OpenRaiser/Intern-Atlas huggingface dataset:
Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design
Venue: Conference ICLR 2025
Year: 2025

Bayesian optimization (BO) is a powerful framework to optimize black-box expensive-to-evaluate functions via sequential interactions. In several important problems (e.g. drug discovery, circuit design, neural architecture search, etc.), though, such functions are defined over large $\textit{combinatorial and unstructured}$ spaces. This makes existing BO algorithms not feasible due to the intractable maximization of the acquisition function over these domains. To address this issue, we propose $\textbf{GameOpt}$, a novel game-theoretical approach to combinatorial BO. $\textbf{GameOpt}$ establishes a cooperative game between the different optimization variables, and selects points that are game $\textit{equilibria}$ of an upper confidence bound acquisition function. These are stable configurations from which no variable has an incentive to deviate$-$ analog to local optima in continuous domains. Crucially, this allows us to efficiently break down the complexity of the combinatorial domain into individual decision sets, making $\textbf{GameOpt}$ scalable to large combinatorial spaces. We demonstrate the application of $\textbf{GameOpt}$ to the challenging $\textit{protein design}$ problem and validate its performance on four real-world protein datasets. Each protein can take up to $20^{X}$ possible configurations, where $X$ is the length of a protein, making standard BO methods infeasible. Instead, our approach iteratively selects informative protein configurations and very quickly discovers highly active protein variants compared to other baselines.
Mechanistic Permutability: Match Features Across Layers
Venue: Conference ICLR 2025
Year: 2025

Understanding how features evolve across layers in deep neural networks is a fundamental challenge in mechanistic interpretability, particularly due to polysemanticity and feature superposition. While Sparse Autoencoders (SAEs) have been used to extract interpretable features from individual layers, aligning these features across layers has remained an open problem. In this paper, we introduce SAE Match, a novel, data-free method for aligning SAE features across different layers of a neural network. Our approach involves matching features by minimizing the mean squared error between the folded parameters of SAEs, a technique that incorporates activation thresholds into the encoder and decoder weights to account for differences in feature scales. Through extensive experiments on the Gemma 2 language model, we demonstrate that our method effectively captures feature evolution across layers, improving feature matching quality. We also show that features persist over several layers and that our approach can approximate hidden states across layers. Our work advances the understanding of feature dynamics in neural networks and provides a new tool for mechanistic interpretability studies.
MANTRA: The Manifold Triangulations Assemblage
Venue: Conference ICLR 2025
Year: 2025

The rising interest in leveraging higher-order interactions present in complex systems has led to a surge in more expressive models exploiting higher-order structures in the data, especially in topological deep learning (TDL), which designs neural networks on higher-order domains such as simplicial complexes. However, progress in this field is hindered by the scarcity of datasets for benchmarking these architectures. To address this gap, we introduce MANTRA, the first large-scale, diverse, and intrinsically higher-order dataset for benchmarking higher-order models, comprising over 43,000 and 250,000 triangulations of surfaces and three-dimensional manifolds, respectively. With MANTRA, we assess several graph- and simplicial complex-based models on three topological classification tasks. We demonstrate that while simplicial complex-based neural networks generally outperform their graph-based counterparts in capturing simple topological invariants, they also struggle, suggesting a rethink of TDL. Thus, MANTRA serves as a benchmark for assessing and advancing topological methods, leading the way for more effective higher-order models.
Layer Swapping for Zero-Shot Cross-Lingual Transfer in Large Language Models
Venue: Conference ICLR 2025
Year: 2025

Model merging, such as model souping, is the practice of combining different models with the same architecture together without further training. In this work, we present a model merging methodology that addresses the difficulty of fine-tuning Large Language Models (LLMs) for target tasks in non-English languages, where task-specific data is often unavailable. We focus on mathematical reasoning and without in-language math data, facilitate cross-lingual transfer by composing language and math capabilities. Starting from the same pretrained model, we fine-tune separate "experts" on math instruction data in English and on generic instruction data in the target language. We then replace the top and bottom transformer layers of the math expert directly with layers from the language expert, which consequently enhances math performance in the target language. The resulting merged models outperform the individual experts and other merging methods on the math benchmark, MGSM, by 10% across four major languages where math instruction data is scarce. In addition, this layer swapping is simple, inexpensive, and intuitive, as it is based on an interpretative analysis of the most important parameter changes during the fine-tuning of each expert. The ability to successfully re-compose LLMs for cross-lingual transfer in this manner opens up future possibilities to combine model expertise, create modular solutions, and transfer reasoning capabilities across languages all post hoc.
Efficient and Accurate Explanation Estimation with Distribution Compression
Venue: Conference ICLR 2025
Year: 2025

