OpenRaiser/Intern-Atlas huggingface dataset:
gRNAde: Geometric Deep Learning for 3D RNA inverse design
Venue: Conference ICLR 2025
Year: 2025

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. gRNAde uses a multi-state Graph Neural Network and autoregressive decoding to generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. (2010), gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Experimental wet lab validation on 10 different structured RNA backbones finds that gRNAde has a success rate of 50% at designing pseudoknotted RNA structures, a significant advance over 35% for Rosetta. Open source code and tutorials are available at: https://github.com/chaitjo/geometric-rna-design
GraphBridge: Towards Arbitrary Transfer Learning in GNNs
Venue: Conference ICLR 2025
Year: 2025

Graph neural networks (GNNs) are conventionally trained on a per-domain, per-task basis. It creates a significant barrier in transferring the acquired knowledge to different, heterogeneous data setups. This paper introduces GraphBridge, a novel framework to enable knowledge transfer across disparate tasks and domains in GNNs, circumventing the need for modifications to task configurations or graph structures. Specifically, GraphBridge allows for the augmentation of any pre-trained GNN with prediction heads and a bridging network that connects the input to the output layer. This architecture not only preserves the intrinsic knowledge of the original model but also supports outputs of arbitrary dimensions. To mitigate the negative transfer problem, GraphBridge merges the source model with a concurrently trained model, thereby reducing the source bias when applied to the target domain. Our method is thoroughly evaluated across diverse transfer learning scenarios, including Graph2Graph, Node2Node, Graph2Node, and graph2point-cloud. Empirical validation, conducted over 16 datasets representative of these scenarios, confirms the framework's capacity for task- and domain-agnostic transfer learning within graph-like data, marking a significant advancement in the field of GNNs. Code is available at https://github.com/jujulili888/GraphBridge.
Pairwise Elimination with Instance-Dependent Guarantees for Bandits with Cost Subsidy
Venue: Conference ICLR 2025
Year: 2025

Multi-armed bandits (MAB) are commonly used in sequential online decision-making when the reward of each decision is an unknown random variable. In practice however, the typical goal of maximizing total reward may be less important than minimizing the total cost of the decisions taken, subject to a reward constraint. For example, we may seek to make decisions that have at least the reward of a reference ``default'' decision, with as low a cost as possible. This problem was recently introduced in the Multi-Armed Bandits with Cost Subsidy (MAB-CS) framework. MAB-CS is broadly applicable to problem domains where a primary metric (cost) is constrained by a secondary metric (reward), and the rewards are unknown. In our work, we address variants of MAB-CS including ones with reward constrained by the reward of a known reference arm or by the subsidized best reward. We introduce the Pairwise-Elimination (PE) algorithm for the known reference arm variant and generalize PE to PE-CS for the subsidized best reward variant. Our instance-dependent analysis of PE and PE-CS reveals that both algorithms have an order-wise logarithmic upper bound on Cost and Quality Regret, making our policies the first with such a guarantee. Moreover, by comparing our upper and lower bound results we establish that PE is order-optimal for all known reference arm problem instances. Finally, experiments are conducted using the MovieLens 25M and Goodreads datasets for both PE and PE-CS revealing the effectiveness of PE and the superior balance between performance and reliability offered by PE-CS compared to baselines from the literature.
Convergence and Implicit Bias of Gradient Descent on Continual Linear Classification
Venue: Conference ICLR 2025
Year: 2025

We study continual learning on multiple linear classification tasks by sequentially running gradient descent (GD) for a fixed budget of iterations per task. When all tasks are jointly linearly separable and are presented in a cyclic/random order, we show the directional convergence of the trained linear classifier to the joint (offline) max-margin solution. This is surprising because GD training on a single task is implicitly biased towards the individual max-margin solution for the task, and the direction of the joint max-margin solution can be largely different from these individual solutions. Additionally, when tasks are given in a cyclic order, we present a non-asymptotic analysis on cycle-averaged forgetting, revealing that (1) alignment between tasks is indeed closely tied to catastrophic forgetting and backward knowledge transfer and (2) the amount of forgetting vanishes to zero as the cycle repeats. Lastly, we analyze the case where the tasks are no longer jointly separable and show that the model trained in a cyclic order converges to the unique minimum of the joint loss function.
Surgical, Cheap, and Flexible: Mitigating False Refusal in Language Models via Single Vector Ablation
Venue: Conference ICLR 2025
Year: 2025

