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Computer Vision · Vision Models & Multimodal

Raphaela Kang, Hongqiao Chen, Georgia Gkioxari, Pietro Perona

Spatio-temporal reasoning is a remarkable capability of Vision Language Models (VLMs), but the underlying mechanisms of such abilities remain largely opaque. We postulate that visual/geometrical and textual representations of spatial structure must be combined at some point in VLM computations. We search for such confluence, and ask whether the identified representation can causally explain aspects of input-output model behavior through a linear model. We show empirically that VLMs encode object locations by linearly binding \textit{spatial IDs to textual activations, then perform reasoning via language tokens. Through rigorous causal interventions we demonstrate that these IDs, which are ubiquitous across the model, can systematically mediate model beliefs at intermediate VLM layers. Additionally, we find that spatial IDs serve as a diagnostic tool for identifying limitations and bottlenecks in existing VLMs. We extend our analysis to video VLMs and identify an analogous linear temporal ID mechanism. By characterizing our proposed spatiotemporal ID mechanism, we elucidate a previously underexplored internal reasoning process in VLMs, toward improved interpretability and the principled design of more aligned and capable models.

Applications · Time Series

Zheng Wang, Kaixuan Zhang, Wanfang Chen, Xiaonan Lu, Longyuan Li, Tobias Schlagenhauf

Time series forecasting remains a critical challenge across numerous domains, yet the effectiveness of complex models often varies unpredictably across datasets. Recent studies highlight the surprising competitiveness of simple linear models, suggesting that their robustness and interpretability warrant deeper theoretical investigation. This paper presents a systematic study of linear models for time series forecasting, with a focus on the role of characteristic roots in temporal dynamics. We begin by analyzing the noise-free setting, where we show that characteristic roots govern long-term behavior and explain how design choices such as instance normalization and channel independence affect model capabilities. We then extend our analysis to the noisy regime, revealing that models tend to produce spurious roots. This leads to the identification of a key data-scaling property: mitigating the influence of noise requires disproportionately large training data, highlighting the need for structural regularization. To address these challenges, we propose two complementary strategies for robust root restructuring. The first uses rank reduction techniques, including Reduced-Rank Regression (RRR) and Direct Weight Rank Reduction (DWRR), to recover the low-dimensional latent dynamics. The second, a novel adaptive method called Root Purge, encourages the model to learn a noise-suppressing null space during training. Extensive experiments on standard benchmarks demonstrate the effectiveness of both approaches, validating our theoretical insights and achieving state-of-the-art results in several settings. Our findings underscore the potential of integrating classical theories for linear systems with modern learning techniques to build robust, interpretable, and data-efficient forecasting models. The code is publicly available at: https://github.com/Wangzzzzzzzz/RootPurge.

Theory · Interpretability and Visualization

Lukas Eisenmann, Alena Brändle, Zahra Monfared, Daniel Durstewitz

Recurrent Neural Networks (RNNs) have found widespread applications in machine learning for time series prediction and dynamical systems reconstruction, and experienced a recent renaissance with improved training algorithms and architectural designs. Understanding why and how trained RNNs produce their behavior is important for scientific and medical applications, and explainable AI more generally. An RNN's dynamical repertoire depends on the topological and geometrical properties of its state space. Stable and unstable manifolds of periodic points play a particularly important role: They dissect a dynamical system's state space into different basins of attraction, and their intersections lead to chaotic dynamics with fractal geometry. Here we introduce a novel algorithm for detecting these manifolds, with a focus on piecewise-linear RNNs (PLRNNs) employing rectified linear units (ReLUs) as their activation function. We demonstrate how the algorithm can be used to trace the boundaries between different basins of attraction, and hence to characterize multistability, a computationally important property. We further show its utility in finding so-called homoclinic points, the intersections between stable and unstable manifolds, and thus establish the existence of chaos in PLRNNs. Finally we show for an empirical example, electrophysiological recordings from a cortical neuron, how insights into the underlying dynamics could be gained through our method.

