Large Language Models (LLMs) demonstrate the ability to solve reasoning and mathematical problems using the Chain-of-Thought (CoT) technique. Expanding CoT length, as seen in models such as DeepSeek-R1, significantly enhances this reasoning for complex problems, but requires costly and high-quality long CoT data and fine-tuning. This work, inspired by the deep thinking paradigm of DeepSeek-R1, utilizes a steering technique to enhance the reasoning ability of an LLM without external datasets. Our method first employs Sparse Autoencoders (SAEs) to extract interpretable features from vanilla CoT. These features are then used to steer the LLM’s internal states during generation. Recognizing that many LLMs do not have corresponding pre-trained SAEs, we further introduce a novel SAE-free steering algorithm, which directly computes steering directions from the residual activations of an LLM, obviating the need for an explicit SAE. Experimental results demonstrate that both our SAE-based and subsequent SAE-free steering algorithms significantly enhance the reasoning capabilities of LLMs.
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Large language models (LLMs) are increasingly integrated into users’ daily lives, leading to a growing demand for personalized outputs.Previous work focuses on leveraging a user’s own history, overlooking inter-user differences that are crucial for effective personalization.While recent work has attempted to model such differences, the reliance on language-based prompts often hampers the effective extraction of meaningful distinctions.To address these issues, we propose Difference-aware Embedding-based Personalization (DEP), a framework that models inter-user differences in the latent space instead of relying on language prompts. DEP constructs soft prompts by contrasting a user’s embedding with those of peers who engaged with similar content, highlighting relative behavioral signals.A sparse autoencoder then filters and compresses both user-specific and difference-aware embeddings, preserving only task-relevant features before injecting them into a frozen LLM.Experiments on personalized review generation show that DEP consistently outperforms baseline methods across multiple metrics.Our code is available at https://github.com/SnowCharmQ/DEP.
Sparse Autoencoders (SAEs) have been proposed as an unsupervised approach to learn a decomposition of a model’s latent space. This enables useful applications, such as fine-grained steering of model outputs without requiring labeled data. Current steering methods identify SAE features to target by analyzing the input tokens that activate them. However, recent work has highlighted that activations alone do not fully describe the effect of a feature on the model’s output. In this work we draw a distinction between two types of features: input features, which mainly capture patterns in the model’s input, and output features, those that have a human-understandable effect on the model’s output. We propose input and output scores to characterize and locate these types of features, and show that high values for both scores rarely co-occur in the same features. These findings have practical implications: After filtering out features with low output scores, steering with SAEs results in a 2–3x improvement, matching the performance of existing supervised methods.
Train One Sparse Autoencoder Across Multiple Sparsity Budgets to Preserve Interpretability and Accuracy
PDF ↗Sparse Autoencoders (SAEs) have proven to be powerful tools for interpreting neural networks by decomposing hidden representations into disentangled, interpretable features via sparsity constraints. However, conventional SAEs are constrained by the fixed sparsity level chosen during training; meeting different sparsity requirements therefore demands separate models and increases the computational footprint during both training and evaluation. We introduce a novel training objective, HierarchicalTopK, which trains a single SAE to optimise reconstructions across multiple sparsity levels simultaneously. Experiments with Gemma-2 2B demonstrate that our approach achieves Pareto-optimal trade-offs between sparsity and explained variance, outperforming traditional SAEs trained at individual sparsity levels. Further analysis shows that HierarchicalTopK preserves high interpretability scores even at higher sparsity. The proposed objective thus closes an important gap between flexibility and interpretability in SAE design.
Mechanistic interpretability of large language models (LLMs) aims to uncover the internal processes of information propagation and reasoning. Sparse autoencoders (SAEs) have demonstrated promise in this domain by extracting interpretable and monosemantic features. However, prior works primarily focus on feature extraction from a single layer, failing to effectively capture activations that span multiple layers. In this paper, we introduce Route Sparse Autoencoder (RouteSAE), a new framework that integrates a routing mechanism with a shared SAE to efficiently extract features from multiple layers. It dynamically assigns weights to activations from different layers, incurring minimal parameter overhead while achieving high interpretability and flexibility for targeted feature manipulation. We evaluate RouteSAE through extensive experiments on Llama-3.2-1B-Instruct. Specifically, under the same sparsity constraint of 64, RouteSAE extracts 22.5% more features than baseline SAEs while achieving a 22.3% higher interpretability score. These results underscore the potential of RouteSAE as a scalable and effective method for LLM interpretability, with applications in feature discovery and model intervention. Our codes are available at https://github.com/swei2001/RouteSAEs.
