OpenRaiser/Intern-Atlas huggingface dataset:
Metalic: Meta-Learning In-Context with Protein Language Models
Venue: Conference ICLR 2025
Year: 2025

Predicting the biophysical and functional properties of proteins is essential for in silico protein design. Machine learning has emerged as a promising technique for such prediction tasks. However, the relative scarcity of in vitro annotations means that these models often have little, or no, specific data on the desired fitness prediction task. As a result of limited data, protein language models (PLMs) are typically trained on general protein sequence modeling tasks, and then fine-tuned, or applied zero-shot, to protein fitness prediction. When no task data is available, the models make strong assumptions about the correlation between the protein sequence likelihood and fitness scores. In contrast, we propose meta-learning over a distribution of standard fitness prediction tasks, and demonstrate positive transfer to unseen fitness prediction tasks. Our method, called Metalic (Meta-Learning In-Context), uses in-context learning and fine-tuning, when data is available, to adapt to new tasks. Crucially, fine-tuning enables considerable generalization, even though it is not accounted for during meta-training. Our fine-tuned models achieve strong results with 18 times fewer parameters than state-of-the-art models. Moreover, our method sets a new state-of-the-art in low-data settings on ProteinGym, an established fitness-prediction benchmark. Due to data scarcity, we believe meta-learning will play a pivotal role in advancing protein engineering.
Sensitivity-Constrained Fourier Neural Operators for Forward and Inverse Problems in Parametric Differential Equations
Venue: Conference ICLR 2025
Year: 2025

Parametric differential equations of the form du/dt = f(u, x, t, p) are fundamental in science and engineering. While deep learning frameworks such as the Fourier Neural Operator (FNO) can efficiently approximate solutions, they struggle with inverse problems, sensitivity estimation (du/dp), and concept drift. We address these limitations by introducing a sensitivity-based regularization strategy, called Sensitivity-Constrained Fourier Neural Operators (SC-FNO). SC-FNO achieves high accuracy in predicting solution paths and consistently outperforms standard FNO and FNO with physics-informed regularization. It improves performance in parameter inversion tasks, scales to high-dimensional parameter spaces (tested with up to 82 parameters), and reduces both data and training requirements. These gains are achieved with a modest increase in training time (30% to 130% per epoch) and generalize across various types of differential equations and neural operators. Code and selected experiments are available at: https://github.com/AMBehroozi/SC_Neural_Operators
DeciMamba: Exploring the Length Extrapolation Potential of Mamba
Venue: Conference ICLR 2025
Year: 2025

Long-range sequence processing poses a significant challenge for Transformers due to their quadratic complexity in input length. A promising alternative is Mamba, which demonstrates high performance and achieves Transformer-level capabilities while requiring substantially fewer computational resources. In this paper we explore the length-generalization capabilities of Mamba, which we find to be relatively limited. Through a series of visualizations and analyses we identify that the limitations arise from a restricted effective receptive field, dictated by the sequence length used during training. To address this constraint, we introduce DeciMamba, a context-extension method specifically designed for Mamba. This mechanism, built on top of a hidden filtering mechanism embedded within the S6 layer, enables the trained model to extrapolate well even without additional training. Empirical experiments over real-world long-range NLP tasks show that DeciMamba can extrapolate to context lengths that are significantly longer than the ones seen during training, while enjoying faster inference.
Fast training and sampling of Restricted Boltzmann Machines
Venue: Conference ICLR 2025
Year: 2025

Restricted Boltzmann Machines (RBMs) are powerful tools for modeling complex systems and extracting insights from data, but their training is hindered by the slow mixing of Markov Chain Monte Carlo (MCMC) processes, especially with highly structured datasets. In this study, we build on recent theoretical advances in RBM training and focus on the stepwise encoding of data patterns into singular vectors of the coupling matrix, significantly reducing the cost of generating new samples and evaluating the quality of the model, as well as the training cost in highly clustered datasets. The learning process is analogous to the thermodynamic continuous phase transitions observed in ferromagnetic models, where new modes in the probability measure emerge in a continuous manner. We leverage the continuous transitions in the training process to define a smooth annealing trajectory that enables reliable and computationally efficient log-likelihood estimates. This approach enables online assessment during training and introduces a novel sampling strategy called Parallel Trajectory Tempering (PTT) that outperforms previously optimized MCMC methods. To mitigate the critical slowdown effect in the early stages of training, we propose a pre-training phase. In this phase, the principal components are encoded into a low-rank RBM through a convex optimization process, facilitating efficient static Monte Carlo sampling and accurate computation of the partition function. Our results demonstrate that this pre-training strategy allows RBMs to efficiently handle highly structured datasets where conventional methods fail. Additionally, our log-likelihood estimation outperforms computationally intensive approaches in controlled scenarios, while the PTT algorithm significantly accelerates MCMC processes compared to conventional methods.
Uncertainty Modeling in Graph Neural Networks via Stochastic Differential Equations
Venue: Conference ICLR 2025
Year: 2025