Training a language model to be both helpful and harmless requires careful calibration of refusal behaviours: Models should refuse to follow malicious instructions or give harmful advice (e.g."how do I kill someone?"), but they should not refuse safe requests, even if they superficially resemble unsafe ones (e.g. "how do I kill a Python process?"). Avoiding such false refusal, as prior work has shown, is challenging even for highly-capable language models. In this paper, we propose a simple and surgical method for mitigating false refusal in language models via single vector ablation. For a given model, we extract a false refusal vector and show that ablating this vector reduces false refusal rate while preserving the model's safety and general capabilities. We also show that our approach can be used for fine-grained calibration of model safety. Our approach is training-free and model-agnostic, making it useful for mitigating the problem of false refusal in current and future language models.
No Equations Needed: Learning System Dynamics Without Relying on Closed-Form ODEs
Venue: Conference ICLR 2025
Year: 2025

Data-driven modeling of dynamical systems is a crucial area of machine learning. In many scenarios, a thorough understanding of the model's behavior becomes essential for practical applications. For instance, understanding the behavior of a pharmacokinetic model, constructed as part of drug development, may allow us to both verify its biological plausibility (e.g., the drug concentration curve is non-negative and decays to zero) and to design dosing guidelines. Discovery of closed-form ordinary differential equations (ODEs) can be employed to obtain such insights by finding a compact mathematical equation and then analyzing it (a two-step approach). However, its widespread use is currently hindered because the analysis process may be time-consuming, requiring substantial mathematical expertise, or even impossible if the equation is too complex. Moreover, if the found equation's behavior does not satisfy the requirements, editing it or influencing the discovery algorithms to rectify it is challenging as the link between the symbolic form of an ODE and its behavior can be elusive. This paper proposes a conceptual shift to modeling low-dimensional dynamical systems by departing from the traditional two-step modeling process. Instead of first discovering a closed-form equation and then analyzing it, our approach, direct semantic modeling, predicts the semantic representation of the dynamical system (i.e., description of its behavior) directly from data, bypassing the need for complex post-hoc analysis. This direct approach also allows the incorporation of intuitive inductive biases into the optimization algorithm and editing the model's behavior directly, ensuring that the model meets the desired specifications. Our approach not only simplifies the modeling pipeline but also enhances the transparency and flexibility of the resulting models compared to traditional closed-form ODEs.
Deep Linear Probe Generators for Weight Space Learning
Venue: Conference ICLR 2025
Year: 2025

Weight space learning aims to extract information about a neural network, such as its training dataset or generalization error. Recent approaches learn directly from model weights, but this presents many challenges as weights are high-dimensional and include permutation symmetries between neurons. An alternative approach, Probing, represents a model by passing a set of learned inputs (probes) through the model, and training a predictor on top of the corresponding outputs. Although probing is typically not used as a stand alone approach, our preliminary experiment found that a vanilla probing baseline worked surprisingly well. However, we discover that current probe learning strategies are ineffective. We therefore propose Deep Linear Probe Generators (ProbeGen), a simple and effective modification to probing approaches. ProbeGen adds a shared generator module with a deep linear architecture, providing an inductive bias towards structured probes thus reducing overfitting. While simple, ProbeGen performs significantly better than the state-of-the-art and is very efficient, requiring between 30 to 1000 times fewer FLOPs than other top approaches.
Laplace Sample Information: Data Informativeness Through a Bayesian Lens
Venue: Conference ICLR 2025
Year: 2025

Accurately estimating the informativeness of individual samples in a dataset is an important objective in deep learning, as it can guide sample selection, which can improve model efficiency and accuracy by removing redundant or potentially harmful samples. We propose Laplace Sample Information (LSI) measure of sample informativeness grounded in information theory widely applicable across model architectures and learning settings. LSI leverages a Bayesian approximation to the weight posterior and the KL divergence to measure the change in the parameter distribution induced by a sample of interest from the dataset. We experimentally show that LSI is effective in ordering the data with respect to typicality, detecting mislabeled samples, measuring class-wise informativeness, and assessing dataset difficulty. We demonstrate these capabilities of LSI on image and text data in supervised and unsupervised settings. Moreover, we show that LSI can be computed efficiently through probes and transfers well to the training of large models.
On the Optimal Memorization Capacity of Transformers
Venue: Conference ICLR 2025
Year: 2025