Social Aspects · Accountability, Transparency and Interpretability

Yuntai Bao, Xuhong Zhang, Jintao Chen, Ge Su, Yuxiang Cai, Hao Peng, SUN Bing, Haiqin Weng, Liu Yan, Jianwei Yin

Intervention-based model steering offers a lightweight and interpretable alternative to prompting and fine-tuning. However, by adapting strong optimization objectives from fine-tuning, current methods are susceptible to overfitting and often underperform, sometimes generating unnatural outputs. We hypothesize that this is because effective steering requires the faithful identification of internal model mechanisms, not the enforcement of external preferences. To this end, we build on the principles of *distributed alignment search (DAS)*, the standard for causal variable localization, to propose a new steering method: **Concept DAS (CDAS)**. While we adopt the core mechanism of DAS, *distributed interchange intervention (DII)*, we introduce a novel distribution matching objective tailored for the steering task by aligning intervened output distributions with counterfactual distributions. CDAS differs from prior work in two main ways: first, it learns interventions via weak-supervised distribution matching rather than probability maximization; second, it uses DIIs that naturally enable bi-directional steering and allow steering factors to be derived from data, reducing the effort required for hyperparameter tuning and resulting in more faithful and stable control. On AxBench, a large-scale model steering benchmark, we show that CDAS does not always outperform preference-optimization methods but may benefit more from increased model scale. In two safety-related case studies, overriding refusal behaviors of safety-aligned models and neutralizing a chain-of-thought backdoor, CDAS achieves systematic steering while maintaining general model utility. These results indicate that CDAS is complementary to preference-optimization approaches and conditionally constitutes a robust approach to intervention-based model steering.

Tommaso Mencattini, Riccardo Cadei, Francesco Locatello

Randomized Controlled Trials are one of the pillars of science; nevertheless, they rely on hand-crafted hypotheses and expensive analysis. Such constraints prevent causal effect estimation at scale, potentially anchoring on popular yet incomplete hypotheses. We propose to discover the unknown effects of a treatment directly from data. For this, we turn unstructured data from a trial into meaningful representations via pretrained foundation models and interpret them via a Sparse Auto Encoder. However, discovering significant causal effects at the neural level is not trivial due to multiple-testing issues and effects entanglement. To address these challenges, we introduce _Neural Effect Search_, a novel recursive procedure solving both issues by progressive stratification. After assessing the robustness of our algorithm on semi-synthetic experiments, we showcase, in the context of experimental ecology, the first successful unsupervised causal effect identification on a real-world scientific trial.

Theory · Everything Else

Jiale Chen, Yalda Shabanzadeh, Elvir Crnčević, Torsten Hoefler, Dan Alistarh

Quantizing the weights of large language models (LLMs) from 16-bit to lower bitwidth is the de facto approach to deploy massive transformers onto more affordable accelerators. While GPTQ emerged as one of the standard methods for one-shot post-training quantization at LLM scale, its inner workings are described as a sequence of algebraic updates that obscure geometric meaning or worst-case guarantees. In this work, we show that, when executed back-to-front (from the last to first dimension) for a linear layer, GPTQ is mathematically identical to Babai's nearest plane algorithm for the classical closest vector problem (CVP) on a lattice defined by the Hessian matrix of the layer's inputs. This equivalence is based on a sophisticated mathematical argument, and has two analytical consequences: first, the GPTQ error propagation step gains an intuitive geometric interpretation; second, GPTQ inherits the error upper bound of Babai's algorithm under the assumption that no weights are clipped. Leveraging this bound, we design post-training quantization methods that avoid clipping, and outperform the original GPTQ. In addition, we provide efficient GPU inference kernels for the resulting representation. Taken together, these results place GPTQ on a firm theoretical footing and open the door to importing decades of progress in lattice algorithms towards the design of future quantization algorithms for billion-parameter models. Source code is available at https://github.com/IST-DASLab/GPTQ-Babai.