We propose a novel Stochastic Differential Equation (SDE) framework to address the problem of learning uncertainty-aware representations for graph-structured data. While Graph Neural Ordinary Differential Equations (GNODEs) have shown promise in learning node representations, they lack the ability to quantify uncertainty. To address this, we introduce Latent Graph Neural Stochastic Differential Equations (LGNSDE), which enhance GNODE by embedding randomness through a Bayesian prior-posterior mechanism for epistemic uncertainty and Brownian motion for aleatoric uncertainty. By leveraging the existence and uniqueness of solutions to graph-based SDEs, we prove that the variance of the latent space bounds the variance of model outputs, thereby providing theoretically sensible guarantees for the uncertainty estimates. Furthermore, we show mathematically that LGNSDEs are robust to small perturbations in the input, maintaining stability over time. Empirical results across several benchmarks demonstrate that our framework is competitive in out-of-distribution detection, robustness to noise, and active learning, underscoring the ability of LGNSDEs to quantify uncertainty reliably. Code is available at \href{https://github.com/Richard-Bergna/GraphNeuralSDE}{\texttt{github.com/Richard-Bergna/GraphNeuralSDE}}.
Straight to Zero: Why Linearly Decaying the Learning Rate to Zero Works Best for LLMs
Venue: Conference ICLR 2025
Year: 2025

LLMs are commonly trained with a learning rate (LR) warmup, followed by cosine decay to 10% of the maximum (10x decay). In a large-scale empirical study, we show that under an optimal peak LR, a simple linear decay-to-zero (D2Z) schedule consistently outperforms other schedules when training at compute-optimal dataset sizes. D2Z is superior across a range of model sizes, batch sizes, datasets, and vocabularies. Benefits increase as dataset size increases. Leveraging a novel interpretation of AdamW as an exponential moving average of weight updates, we show how linear D2Z optimally balances the demands of early training (moving away from initial conditions) and late training (averaging over more updates in order to mitigate gradient noise). In experiments, a 610M-parameter model trained for 80 tokens-per-parameter (TPP) using D2Z achieves lower loss than when trained for 200 TPP using 10x decay, corresponding to an astonishing 60% compute savings. Models such as Llama2-7B, trained for 286 TPP with 10x decay, could likely have saved a majority of compute by training with D2Z.
Boosting Latent Diffusion with Perceptual Objectives
Venue: Conference ICLR 2025
Year: 2025

Latent diffusion models (LDMs) power state-of-the-art high-resolution generative image models. LDMs learn the data distribution in the latent space of an autoencoder (AE) and produce images by mapping the generated latents into RGB image space using the AE decoder. While this approach allows for efficient model training and sampling, it induces a disconnect between the training of the diffusion model and the decoder, resulting in a loss of detail in the generated images. To remediate this disconnect, we propose to leverage the internal features of the decoder to define a latent perceptual loss (LPL). This loss encourages the models to create sharper and more realistic images. Our loss can be seamlessly integrated with common autoencoders used in latent diffusion models, and can be applied to different generative modeling paradigms such as DDPM with epsilon and velocity prediction, as well as flow matching. Extensive experiments with models trained on three datasets at 256 and 512 resolution show improved quantitative -- with boosts between 6% and 20% in FID -- and qualitative results when using our perceptual loss.
Halton Scheduler for Masked Generative Image Transformer
Venue: Conference ICLR 2025
Year: 2025

Masked Generative Image Transformers (MaskGIT) have emerged as a scalable and efficient image generation framework, able to deliver high-quality visuals with low inference costs. However, MaskGIT's token unmasking scheduler, an essential component of the framework, has not received the attention it deserves. We analyze the sampling objective in MaskGIT, based on the mutual information between tokens, and elucidate its shortcomings. We then propose a new sampling strategy based on our Halton scheduler instead of the original Confidence scheduler. More precisely, our method selects the token's position according to a quasi-random, low-discrepancy Halton sequence. Intuitively, that method spreads the tokens spatially, progressively covering the image uniformly at each step. Our analysis shows that it allows reducing non-recoverable sampling errors, leading to simpler hyper-parameters tuning and better quality images. Our scheduler does not require retraining or noise injection and may serve as a simple drop-in replacement for the original sampling strategy. Evaluation of both class-to-image synthesis on ImageNet and text-to-image generation on the COCO dataset demonstrates that the Halton scheduler outperforms the Confidence scheduler quantitatively by reducing the FID and qualitatively by generating more diverse and more detailed images. Our code is at https://github.com/valeoai/Halton-MaskGIT.
Tell me about yourself: LLMs are aware of their learned behaviors
Venue: Conference ICLR 2025
Year: 2025

