation shifts. We develop a reproducible causal pipeline to localize and test these sparse visual thought circuits in Qwen3-VL-8B. On a controlled synthetic benchmark with seven task types and three difficulty levels, linear probes identify a mid decoder locus for task type information. We train SAEs at this layer, construct task-selective sets via an explicit rule, and perform inference time scaling and ablation while quantifying accuracy and drift. Our findings-validated with bootstrapped subsamples and permutation controls, and replicated across multiple VLM families and five diverse datasets clarify the boundaries of SAE feature composability and provide a rigorous diagnostic framework for more reliable VLM control.

Sparse Autoencoders for Interpretable Medical Image Representation Learning

Vision foundation models (FMs) achieve state-of-the-art performance in medical imaging. However, they encode information in abstract latent representations that clinicians cannot interrogate or verify. The goal of this study is to investigate Sparse Autoencoders (SAEs) for replacing opaque FM image representations with human-interpretable, sparse features. We train SAEs on embeddings from BiomedParse (biomedical) and DINOv3 (general-purpose) using 909,873 CT and MRI 2D image slices from the TotalSegmentator dataset. We find that learned sparse features: (a) reconstruct original embeddings with high fidelity (R2 up to 0.941) and recover up to 87.8% of downstream performance using only 10 features (99.4% dimensionality reduction), (b) preserve semantic fidelity in image retrieval tasks, (c) correspond to specific concepts that can be expressed in language using large language model (LLM)-based auto-interpretation. (d) bridge clinical language and abstract latent representations in zero-shot language-driven image retrieval. Our work indicates SAEs are a promising pathway towards interpretable, concept-driven medical vision systems. Code repository: https://github.com/pwesp/sail.