SAE-SSV: Supervised Steering in Sparse Representation Spaces for Reliable Control of Language Models
PDF ↗Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but controlling their behavior reliably remains challenging, especially in open-ended generation settings. This paper introduces a novel supervised steering approach that operates in sparse, interpretable representation spaces. We employ sparse autoencoders (SAEs) to obtain sparse latent representations that aim to disentangle semantic attributes from model activations. Then we train linear classifiers to identify a small subspace of task-relevant dimensions in latent representations. Finally, we learn supervised steering vectors constrained to this subspace, optimized to align with target behaviors. Experiments across sentiment, truthfulness, and politics polarity steering tasks with multiple LLMs demonstrate that our supervised steering vectors achieve higher success rates with minimal degradation in generation quality compared to existing methods. Further analysis reveals that a notably small subspace is sufficient for effective steering, enabling more targeted and interpretable interventions.
Sparse Autoencoders (SAEs) have recently emerged as powerful tools for interpreting and steering the internal representations of large language models (LLMs). However, conventional approaches to analyzing SAEs typically rely solely on input-side activations, without considering the influence between each latent feature and the model’s output. This work is built on two key hypotheses: (1) activated latents do not contribute equally to the construction of the model’s output, and (2) only latents with high influence are effective for model steering. To validate these hypotheses, we propose Gradient Sparse Autoencoder (GradSAE), a simple yet effective method that identifies the most influential latents by incorporating output-side gradient information.
Computer Vision · 3D Rendering & Reconstruction
Self-supervised pre-training is essential for 3D point cloud representation learning, as annotating their irregular, topology-free structures is costly and labor-intensive. Masked autoencoders (MAEs) offer a promising framework but rely on explicit positional embeddings, such as patch center coordinates, which leak geometric information and limit data-driven structural learning. In this work, we propose Point-MaDi, a novel Point cloud Masked autoencoding Diffusion framework for pre-training that integrates a dual-diffusion pretext task into an MAE architecture to address this issue. Specifically, we introduce a center diffusion mechanism in the encoder, noising and predicting the coordinates of both visible and masked patch centers without ground-truth positional embeddings. These predicted centers are processed using a transformer with self-attention and cross-attention to capture intra- and inter-patch relationships. In the decoder, we design a conditional patch diffusion process, guided by the encoder's latent features and predicted centers to reconstruct masked patches directly from noise. This dual-diffusion design drives comprehensive global semantic and local geometric representations during pre-training, eliminating external geometric priors. Extensive experiments on ScanObjectNN, ModelNet40, ShapeNetPart, S3DIS, and ScanNet demonstrate that Point-MaDi achieves superior performance across downstream tasks, surpassing Point-MAE by 5.51\% on OBJ-BG, 5.17\% on OBJ-ONLY, and 4.34\% on PB-T50-RS for 3D object classification on the ScanObjectNN dataset.
Deep Learning · Generative Models and Autoencoders
Large language model (LLM) routers improve the efficiency of multi-model systems by directing each query to the most appropriate model while leveraging the diverse strengths of heterogeneous LLMs. Most existing approaches frame routing as a classification problem based solely on the input query. While this reduces overhead by avoiding inference across all models, it overlooks valuable information that could be gleaned from potential outputs and fails to capture implicit intent or contextual nuances that often emerge only during response generation. These limitations can result in suboptimal routing decisions, particularly for complex or ambiguous queries that require deeper semantic understanding. To address this challenge, we propose Lookahead, a routing framework that "foresees" potential model outputs by predicting their latent representations and uses these predictions to guide model selection, thus enabling more informed routing without full inference. Within this framework, we implement two approaches based on causal and masked language models. Empirical evaluations across seven public benchmarks—spanning instruction following, mathematical reasoning, and code generation—show that Lookahead consistently outperforms existing routing baselines, achieving an average performance gain of 7.7\% over the state-of-the-art. Our code is available at https://github.com/huangcb01/lookahead-routing.