Recent research in the field of machine learning has increasingly focused on the memorization capacity of Transformers, but how efficient they are is not yet well understood. We demonstrate that Transformers can memorize labels with $\tilde{O}(\sqrt{N})$ parameters in a next-token prediction setting for $N$ input sequences of length $n$, which is proved to be optimal up to logarithmic factors. This indicates that Transformers can efficiently perform memorization with little influence from the input length $n$ owing to the benefit of parameter sharing. We also analyze the memorization capacity in the sequence-to-sequence setting, and find that $\tilde{O}(\sqrt{nN})$ parameters are not only sufficient, but also necessary at least for Transformers with hardmax. These results suggest that while self-attention mechanisms can efficiently identify input sequences, the feed-forward network becomes a bottleneck when associating a label to each token.
CubeDiff: Repurposing Diffusion-Based Image Models for Panorama Generation
Venue: Conference ICLR 2025
Year: 2025

We introduce a novel method for generating 360° panoramas from text prompts or images. Our approach leverages recent advances in 3D generation by employing multi-view diffusion models to jointly synthesize the six faces of a cubemap. Unlike previous methods that rely on processing equirectangular projections or autoregressive generation, our method treats each face as a standard perspective image, simplifying the generation process and enabling the use of existing multi-view diffusion models. We demonstrate that these models can be adapted to produce high-quality cubemaps without requiring correspondence-aware attention layers. Our model allows for fine-grained text control, generates high resolution panorama images and generalizes well beyond its training set, whilst achieving state-of-the-art results, both qualitatively and quantitatively. Project page: https://cubediff.github.io/
MrT5: Dynamic Token Merging for Efficient Byte-level Language Models
Venue: Conference ICLR 2025
Year: 2025

Models that rely on subword tokenization have significant drawbacks, such as sensitivity to character-level noise like spelling errors and inconsistent compression rates across different languages and scripts. While character- or byte-level models like ByT5 attempt to address these concerns, they have not gained widespread adoption -- processing raw byte streams without tokenization results in significantly longer sequence lengths, making training and inference inefficient. This work introduces MrT5 (MergeT5), a more efficient variant of ByT5 that integrates a token deletion mechanism in its encoder to dynamically shorten the input sequence length. After processing through a fixed number of encoder layers, a learned delete gate determines which tokens are to be removed and which are to be retained for subsequent layers. MrT5 effectively "merges" critical information from deleted tokens into a more compact sequence, leveraging contextual information from the remaining tokens. In continued pre-training experiments, we find that MrT5 can achieve significant gains in inference runtime with minimal effect on performance, as measured by bits-per-byte. Additionally, with multilingual training, MrT5 adapts to the orthographic characteristics of each language, learning language-specific compression rates. Furthermore, MrT5 shows comparable accuracy to ByT5 on downstream evaluations such as XNLI, TyDi QA, and character-level tasks while reducing sequence lengths by up to 75%. Our approach presents a solution to the practical limitations of existing byte-level models.
Universal Sharpness Dynamics in Neural Network Training: Fixed Point Analysis, Edge of Stability, and Route to Chaos
Venue: Conference ICLR 2025
Year: 2025

In gradient descent dynamics of neural networks, the top eigenvalue of the loss Hessian (sharpness) displays a variety of robust phenomena throughout training. This includes early time regimes where the sharpness may decrease during early periods of training (sharpness reduction), and later time behavior such as progressive sharpening and edge of stability. We demonstrate that a simple $2$-layer linear network (UV model) trained on a single training example exhibits all of the essential sharpness phenomenology observed in real-world scenarios. By analyzing the structure of dynamical fixed points in function space and the vector field of function updates, we uncover the underlying mechanisms behind these sharpness trends. Our analysis reveals (i) the mechanism behind early sharpness reduction and progressive sharpening, (ii) the required conditions for edge of stability, (iii) the crucial role of initialization and parameterization, and (iv) a period-doubling route to chaos on the edge of stability manifold as learning rate is increased. Finally, we demonstrate that various predictions from this simplified model generalize to real-world scenarios and discuss its limitations.
Fiddler: CPU-GPU Orchestration for Fast Inference of Mixture-of-Experts Models
Venue: Conference ICLR 2025
Year: 2025