We discover a theoretical connection between explanation estimation and distribution compression that significantly improves the approximation of feature attributions, importance, and effects. While the exact computation of various machine learning explanations requires numerous model inferences and becomes impractical, the computational cost of approximation increases with an ever-increasing size of data and model parameters. We show that the standard i.i.d. sampling used in a broad spectrum of algorithms for post-hoc explanation leads to an approximation error worthy of improvement. To this end, we introduce Compress Then Explain (CTE), a new paradigm of sample-efficient explainability. It relies on distribution compression through kernel thinning to obtain a data sample that best approximates its marginal distribution. CTE significantly improves the accuracy and stability of explanation estimation with negligible computational overhead. It often achieves an on-par explanation approximation error 2-3x faster by using fewer samples, i.e. requiring 2-3x fewer model evaluations. CTE is a simple, yet powerful, plug-in for any explanation method that now relies on i.i.d. sampling.
Matcha: Mitigating Graph Structure Shifts with Test-Time Adaptation
Venue: Conference ICLR 2025
Year: 2025

Powerful as they are, graph neural networks (GNNs) are known to be vulnerable to distribution shifts. Recently, test-time adaptation (TTA) has attracted attention due to its ability to adapt a pre-trained model to a target domain, without re-accessing the source domain. However, existing TTA algorithms are primarily designed for attribute shifts in vision tasks, where samples are independent. These methods perform poorly on graph data that experience structure shifts, where node connectivity differs between source and target graphs. We attribute this performance gap to the distinct impact of node attribute shifts versus graph structure shifts: the latter significantly degrades the quality of node representations and blurs the boundaries between different node categories. To address structure shifts in graphs, we propose Matcha, an innovative framework designed for effective and efficient adaptation to structure shifts by adjusting the htop-aggregation parameters in GNNs. To enhance the representation quality, we design a prediction-informed clustering loss to encourage the formation of distinct clusters for different node categories. Additionally, Matcha seamlessly integrates with existing TTA algorithms, allowing it to handle attribute shifts effectively while improving overall performance under combined structure and attribute shifts. We validate the effectiveness of Matcha on both synthetic and real-world datasets, demonstrating its robustness across various combinations of structure and attribute shifts. Our code is available at https://github.com/baowenxuan/Matcha .
Homomorphism Counts as Structural Encodings for Graph Learning
Venue: Conference ICLR 2025
Year: 2025

Graph Transformers are popular neural networks that extend the well-known Transformer architecture to the graph domain. These architectures operate by applying self-attention on graph nodes and incorporating graph structure through the use of positional encodings (e.g., Laplacian positional encoding) or structural encodings (e.g., random-walk structural encoding). The quality of such encodings is critical, since they provide the necessary $\textit{graph inductive biases}$ to condition the model on graph structure. In this work, we propose $\textit{motif structural encoding}$ (MoSE) as a flexible and powerful structural encoding framework based on counting graph homomorphisms. Theoretically, we compare the expressive power of MoSE to random-walk structural encoding and relate both encodings to the expressive power of standard message passing neural networks. Empirically, we observe that MoSE outperforms other well-known positional and structural encodings across a range of architectures, and it achieves state-of-the-art performance on a widely studied molecular property prediction dataset.
Glimpse: Enabling White-Box Methods to Use Proprietary Models for Zero-Shot LLM-Generated Text Detection
Venue: Conference ICLR 2025
Year: 2025

Advanced large language models (LLMs) can generate text almost indistinguishable from human-written text, highlighting the importance of LLM-generated text detection. However, current zero-shot techniques face challenges as white-box methods are restricted to use weaker open-source LLMs, and black-box methods are limited by partial observation from stronger proprietary LLMs. It seems impossible to enable white-box methods to use proprietary models because API-level access to the models neither provides full predictive distributions nor inner embeddings. To traverse the divide, we propose **Glimpse**, a probability distribution estimation approach, predicting the full distributions from partial observations. Despite the simplicity of Glimpse, we successfully extend white-box methods like Entropy, Rank, Log-Rank, and Fast-DetectGPT to latest proprietary models. Experiments show that Glimpse with Fast-DetectGPT and GPT-3.5 achieves an average AUROC of about 0.95 in five latest source models, improving the score by 51% relative to the remaining space of the open source baseline. It demonstrates that the latest LLMs can effectively detect their own outputs, suggesting that advanced LLMs may be the best shield against themselves. We release our code and data at https://github.com/baoguangsheng/glimpse.
SigDiffusions: Score-Based Diffusion Models for Time Series via Log-Signature Embeddings
Venue: Conference ICLR 2025
Year: 2025