Deep Learning · Graph Neural Networks

Devvrat Joshi, Islem Rekik

Automated knowledge graph (KG) construction is essential for navigating the rapidly expanding body of scientific literature. However, existing approaches face persistent challenges: they struggle to recognize long multi-word entities, often fail to generalize across domains, and typically overlook the hierarchical and logically constrained nature of scientific knowledge. While general-purpose large language models (LLMs) offer some adaptability, they are computationally expensive and yield inconsistent accuracy on specialized, domain-heavy tasks such as scientific knowledge graph construction. As a result, current KGs are shallow and inconsistent, limiting their utility for exploration and synthesis. We propose a two-stage framework for scalable, zero-shot scientific KG construction. The first stage, Z-NERD, introduces (i) Orthogonal Semantic Decomposition (OSD), which promotes domain-agnostic entity recognition by isolating semantic “turns” in text, and (ii) a Multi-Scale TCQK attention mechanism that captures coherent multi-word entities through n-gram–aware attention heads. The second stage, HGNet, performs relation extraction with hierarchy-aware message passing, explicitly modeling parent, child, and peer relations. To enforce global consistency, we introduce two complementary objectives: a Differentiable Hierarchy Loss to discourage cycles and shortcut edges, and a Continuum Abstraction Field (CAF) Loss that embeds abstraction levels along a learnable axis in Euclidean space. To the best of our knowledge, this is the first approach to formalize hierarchical abstraction as a continuous property within standard Euclidean embeddings, offering a simpler and more interpretable alternative to hyperbolic methods. To address data scarcity, we also release SPHERE, a large-scale, multi-domain benchmark for hierarchical relation extraction. Our framework establishes a new state of the art on benchmarks such as SciERC, SciER and SPHERE benchmarks, improving named entity recognition (NER) by 8.08\% and relation extraction (RE) by 5.99\% on the official out-of-distrubtion test sets. In zero-shot settings, the gains are even more pronounced, with improvements of 10.76\% for NER and 26.2\% for RE, marking a significant step toward reliable and scalable scientific knowledge graph construction.

Applications · Robotics

Chengyang He, Xu Liu, Gadiel Sznaier Camps, Joseph Bruno, Guillaume Sartoretti, Mac Schwager

Diffusion policies for visuomotor robot manipulation tasks achieve remarkable dexterity and robustness while only training on a small number of task demonstrations. However, the reason for this performance remains a mystery. In this paper, we offer a surprising hypothesis: diffusion policies essentially memorize an action lookup table---\emph{and this is beneficial}. We posit that, at runtime, diffusion policies find the closest training image to the test image in a latent space, and recall the associated training action (i.e. action chunk), offering reactivity without the need for action generalization. This is effective in the sparse data regime, where there is not enough data density for the model to learn action generalization. We support this claim with systematic empirical evidence, showing that even when conditioned on highly out of distribution (OOD) images, Diffusion Policy still outputs an action chunk from the training data. We evaluate and compare three representative policy families on the same data set: Diffusion Policy, Action Chunking with Transformers (ACT), and GR00T, a pre-trained generalist Vision-Language-Action (VLA) model. We show that Diffusion Policy gives strong action memorization giving surprising robustness in OOD regimes, ACT shows action interpolation with poor robustness in OOD regimes, and GR00T (benefiting from substantial pre-training) shows both action interpolation and OOD robustness. As a simple alternative to Diffusion Policy, we introduce the Action Lookup Table (ALT) policy, showing that an explicit lookup table policy can perform comparably in this low data regime. Despite its simplicity, ALT attains Diffusion Policy–level performance while also providing faster inference and explicit OOD detection via latent-distance thresholds. These results reframe diffusion policies for robot manipulation as reactive memory retrieval under data sparsity, and provide practical tools for interpreting, evaluating, and monitoring such policies. More information can be found at: \url{https://stanfordmsl.github.io/alt/}.

Deep Learning · Everything Else

Xu Wang, Yan Hu, Wang Benyou, Difan Zou

Sparse Autoencoders (SAEs) are widely used to steer large language models (LLMs), based on the assumption that their interpretable features naturally enable effective model behavior steering. Yet a fundamental question remains: does higher interpretability imply better steering utility? To answer this, we train 90 SAEs across three LLMs (Gemma-2-2B, Qwen-2.5-3B, Gemma-2-9B), spanning five architectures and six sparsity levels. We evaluate interpretability with SAEBench (Karvonen et al., 2025) and steering utility with AxBench (Wu et al., 2025), and analyze rank agreement via Kendall’s rank coefficient $\tau_b$. Our analysis reveals only a relatively weak positive association ($\tau_b \approx 0.298$), indicating that interpretability is an insufficient proxy for steering performance. We conjecture the interpretability–utility gap stems from feature selection: not all SAE features are equally effective for steering. To identify features that truly steer LLM behavior, we propose a novel selection criterion, $\Delta$ Token Confidence, which measures how much amplifying a feature changes the next-token distribution. Our method improves steering performance on three LLMs by **52.52\%** compared to the best prior output score–based criterion (Arad et al., 2025). Strikingly, after selecting features with high $\Delta$ Token Confidence, the correlation between interpretability and utility vanishes ($\tau_b \approx 0$) and can even become negative, further highlighting their divergence for the most effective steering features.