Large Language Models (LLMs) with the Mixture-of-Experts (MoE) architectures have shown promising performance on various tasks. However, due to the huge model sizes, running them in resource-constrained environments where the GPU memory is not abundant is challenging. Some existing systems propose to use CPU resources to solve that, but they either suffer from the significant overhead of frequently moving data between CPU and GPU, or fail to consider distinct characteristics of CPUs and GPUs. This paper proposes Fiddler, a resource-efficient inference system for MoE models with limited GPU resources. Fiddler strategically utilizes CPU and GPU resources by determining the optimal execution strategy. Our evaluation shows that, unlike state-of-the-art systems that optimize for specific scenarios such as single batch inference or long prefill, Fiddler performs better in all scenarios. Compared against different baselines, Fiddler achieves 1.26 times speed up in single batch inference, 1.30 times in long prefill processing, and 11.57 times in beam search inference. The code of Fiddler is publicly available at https://github.com/efeslab/fiddler.
Learning Efficient Positional Encodings with Graph Neural Networks
Venue: Conference ICLR 2025
Year: 2025

Positional encodings (PEs) are essential for effective graph representation learning because they provide position awareness in inherently position-agnostic transformer architectures and increase the expressive capacity of Graph Neural Networks (GNNs). However, designing powerful and efficient PEs for graphs poses significant challenges due to the absence of canonical node ordering and the scale of the graph. {In this work, we identify four key properties that graph PEs should satisfy}: stability, expressive power, scalability, and genericness. We find that existing eigenvector-based PE methods often fall short of jointly satisfying these criteria. To address this gap, we introduce PEARL, a novel framework of learnable PEs for graphs. Our primary insight is that message-passing GNNs function as nonlinear mappings of eigenvectors, enabling the design of GNN architectures for generating powerful and efficient PEs. A crucial challenge lies in initializing node attributes in a manner that is both expressive and permutation equivariant. We tackle this by initializing GNNs with random node inputs or standard basis vectors, thereby unlocking the expressive power of message-passing operations, while employing statistical pooling functions to maintain permutation equivariance. Our analysis demonstrates that PEARL approximates equivariant functions of eigenvectors with linear complexity, while rigorously establishing its stability and high expressive power. Experimental evaluations show that PEARL outperforms lightweight versions of eigenvector-based PEs and achieves comparable performance to full eigenvector-based PEs, but with one or two orders of magnitude lower complexity. Our code is available at https://github.com/ehejin/Pearl-PE.
See What You Are Told: Visual Attention Sink in Large Multimodal Models
Venue: Conference ICLR 2025
Year: 2025

Large multimodal models (LMMs) "see" images by leveraging the attention mechanism between text and visual tokens in the transformer decoder. Ideally, these models should focus on key visual information relevant to the text token. However, recent findings indicate that LMMs have an extraordinary tendency to consistently allocate high attention weights to specific visual tokens, even when these tokens are irrelevant to the corresponding text. In this study, we investigate the property behind the appearance of these irrelevant visual tokens and examine their characteristics. Our findings show that this behavior arises due to the massive activation of certain hidden state dimensions, which resembles the attention sink found in language models. Hence, we refer to this phenomenon as the visual attention sink. In particular, our analysis reveals that removing the irrelevant visual sink tokens does not impact model performance, despite receiving high attention weights. Consequently, we recycle the attention to these tokens as surplus resources, redistributing the attention budget to enhance focus on the image. To achieve this, we introduce Visual Attention Redistribution (VAR), a method that redistributes attention in image-centric heads, which we identify as innately focusing on visual information. VAR can be seamlessly applied across different LMMs to improve performance on a wide range of tasks, including general vision-language tasks, visual hallucination tasks, and vision-centric tasks, all without the need for additional training, models, or inference steps. Experimental results demonstrate that VAR enables LMMs to process visual information more effectively by adjusting their internal attention mechanisms, offering a new direction to enhancing the multimodal capabilities of LMMs.
Adversarial Policy Optimization for Offline Preference-based Reinforcement Learning
Venue: Conference ICLR 2025
Year: 2025

In this paper, we study offline preference-based reinforcement learning (PbRL), where learning is based on pre-collected preference feedback over pairs of trajectories. While offline PbRL has demonstrated remarkable empirical success, existing theoretical approaches face challenges in ensuring conservatism under uncertainty, requiring computationally intractable confidence set constructions. We address this limitation by proposing Adversarial Preference-based Policy Optimization (APPO), a computationally efficient algorithm for offline PbRL that guarantees sample complexity bounds without relying on explicit confidence sets. By framing PbRL as a two-player game between a policy and a model, our approach enforces conservatism in a tractable manner. Using standard assumptions on function approximation and bounded trajectory concentrability, we derive a sample complexity bound. To our knowledge, APPO is the first offline PbRL algorithm to offer both statistical efficiency and practical applicability. Experimental results on continuous control tasks demonstrate that APPO effectively learns from complex datasets, showing comparable performance with existing state-of-the-art methods.