Score-based diffusion models have recently emerged as state-of-the-art generative models for a variety of data modalities. Nonetheless, it remains unclear how to adapt these models to generate long multivariate time series. Viewing a time series as the discretisation of an underlying continuous process, we introduce SigDiffusion, a novel diffusion model operating on log-signature embeddings of the data. The forward and backward processes gradually perturb and denoise log-signatures while preserving their algebraic structure. To recover a signal from its log-signature, we provide new closed-form inversion formulae expressing the coefficients obtained by expanding the signal in a given basis (e.g. Fourier or orthogonal polynomials) as explicit polynomial functions of the log-signature. Finally, we show that combining SigDiffusions with these inversion formulae results in high-quality long time series generation, competitive with the current state-of-the-art on various datasets of synthetic and real-world examples.
Round and Round We Go! What makes Rotary Positional Encodings useful?
Venue: Conference ICLR 2025
Year: 2025

Positional Encodings (PEs) are a critical component of Transformer-based Large Language Models (LLMs), providing the attention mechanism with important sequence-position information. One of the most popular types of encoding used today in LLMs are Rotary Positional Encodings (RoPE), that rotate the queries and keys based on their relative distance. A common belief is that RoPE is useful because it helps to decay token dependency as relative distance increases. In this work, we argue that this is unlikely to be the core reason. We study the internals of a trained Gemma 7B model to understand how RoPE is being used at a mechanical level. We find that Gemma learns to use RoPE to construct robust "positional" attention patterns by exploiting the highest frequencies. We also find that, in general, Gemma greatly prefers to use the lowest frequencies of RoPE, which we suspect are used to carry semantic information. We mathematically prove interesting behaviours of RoPE and conduct experiments to verify our findings, proposing a modification of RoPE that fixes some highlighted issues and improves performance. We believe that this work represents an interesting step in better understanding PEs in LLMs, which we believe holds crucial value for scaling LLMs to large sizes and context lengths.
Dream to Manipulate: Compositional World Models Empowering Robot Imitation Learning with Imagination
Venue: Conference ICLR 2025
Year: 2025

A world model provides an agent with a representation of its environment, enabling it to predict the causal consequences of its actions. Current world models typically cannot directly and explicitly imitate the actual environment in front of a robot, often resulting in unrealistic behaviors and hallucinations that make them unsuitable for real-world robotics applications. To overcome those challenges, we propose to rethink robot world models as learnable digital twins. We introduce DreMa, a new approach for constructing digital twins automatically using learned explicit representations of the real world and its dynamics, bridging the gap between traditional digital twins and world models. DreMa replicates the observed world and its structure by integrating Gaussian Splatting and physics simulators, allowing robots to imagine novel configurations of objects and to predict the future consequences of robot actions thanks to its compositionality. We leverage this capability to generate new data for imitation learning by applying equivariant transformations to a small set of demonstrations. Our evaluations across various settings demonstrate significant improvements in accuracy and robustness by incrementing actions and object distributions, reducing the data needed to learn a policy and improving the generalization of the agents. As a highlight, we show that a real Franka Emika Panda robot, powered by DreMa's imagination, can successfully learn novel physical tasks from just a single example per task variation (one-shot policy learning). Our project page can be found in: https://dreamtomanipulate.github.io/.
Intrinsic Dimension Correlation: uncovering nonlinear connections in multimodal representations
Venue: Conference ICLR 2025
Year: 2025

To gain insight into the mechanisms behind machine learning methods, it is crucial to establish connections among the features describing data points. However, these correlations often exhibit a high-dimensional and strongly nonlinear nature, which makes them challenging to detect using standard methods. This paper exploits the entanglement between intrinsic dimensionality and correlation to propose a metric that quantifies the (potentially nonlinear) correlation between high-dimensional manifolds. We first validate our method on synthetic data in controlled environments, showcasing its advantages and drawbacks compared to existing techniques. Subsequently, we extend our analysis to large-scale applications in neural network representations. Specifically, we focus on latent representations of multimodal data, uncovering clear correlations between paired visual and textual embeddings, whereas existing methods struggle significantly in detecting similarity. Our results indicate the presence of highly nonlinear correlation patterns between latent manifolds.
GenVP: Generating Visual Puzzles with Contrastive Hierarchical VAEs
Venue: Conference ICLR 2025
Year: 2025

Raven's Progressive Matrices (RPMs) is an established benchmark to examine the ability to perform high-level abstract visual reasoning (AVR). Despite the current success of algorithms that solve this task, humans can generalize beyond a given puzzle and create new puzzles given a set of rules, whereas machines remain locked in solving a fixed puzzle from a curated choice list. We propose Generative Visual Puzzles (GenVP), a framework to model the entire RPM generation process, a substantially more challenging task. Our model's capability spans from generating multiple solutions for one specific problem prompt to creating complete new puzzles out of the desired set of rules. Experiments on five different datasets indicate that GenVP achieves state-of-the-art (SOTA) performance both in puzzle-solving accuracy and out-of-distribution (OOD) generalization in 22 OOD scenarios. Compared to SOTA generative approaches, which struggle to solve RPMs when the feasible solution space increases, GenVP efficiently generalizes to these challenging setups. Moreover, our model demonstrates the ability to produce a wide range of complete RPMs given a set of abstract rules by effectively capturing the relationships between abstract rules and visual object properties.
Explain Yourself, Briefly! Self-Explaining Neural Networks with Concise Sufficient Reasons
Venue: Conference ICLR 2025
Year: 2025