Computer Vision · 3D Rendering & Reconstruction

Zhongwen Wang, Han Ling, Weihao Zhang, Yinghui Sun, Quansen Sun

We propose ETGS, a method for reconstructing dynamic thermal scenes by embedding explicit thermodynamic modeling into 3D Gaussian Splatting. Each Gaussian is equipped with physically interpretable thermal parameters, and its thermodynamics evolution is described by a first-order heat-transfer ODE with an analytical closed-form solution. This formulation avoids numerical integration, enables efficient rendering at arbitrary timestamps, and naturally handles irregular sampling and out-of-order observations. We also introduce the Rapid Heat Dynamics (RHD) dataset, which provides millisecond-aligned RGB–IR image pairs covering typical thermal processes such as cooling, warming, heating, and heat transfer. Experiments on RHD show that ETGS captures rapid thermal dynamics more accurately than existing static and dynamic baselines, while maintaining training and rendering efficiency close to that of static 3DGS. Code and dataset are available at https://github.com/jankin-wang/ETGS.

Computer Vision · Vision Models & Multimodal

Minji Kim, Taekyung Kim, Bohyung Han

Video Large Language Models (VideoLLMs) extend the capabilities of vision-language models to spatiotemporal inputs, enabling tasks such as video question answering (VideoQA). Despite recent advances in VideoLLMs, their internal mechanisms on where and how they extract and propagate video and textual information remain less explored. In this study, we investigate the internal information flow of VideoLLMs using mechanistic interpretability techniques. Our analysis reveals consistent patterns across diverse VideoQA tasks: (1) temporal reasoning in VideoLLMs initiates with active cross-frame interactions in early-to-middle layers, (2) followed by progressive video-language integration in middle layers. This is facilitated by alignment between video representations and linguistic embeddings containing temporal concepts. (3) Upon completion of this integration, the model is ready to generate correct answers in middle-to-late layers. (4) Based on our analysis, we show that VideoLLMs retain their VideoQA performance by selecting these effective information pathways while suppressing a substantial amount of attention edges, e.g., 58% in LLaVA-NeXT-7B-Video-FT. These findings provide a blueprint for how VideoLLMs perform temporal reasoning and offer practical insights for improving model interpretability and downstream generalization.

General Machine Learning · Causality

Josh Givens, Song Liu, Henry W J Reeve, Katarzyna Reluga

Within heterogeneous treatment effect (HTE) analysis, various estimands have been proposed to capture the effect of a treatment conditional on covariates. Recently, the conditional quantile comparator (CQC) has emerged as a promising estimand, offering quantile-level summaries akin to the conditional quantile treatment effect (CQTE) while preserving some interpretability of the conditional average treatment effect (CATE). It achieves this by summarising the treated response conditional on both the covariates and the untreated response. Despite these desirable properties, the CQC's current estimation is limited by the need to first estimate the difference in conditional cumulative distribution functions and then invert it. This inversion obscures the CQC estimate, hampering our ability to both model and interpret it. To address this, we propose the first direct estimator of the CQC, allowing for explicit modelling and parameterisation. This explicit parameterisation enables better interpretation of our estimate while also providing a means to constrain and inform the model. We show, both theoretically and empirically, that our estimation error depends directly on the complexity of the CQC itself, improving upon the existing estimation procedure. Furthermore, it retains the desirable double robustness property with respect to nuisance parameter estimation. We further show our method to outperform existing procedures in estimation accuracy across multiple data scenarios while varying sample size and nuisance error. Finally, we apply it to real-world data from an employment scheme, uncovering a reduced range of potential earnings improvement as participant age increases.

Theory · Interpretability and Visualization

Jin Hwa Lee, Matthew Smith, Maxwell Adam, Jesse Hoogland

Current training data attribution (TDA) methods treat the influence one sample has on another as static, but neural networks learn in distinct stages that exhibit changing patterns of influence. In this work, we introduce a framework for stagewise data attribution grounded in singular learning theory. We predict that influence can change non-monotonically, including sign flips and sharp peaks at developmental transitions. We first validate these predictions analytically and empirically in a toy model, showing that dynamic shifts in influence directly map to the model's progressive learning of a semantic hierarchy. Finally, we demonstrate these phenomena at scale in language models, where token-level influence changes align with known developmental stages.