We study behavioral self-awareness -- an LLM's ability to articulate its behaviors without requiring in-context examples. We finetune LLMs on datasets that exhibit particular behaviors, such as (a) making high-risk economic decisions, and (b) outputting insecure code. Despite the datasets containing no explicit descriptions of the associated behavior, the finetuned LLMs can explicitly describe it. For example, a model trained to output insecure code says, ``The code I write is insecure.'' Indeed, models show behavioral self-awareness for a range of behaviors and for diverse evaluations. Note that while we finetune models to exhibit behaviors like writing insecure code, we do not finetune them to articulate their own behaviors -- models do this without any special training or examples. Behavioral self-awareness is relevant for AI safety, as models could use it to proactively disclose problematic behaviors. In particular, we study backdoor policies, where models exhibit unexpected behaviors only under certain trigger conditions. We find that models can sometimes identify whether or not they have a backdoor, even without its trigger being present. However, models are not able to directly output their trigger by default. Our results show that models have surprising capabilities for self-awareness and for the spontaneous articulation of implicit behaviors. Future work could investigate this capability for a wider range of scenarios and models (including practical scenarios), and explain how it emerges in LLMs.
PRDP: Progressively Refined Differentiable Physics
Venue: Conference ICLR 2025
Year: 2025

The physics solvers employed for neural network training are primarily iterative, and hence, differentiating through them introduces a severe computational burden as iterations grow large. Inspired by works in bilevel optimization, we show that full accuracy of the network is achievable through physics significantly coarser than fully converged solvers. We propose Progressively Refined Differentiable Physics (PRDP), an approach that identifies the level of physics refinement sufficient for full training accuracy. By beginning with coarse physics, adaptively refining it during training, and stopping refinement at the level adequate for training, it enables significant compute savings without sacrificing network accuracy. Our focus is on differentiating iterative linear solvers for sparsely discretized differential operators, which are fundamental to scientific computing. PRDP is applicable to both unrolled and implicit differentiation. We validate its performance on a variety of learning scenarios involving differentiable physics solvers such as inverse problems, autoregressive neural emulators, and correction-based neural-hybrid solvers. In the challenging example of emulating the Navier-Stokes equations, we reduce training time by 62%.
Efficient Active Imitation Learning with Random Network Distillation
Venue: Conference ICLR 2025
Year: 2025

Developing agents for complex and underspecified tasks, where no clear objective exists, remains challenging but offers many opportunities. This is especially true in video games, where simulated players (bots) need to play realistically, and there is no clear reward to evaluate them. While imitation learning has shown promise in such domains, these methods often fail when agents encounter out-of-distribution scenarios during deployment. Expanding the training dataset is a common solution, but it becomes impractical or costly when relying on human demonstrations. This article addresses active imitation learning, aiming to trigger expert intervention only when necessary, reducing the need for constant expert input along training. We introduce Random Network Distillation DAgger (RND-DAgger), a new active imitation learning method that limits expert querying by using a learned state-based out-of-distribution measure to trigger interventions. This approach avoids frequent expert-agent action comparisons, thus making the expert intervene only when it is useful. We evaluate RND-DAgger against traditional imitation learning and other active approaches in 3D video games (racing and third-person navigation) and in a robotic locomotion task and show that RND-DAgger surpasses previous methods by reducing expert queries. https://sites.google.com/view/rnd-dagger
Scaling Optimal LR Across Token Horizons
Venue: Conference ICLR 2025
Year: 2025

State-of-the-art LLMs are powered by scaling -- scaling model size, dataset size and cluster size. It is economically infeasible to extensively tune hyperparameter for the largest runs. Instead, approximately optimal hyperparameters must be inferred or \textit{transferred} from smaller experiments. Hyperparameter transfer across model sizes has been studied in Yang et al. However, hyperparameter transfer across dataset size -- or token horizon -- has not been studied yet. To remedy this we conduct a large scale empirical study on how optimal learning rate (LR) depends on token horizon in LLM training. We first demonstrate that the optimal LR changes significantly with token horizon -- longer training necessitates smaller LR. Secondly we demonstrate the the optimal LR follows a scaling law, and that the optimal LR for longer horizons can be accurately estimated from shorter horizons via such scaling laws. We also provide a rule-of-thumb for transferring LR across token horizons with zero overhead over current practices. Lastly we provide evidence that LLama-1 used too high LR, and estimate the performance hit from this. We thus argue that hyperparameter transfer across data size is an important and overlooked component of LLM training.
u-μP: The Unit-Scaled Maximal Update Parametrization
Venue: Conference ICLR 2025
Year: 2025