Deep Learning · Generative Models and Autoencoders
Recent advances in diffusion language models (DLMs) have presented a promising alternative to traditional autoregressive large language models (LLMs). However, DLMs still lag behind LLMs in reasoning performance, especially as the number of denoising steps decreases. Our analysis reveals that this shortcoming arises primarily from the independent generation of masked tokens across denoising steps, which fails to capture the token correlation. In this paper, we define two types of token correlation: intra-sequence correlation and inter-sequence correlation, and demonstrate that enhancing these correlations improves reasoning performance. To this end, we propose a Multi-Reward Optimization (MRO) approach, which encourages DLMs to consider the token correlation during the denoising process. More specifically, our MRO approach leverages test-time scaling, reject sampling, and reinforcement learning to directly optimize the token correlation with multiple elaborate rewards. Additionally, we introduce group step and importance sampling strategies to mitigate reward variance and enhance sampling efficiency. Through extensive experiments, we demonstrate that MRO not only improves reasoning performance but also achieves significant sampling speedups while maintaining high performance on reasoning benchmarks.
Computer Vision · Vision Models & Multimodal
Prior work using Masked Autoencoders (MAEs) typically relies on random patch masking based on the assumption that images have significant redundancies across different channels, allowing for the reconstruction of masked content using cross-channel correlations. However, this assumption does not hold in Multi-Channel Imaging (MCI), where channels may provide complementary information with minimal feature overlap. Thus, these MAEs primarily learn local structures within individual channels from patch reconstruction, failing to fully leverage cross-channel interactions and limiting their MCI effectiveness. In this paper, we present ChA-MAEViT, an MAE-based method that enhances feature learning across MCI channels via four key strategies: (1) dynamic channel-patch masking, which compels the model to reconstruct missing channels in addition to masked patches, thereby enhancing cross-channel dependencies and improving robustness to varying channel configurations; (2) memory tokens, which serve as long-term memory aids to promote information sharing across channels, addressing the challenges of reconstructing structurally diverse channels; (3) hybrid token fusion module, which merges fine-grained patch tokens with a global class token to capture richer representations; and (4) Channel-Aware Decoder, a lightweight decoder utilizes channel tokens to effectively reconstruct image patches. Experiments on satellite and microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, show that ChA-MAEViT significantly outperforms state-of-the-art MCI-ViTs by 3.0-21.5%, highlighting the importance of cross-channel interactions in MCI. Our code is publicly available at https://github.com/chaudatascience/cha_mae_vit.
Deep Learning · Generative Models and Autoencoders
Prompting is the primary method by which we study and control large language models. It is also one of the most powerful: nearly every major capability attributed to LLMs—few-shot learning, chain-of-thought, constitutional AI—was first unlocked through prompting. Yet prompting is rarely treated as science and is frequently frowned upon as alchemy. We argue that this is a category error. If we treat LLMs as a new kind of organism—complex, opaque, and trained rather than programmed—then prompting is not a workaround. It is behavioral science. Mechanistic interpretability peers into the neural substrate, prompting probes the model in its native interface: language. We argue that prompting is not inferior, but rather a key component in the science of LLMs.
Deep Learning · Generative Models and Autoencoders
We propose an inference-time scaling approach for pretrained flow models. Recently, inference-time scaling has gained significant attention in LLMs and diffusion models, improving sample quality or better aligning outputs with user preferences by leveraging additional computation. For diffusion models, particle sampling has allowed more efficient scaling due to the stochasticity at intermediate denoising steps. On the contrary, while flow models have gained popularity as an alternative to diffusion models--offering faster generation and high-quality outputs--efficient inference-time scaling methods used for diffusion models cannot be directly applied due to their deterministic generative process. To enable efficient inference-time scaling for flow models, we propose three key ideas: 1) SDE-based generation, enabling particle sampling in flow models, 2) Interpolant conversion, broadening the search space and enhancing sample diversity, and 3) Rollover Budget Forcing (RBF), an adaptive allocation of computational resources across timesteps to maximize budget utilization. Our experiments show that SDE-based generation and variance-preserving (VP) interpolant-based generation, improves the performance of particle sampling methods for inference-time scaling in flow models. Additionally, we demonstrate that RBF with VP-SDE achieves the best performance, outperforming all previous inference-time scaling approaches.