Applications · Neuroscience, Cognitive Science

Takuya Matsuyama, Shinji Nishimoto, Yu Takagi

Understanding the properties of neural populations (or voxels) in the human brain can advance our comprehension of human perceptual and cognitive processing capabilities and contribute to developing brain-inspired computer models. Recent encoding models using deep neural networks (DNNs) have successfully predicted voxel-wise activity. However, interpreting the properties that explain voxel responses remains challenging because of the black-box nature of DNNs. As a solution, we propose LLM-assisted Visual Cortex Captioning (LaVCa), a data-driven approach that leverages large language models (LLMs) to generate natural-language captions for images to which voxels are selective. By applying LaVCa for image-evoked brain activity, we demonstrate that LaVCa generates captions that describe voxel selectivity more accurately than the previous approaches. The captions generated by LaVCa quantitatively capture more detailed properties than the existing method at both the inter-voxel and intra-voxel levels. Furthermore, we find richer representational content within cortical regions that prior neuroimaging studies have deemed selective for simpler categories. These findings offer profound insights into human visual representations by assigning detailed captions throughout the visual cortex while highlighting the potential of LLM-based methods in understanding brain representations.

Social Aspects · Accountability, Transparency and Interpretability

Gabriel Laberge, Ola Ahmad

Post-hoc explanations aim at understanding which input features (or groups thereof) are the most impactful toward certain model decisions. Many such methods have been proposed (ArchAttribute, Occlusion, SHAP, RISE, LIME, Integrated Gradient) and it is hard for practitioners to understand the differences between them. Even worse, faithfulness metrics, often used to quantitatively compare explanation methods, also exhibit inconsistencies. To address these issues, recent work has unified explanation methods through the lens of Functional Decomposition. We extend such work to scenarios where input features are partitioned into groups (e.g. pixel patches) and prove that disagreements between explanation methods and faithfulness metrics are caused by between-group interactions. Crucially, getting rid of between-group interactions leads to a single explanation that is optimal according to all faithfulness metrics. We finally show how to reduce the disagreements by grouping features on tabular/image data.

Applications · Genetics, Cell Biology, Health, etc

Jiahao Li, Jiayi Dong, Peng Ye, Xiaochi Zhou, Haohai Lu, Fei Wang

Modeling single-cell gene expression across diverse biological and technical conditions is crucial for characterizing cellular states and simulating unseen scenarios. Existing methods often treat genes as independent tokens, overlooking their high-level biological relationships and leading to poor performance. We introduce SAVE, a unified generative framework based on conditional Transformers for multi-condition single-cell modeling. SAVE leverages a coarse-grained representation by grouping semantically related genes into blocks, capturing higher-order dependencies among gene modules. A Flow Matching mechanism and condition-masking strategy further enhance flexible simulation and enable generalization to unseen condition combinations. We evaluate SAVE on a range of benchmarks, including conditional generation, batch effect correction, and perturbation prediction. SAVE consistently outperforms state-of-the-art methods in generation fidelity and extrapolative generalization, especially in low-resource or combinatorially held-out settings. Overall, SAVE offers a scalable and generalizable solution for modeling complex single-cell data, with broad utility in virtual cell synthesis and biological interpretation.

Social Aspects · Trustworthy Machine Learning

Matthieu Bou, Nyal Patel, Arjun Jagota, Satyapriya Krishna, Sonali Parbhoo

The objectives that Large Language Models (LLMs) implicitly optimize remain dangerously opaque, making trustworthy alignment and auditing a grand challenge. While Inverse Reinforcement Learning (IRL) can infer reward functions from behaviour, existing approaches either produce a single, overconfident reward estimate or fail to address the fundamental ambiguity of the task (non-identifiability). This paper introduces a principled auditing framework that re-frames reward inference from a simple estimation task to a comprehensive process for verification. Our framework leverages Bayesian IRL to not only recover a distribution over objectives but to enable three critical audit capabilities: (i) Quantifying and systematically reducing non-identifiability by demonstrating posterior contraction over sequential rounds of evidence; (ii) Providing actionable, uncertainty-aware diagnostics that expose spurious shortcuts and identify out-of-distribution prompts where the inferred objective cannot be trusted; and (iii) Validating policy-level utility by showing that the refined, low-uncertainty reward can be used directly in RLHF to achieve training dynamics and toxicity reductions comparable to the ground-truth alignment process. Empirically, our framework successfully audits a detoxified LLM and generalizes beyond detoxification to a helpfulness preference setting, yielding a well-calibrated and interpretable objective that strengthens alignment guarantees. Overall, this work provides a practical toolkit for auditors, safety teams, and regulators to verify what LLMs are truly trying to achieve, moving us toward more trustworthy and accountable AI.