The Maximal Update Parametrization ($μ$P) aims to make the optimal hyperparameters (HPs) of a model independent of its size, allowing them to be swept using a cheap proxy model rather than the full-size target model. We present a new scheme, u-$μ$P, which improves upon $μ$P by combining it with Unit Scaling, a method for designing models that makes them easy to train in low-precision. The two techniques have a natural affinity: $μ$P ensures that the scale of activations is independent of model size, and Unit Scaling ensures that activations, weights and gradients begin training with a scale of one. This synthesis opens the door to a simpler scheme, whose default values are near-optimal. This in turn facilitates a more efficient sweeping strategy, with u-$μ$P models reaching a loss that is equal to or lower than comparable $μ$P models and working out-of-the-box in FP8.
Underdamped Diffusion Bridges with Applications to Sampling
Venue: Conference ICLR 2025
Year: 2025

We provide a general framework for learning diffusion bridges that transport prior to target distributions. It includes existing diffusion models for generative modeling, but also underdamped versions with degenerate diffusion matrices, where the noise only acts in certain dimensions. Extending previous findings, our framework allows to rigorously show that score matching in the underdamped case is indeed equivalent to maximizing a lower bound on the likelihood. Motivated by superior convergence properties and compatibility with sophisticated numerical integration schemes of underdamped stochastic processes, we propose \emph{underdamped diffusion bridges}, where a general density evolution is learned rather than prescribed by a fixed noising process. We apply our method to the challenging task of sampling from unnormalized densities without access to samples from the target distribution. Across a diverse range of sampling problems, our approach demonstrates state-of-the-art performance, notably outperforming alternative methods, while requiring significantly fewer discretization steps and no hyperparameter tuning.
End-to-end Learning of Gaussian Mixture Priors for Diffusion Sampler
Venue: Conference ICLR 2025
Year: 2025

Diffusion models optimized via variational inference (VI) have emerged as a promising tool for generating samples from unnormalized target densities. These models create samples by simulating a stochastic differential equation, starting from a simple, tractable prior, typically a Gaussian distribution. However, when the support of this prior differs greatly from that of the target distribution, diffusion models often struggle to explore effectively or suffer from large discretization errors. Moreover, learning the prior distribution can lead to mode-collapse, exacerbated by the mode-seeking nature of reverse Kullback-Leibler divergence commonly used in VI. To address these challenges, we propose end-to-end learnable Gaussian mixture priors (GMPs). GMPs offer improved control over exploration, adaptability to target support, and increased expressiveness to counteract mode collapse. We further leverage the structure of mixture models by proposing a strategy to iteratively refine the model by adding mixture components during training. Our experimental results demonstrate significant performance improvements across a diverse range of real-world and synthetic benchmark problems when using GMPs without requiring additional target evaluations.
Revisiting Convolution Architecture in the Realm of DNA Foundation Models
Venue: Conference ICLR 2025
Year: 2025

In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there is a lack of comparison between these recent approaches and the classical architecture convolutional networks (CNNs) on foundation model benchmarks. This raises the question: are CNNs truly being surpassed by these recent approaches based on transformer and SSM architectures? In this paper, we develop a simple but well-designed CNN-based method termed ConvNova. ConvNova identifies and proposes three effective designs: 1) dilated convolutions, 2) gated convolutions, and 3) a dual-branch framework for gating mechanisms. Through extensive empirical experiments, we demonstrate that ConvNova significantly outperforms recent methods on more than half of the tasks across several foundation model benchmarks. For example, in histone-related tasks, ConvNova exceeds the second-best method by an average of 5.8%, while generally utilizing fewer parameters and enabling faster computation. In addition, the experiments observed findings that may be related to biological characteristics. This indicates that CNNs are still a strong competitor compared to Transformers and SSMs. We anticipate that this work will spark renewed interest in CNN-based methods for DNA foundation models.
Depth Pro: Sharp Monocular Metric Depth in Less Than a Second
Venue: Conference ICLR 2025
Year: 2025

We present a foundation model for zero-shot metric monocular depth estimation. Our model, Depth Pro, synthesizes high-resolution depth maps with unparalleled sharpness and high-frequency details. The predictions are metric, with absolute scale, without relying on the availability of metadata such as camera intrinsics. And the model is fast, producing a 2.25-megapixel depth map in 0.3 seconds on a standard GPU. These characteristics are enabled by a number of technical contributions, including an efficient multi-scale vision transformer for dense prediction, a training protocol that combines real and synthetic datasets to achieve high metric accuracy alongside fine boundary tracing, dedicated evaluation metrics for boundary accuracy in estimated depth maps, and state-of-the-art focal length estimation from a single image. Extensive experiments analyze specific design choices and demonstrate that Depth Pro outperforms prior work along multiple dimensions. We release code and weights at https://github.com/apple/ml-depth-pro