Deep Learning · Generative Models and Autoencoders
Maritime object detection is essential for navigation safety, surveillance, and autonomous operations, yet constrained by two key challenges: the scarcity of annotated maritime data and poor generalization across various maritime attributes (e.g., object category, viewpoint, location, and imaging environment). To address these challenges, we propose Neptune-X, a data-centric generative-selection framework that enhances training effectiveness by leveraging synthetic data generation with task-aware sample selection. From the generation perspective, we develop X-to-Maritime, a multi-modality-conditioned generative model that synthesizes diverse and realistic maritime scenes. A key component is the Bidirectional Object-Water Attention module, which captures boundary interactions between objects and their aquatic surroundings to improve visual fidelity. To further improve downstream tasking performance, we propose Attribute-correlated Active Sampling, which dynamically selects synthetic samples based on their task relevance. To support robust benchmarking, we construct the Maritime Generation Dataset, the first dataset tailored for generative maritime learning, encompassing a wide range of semantic conditions. Extensive experiments demonstrate that our approach sets a new benchmark in maritime scene synthesis, significantly improving detection accuracy, particularly in challenging and previously underrepresented settings. The code is available at https://github.com/gy65896/Neptune-X.
Deep Learning · Generative Models and Autoencoders
Process reward models (PRMs) offer fine-grained, step-level evaluations that facilitate deeper reasoning processes in large language models (LLMs), proving effective in complex tasks like mathematical reasoning. However, developing PRMs is challenging due to the high cost and limited scalability of human-annotated data. Synthetic data from Monte Carlo (MC) estimation is a promising alternative but suffers from a high noise ratio, which can cause overfitting and hinder large-scale training. In this work, we conduct a preliminary study on the noise distribution in synthetic data from MC estimation, identifying that annotation models tend to both underestimate and overestimate step correctness due to limitations in their annotation capabilities. Building on these insights, we propose {\bf S}elf-Denoising Monte {\bf C}arlo {\bf An}notation (\textsc{Scan}), an efficient data synthesis and noise-tolerant learning framework. Our key findings indicate that: (1) Even lightweight models (e.g., 1.5B parameters) can produce high-quality annotations through self-denoising strategy, enabling PRMs to achieve superior performance with only 6\% the inference cost required by vanilla MC estimation. (2) With our robust learning strategy, PRMs can effectively learn from this weak supervision, achieving a 39.2 F1 score improvement (from 19.9 to 59.1) in ProcessBench. Despite using only a compact synthetic dataset, our models surpass strong baselines, including those trained on large-scale human-annotated datasets such as PRM800K. Furthermore, performance continues to improve as we scale up the synthetic data, highlighting the potential of \textsc{Scan} for scalable, cost-efficient, and robust PRM training.
Applications · Chemistry and Drug Discovery
Coordinate denoising has emerged as a promising method for 3D molecular pretraining due to its theoretical connection to learning molecular force field. However, existing denoising methods rely on oversimplied molecular dynamics that assume atomic motions to be isotropic and homoscedastic. To address these limitations, we propose a novel denoising framework AniDS: Anisotropic Variational Autoencoder for 3D Molecular Denoising. AniDS introduces a structure-aware anisotropic noise generator that can produce atom-specific, full covariance matrices for Gaussian noise distributions to better reflect directional and structural variability in molecular systems. These covariances are derived from pairwise atomic interactions as anisotropic corrections to an isotropic base. Our design ensures that the resulting covariance matrices are symmetric, positive semi-definite, and SO(3)-equivariant, while providing greater capacity to model complex molecular dynamics. Extensive experiments show that AniDS outperforms prior isotropic and homoscedastic denoising models and other leading methods on the MD17 and OC22 benchmarks, achieving average relative improvements of 8.9% and 6.2% in force prediction accuracy. Our case study on a crystal and molecule structure shows that AniDS adaptively suppresses noise along the bonding direction, consistent with physicochemical principles. Our code is available at https://github.com/ZeroKnighting/AniDS.