*Minimal sufficient reasons* represent a prevalent form of explanation - the smallest subset of input features which, when held constant at their corresponding values, ensure that the prediction remains unchanged. Previous *post-hoc* methods attempt to obtain such explanations but face two main limitations: (1) Obtaining these subsets poses a computational challenge, leading most scalable methods to converge towards suboptimal, less meaningful subsets; (2) These methods heavily rely on sampling out-of-distribution input assignments, potentially resulting in counterintuitive behaviors. To tackle these limitations, we propose in this work a self-supervised training approach, which we term *sufficient subset training* (SST). Using SST, we train models to generate concise sufficient reasons for their predictions as an integral part of their output. Our results indicate that our framework produces succinct and faithful subsets substantially more efficiently than competing post-hoc methods, while maintaining comparable predictive performance.
Physics-Informed Diffusion Models
Venue: Conference ICLR 2025
Year: 2025

Generative models such as denoising diffusion models are quickly advancing their ability to approximate highly complex data distributions. They are also increasingly leveraged in scientific machine learning, where samples from the implied data distribution are expected to adhere to specific governing equations. We present a framework that unifies generative modeling and partial differential equation fulfillment by introducing a first-principle-based loss term that enforces generated samples to fulfill the underlying physical constraints. Our approach reduces the residual error by up to two orders of magnitude compared to previous work in a fluid flow case study and outperforms task-specific frameworks in relevant metrics for structural topology optimization. We also present numerical evidence that our extended training objective acts as a natural regularization mechanism against overfitting. Our framework is simple to implement and versatile in its applicability for imposing equality and inequality constraints as well as auxiliary optimization objectives.
E(n) Equivariant Topological Neural Networks
Venue: Conference ICLR 2025
Year: 2025

Graph neural networks excel at modeling pairwise interactions, but they cannot flexibly accommodate higher-order interactions and features. Topological deep learning (TDL) has emerged recently as a promising tool for addressing this issue. TDL enables the principled modeling of arbitrary multi-way, hierarchical higher-order interactions by operating on combinatorial topological spaces, such as simplicial or cell complexes, instead of graphs. However, little is known about how to leverage geometric features such as positions and velocities for TDL. This paper introduces E(n)-Equivariant Topological Neural Networks (ETNNs), which are E(n)-equivariant message-passing networks operating on combinatorial complexes, formal objects unifying graphs, hypergraphs, simplicial, path, and cell complexes. ETNNs incorporate geometric node features while respecting rotation, reflection, and translation equivariance. Moreover, being TDL models, ETNNs are natively ready for settings with heterogeneous interactions. We provide a theoretical analysis to show the improved expressiveness of ETNNs over architectures for geometric graphs. We also show how E(n)-equivariant variants of TDL models can be directly derived from our framework. The broad applicability of ETNNs is demonstrated through two tasks of vastly different scales: i) molecular property prediction on the QM9 benchmark and ii) land-use regression for hyper-local estimation of air pollution with multi-resolution irregular geospatial data. The results indicate that ETNNs are an effective tool for learning from diverse types of richly structured data, as they match or surpass SotA equivariant TDL models with a significantly smaller computational burden, thus highlighting the benefits of a principled geometric inductive bias. Our implementation of ETNNs can be found at https://github.com/NSAPH-Projects/topological-equivariant-networks.
Efficient Model-Based Reinforcement Learning Through Optimistic Thompson Sampling
Venue: Conference ICLR 2025
Year: 2025

Learning complex robot behavior through interactions with the environment necessitates principled exploration. Effective strategies should prioritize exploring regions of the state-action space that maximize rewards, with optimistic exploration emerging as a promising direction aligned with this idea and enabling sample-efficient reinforcement learning. However, existing methods overlook a crucial aspect: the need for optimism to be informed by a belief connecting the reward and state. To address this, we propose a practical, theoretically grounded approach to optimistic exploration based on Thompson sampling. Our model structure is the first that allows for reasoning about joint uncertainty over transitions and rewards. We apply our method on a set of MuJoCo and VMAS continuous control tasks. Our experiments demonstrate that optimistic exploration significantly accelerates learning in environments with sparse rewards, action penalties, and difficult-to-explore regions. Furthermore, we provide insights into when optimism is beneficial and emphasize the critical role of model uncertainty in guiding exploration.