Theory · Interpretability and Visualization

Dmitrii Krasheninnikov, Richard E Turner, David Krueger

We show that language models' activations linearly encode when information was learned during training. Our setup involves creating a model with a known training order by sequentially fine-tuning Llama-3.2-1B on six disjoint but otherwise similar datasets about named entities. We find that the average activations of test samples corresponding to the six training datasets encode the training order: when projected into a 2D subspace, these centroids are arranged exactly in the order of training and lie on a straight line. Further, we show that linear probes can accurately (approx. 90%) distinguish "early" vs. "late" entities, generalizing to entities unseen during the probes' own training. The model can also be fine-tuned to explicitly report an unseen entity's training stage (approx. 80% accuracy). Notably, the training-order encoding does not seem attributable to simple differences in activation magnitudes, losses, or model confidence. Our paper shows that models can differentiate information by its acquisition time, and carries significant implications for how they might manage conflicting data and respond to knowledge modifications.

Social Aspects · Fairness, Equity, Justice and Safety

Weidi Luo, Tianyu Lu, Qiming Zhang, Xiaogeng Liu, Bin Hu, Yue Zhao, Jieyu Zhao, Song Gao, Patrick McDaniel, Zhen Xiang 等

Recent advances in multi-modal large reasoning models (MLRMs) have shown significant ability to interpret complex visual content. While these models possess impressive reasoning capabilities, they also introduce novel and underexplored privacy risks. In this paper, we identify a novel category of privacy leakage in MLRMs: Adversaries can infer sensitive geolocation information, such as users' home addresses or neighborhoods, from user-generated images, including selfies captured in private settings. To formalize and evaluate these risks, we propose a three-level privacy risk framework that categorizes image based on contextual sensitivity and potential for geolocation inference. We further introduce DoxBench, a curated dataset of 500 real-world images reflecting diverse privacy scenarios divided into 6 categories. Our evaluation across 13 advanced MLRMs and MLLMs demonstrates that most of these models outperform non-expert humans in geolocation inference and can effectively leak location-related private information. This significantly lowers the barrier for adversaries to obtain users' sensitive geolocation information. We further analyze and identify two primary factors contributing to this vulnerability: (1) MLRMs exhibit strong geolocation reasoning capabilities by leveraging visual clues in combination with their internal world knowledge; and (2) MLRMs frequently rely on privacy-related visual clues for inference without any built-in mechanisms to suppress or avoid such usage. To better understand and demonstrate real-world attack feasibility, we propose GeoMiner, a collaborative attack framework that decomposes the prediction process into two stages consisting of clue extraction and reasoning to improve geolocation performance. Our findings highlight the urgent need to reassess inference-time privacy risks in MLRMs to better protect users' sensitive information.

Social Aspects · Accountability, Transparency and Interpretability

Borui Yang, Mingxuan Ma, Liyao Xiang, Nan Chen, Xin Zhang, Linghe Kong, Xinghao Jiang

Code language models (LMs) represent valuable intellectual property (IP) as their training involves immense investments, including large-scale code corpora, proprietary annotations, extensive computational resources, and specialized designs. Hence the threat of model IP infringements such as unauthorized redistribution or model theft has become increasingly concerning. While neural network watermarking has been widely studied as a measure to support model ownership verification, watermarking code LMs is particularly challenging due to the seemingly conflicting requirements of code generation: adhering to strict syntactic rules and semantic consistency while allowing flexible changes to embed watermarks, keeping high fidelity of the generated content while being robust to extraction attacks, etc. To resolve the issues, we propose CodeGenGuard, a watermarking framework for code LMs. CodeGenGuard leverages semantic-preserving transformations (SPTs) to encode the watermark and incorporates a dead-code-based data augmentation pipeline to diversify SPT patterns. To improve robustness, we incorporate an efficient dual-LoRA shadow training scheme and an optimizable trigger prompt that learns to extract watermark from both the watermarked and the shadow models. As most SPTs take place in specific contexts, we implant auxiliary prompts during verification to encourage the generation of the context, further enhancing the detection rate. Evaluation results on representative code generation models demonstrate that CodeGenGuard achieves superior watermarking performance to the state-of-the-art.