Deep Learning · Generative Models and Autoencoders
While humans effortlessly draw visual objects and shapes by adaptively allocating attention based on their complexity, existing multimodal large language models (MLLMs) remain constrained by rigid token representations. Bridging this gap, we propose ALTo, an adaptive length tokenizer for autoregressive mask generation. To achieve this, a novel token length predictor is designed, along with a length regularization term and a differentiable token chunking strategy. We further build ALToLLM that seamlessly integrates ALTo into MLLM. Preferences on the trade-offs between mask quality and efficiency is implemented by group relative policy optimization (GRPO). Experiments demonstrate that ALToLLM achieves state-of-the-art performance with adaptive token cost on popular segmentation benchmarks. Code and models will be released.
Deep Learning · Generative Models and Autoencoders
Discrete diffusion models (DDMs) have shown powerful generation ability for discrete data modalities like text and molecules. However, their practical application is hindered by inefficient sampling, requiring a large number of sampling steps. Accelerating DDMs by using larger step sizes typically introduces significant problems in generation quality, as it amplifies the impact of both the compounding decoding error due to factorized predictions and discretization error from numerical approximations, leading to a significant decrease in sampling quality. To address these challenges, we propose learnable sampler distillation (LSD), a novel approach to train fast and high-fidelity samplers for DDMs. LSD employs a distillation approach where a student sampler with a few steps learns to align its intermediate score trajectory with that of a high-quality teacher sampler with numerous steps. This alignment is achieved by optimizing learnable sampler coefficients that adaptively adjust sampling dynamics. Additionally, we further propose LSD+, which also learns time schedules that allocate steps non-uniformly. Experiments across text generation, image generation, and synthetic tasks demonstrate that our proposed approaches outperform existing samplers for DDMs, achieving substantially higher sampling quality with significantly fewer sampling steps.
Deep Learning · Generative Models and Autoencoders
Large language models (LLMs) often produce reasoning steps that are superficially coherent yet internally inconsistent, leading to unreliable outputs. Since such failures typically arise from implicit or poorly-grounded knowledge, we introduce \emph{Grounded Reasoning in Dependency (GRiD)}, a novel dependency-aware reasoning framework that explicitly grounds reasoning steps in structured knowledge. GRiD represents reasoning as a graph consisting of interconnected knowledge extraction nodes and reasoning nodes, enforcing logical consistency through explicit dependencies. Each reasoning step is validated via a lightweight, step-wise verifier that ensures logical correctness relative to its premises. Extensive experiments across diverse reasoning benchmarks—including StrategyQA, CommonsenseQA, GPQA, and TruthfulQA—demonstrate that GRiD substantially improves reasoning accuracy, consistency, and faithfulness compared to recent state-of-the-art structured reasoning methods. Notably, GRiD enhances performance even when applied purely as a lightweight verification module at inference time, underscoring its generalizability and practical utility. Code is available at: https://github.com/cure-lab/GRiD.
Deep Learning · Generative Models and Autoencoders
Diffusion models have emerged as a promising alternative to autoregressive models in modeling discrete categorical data. However, diffusion models that directly work on discrete data space fail to fully exploit the power of iterative refinement, as the signals are lost during transitions between discrete states. Existing continuous diffusion models for discrete data underperform compared to discrete methods, and the lack of a clear connection between the two approaches hinders the development of effective diffusion models for discrete data. In this work, we propose a continuous diffusion model for language modeling that incorporates the geometry of the underlying categorical distribution. We establish a connection between the discrete diffusion and continuous flow on the statistical manifold, and building on this analogy, introduce a simple diffusion process that generalizes existing discrete diffusion models. We further propose a simulation-free training framework based on radial symmetry, along with a simple technique to address the high dimensionality of the manifold. Comprehensive experiments on language modeling benchmarks and other modalities show that our method outperforms existing discrete diffusion models and approaches the performance of autoregressive models.