OpenRaiser/Intern-Atlas huggingface dataset:
Multi-domain Distribution Learning for De Novo Drug Design
Venue: Conference ICLR 2025
Year: 2025

We introduce DrugFlow, a generative model for structure-based drug design that integrates continuous flow matching with discrete Markov bridges, demonstrating state-of-the-art performance in learning chemical, geometric, and physical aspects of three-dimensional protein-ligand data. We endow DrugFlow with an uncertainty estimate that is able to detect out-of-distribution samples. To further enhance the sampling process towards distribution regions with desirable metric values, we propose a joint preference alignment scheme applicable to both flow matching and Markov bridge frameworks. Furthermore, we extend our model to also explore the conformational landscape of the protein by jointly sampling side chain angles and molecules.
Residual Connections and Normalization Can Provably Prevent Oversmoothing in GNNs
Venue: Conference ICLR 2025
Year: 2025

Residual connections and normalization layers have become standard design choices for graph neural networks (GNNs), and were proposed as solutions to the mitigate the oversmoothing problem in GNNs. However, how exactly these methods help alleviate the oversmoothing problem from a theoretical perspective is not well understood. In this work, we provide a formal and precise characterization of (linearized) GNNs with residual connections and normalization layers. We establish that (a) for residual connections, the incorporation of the initial features at each layer can prevent the signal from becoming too smooth, and determines the subspace of possible node representations; (b) batch normalization prevents a complete collapse of the output embedding space to a one-dimensional subspace through the individual rescaling of each column of the feature matrix. This results in the convergence of node representations to the top-$k$ eigenspace of the message-passing operator; (c) moreover, we show that the centering step of a normalization layer -- which can be understood as a projection -- alters the graph signal in message-passing in such a way that relevant information can become harder to extract. We therefore introduce a novel, principled normalization layer called GraphNormv2 in which the centering step is learned such that it does not distort the original graph signal in an undesirable way. Experimental results confirm the effectiveness of our method.
World Model on Million-Length Video And Language With Blockwise RingAttention
Venue: Conference ICLR 2025
Year: 2025

Enabling long-context understanding remains a key challenge in scaling existing sequence models -- a crucial component in developing generally intelligent models that can process and operate over long temporal horizons that potentially consist of millions of tokens. In this paper, we aim to address these challenges by providing a comprehensive exploration of the full development process for producing 1M context language models and video-language models, setting new benchmarks in language retrieval and new capabilities in long video understanding. We detail our long context data curation process, progressive context extension from 4K to 1M tokens, and present an efficient open-source implementation for scalable training on long sequences. Additionally, we open-source a family of 7B parameter models capable of processing long text documents and videos exceeding 1M tokens.
Provably Reliable Conformal Prediction Sets in the Presence of Data Poisoning
Venue: Conference ICLR 2025
Year: 2025

Conformal prediction provides model-agnostic and distribution-free uncertainty quantification through prediction sets that are guaranteed to include the ground truth with any user-specified probability. Yet, conformal prediction is not reliable under poisoning attacks where adversaries manipulate both training and calibration data, which can significantly alter prediction sets in practice. As a solution, we propose reliable prediction sets (RPS): the first efficient method for constructing conformal prediction sets with provable reliability guarantees under poisoning. To ensure reliability under training poisoning, we introduce smoothed score functions that reliably aggregate predictions of classifiers trained on distinct partitions of the training data. To ensure reliability under calibration poisoning, we construct multiple prediction sets, each calibrated on distinct subsets of the calibration data. We then aggregate them into a majority prediction set, which includes a class only if it appears in a majority of the individual sets. Both proposed aggregations mitigate the influence of datapoints in the training and calibration data on the final prediction set. We experimentally validate our approach on image classification tasks, achieving strong reliability while maintaining utility and preserving coverage on clean data. Overall, our approach represents an important step towards more trustworthy uncertainty quantification in the presence of data poisoning.
A Probabilistic Perspective on Unlearning and Alignment for Large Language Models
Venue: Conference ICLR 2025
Year: 2025

Comprehensive evaluation of Large Language Models (LLMs) is an open research problem. Existing evaluations rely on deterministic point estimates generated via greedy decoding. However, we find that deterministic evaluations fail to capture the whole output distribution of a model, yielding inaccurate estimations of model capabilities. This is particularly problematic in critical contexts such as unlearning and alignment, where precise model evaluations are crucial. To remedy this, we introduce the first formal probabilistic evaluation framework for LLMs. Namely, we propose novel metrics with high probability guarantees concerning the output distribution of a model. Our metrics are application-independent and allow practitioners to make more reliable estimates about model capabilities before deployment. Our experimental analysis reveals that deterministic evaluations falsely indicate successful unlearning and alignment, whereas our probabilistic evaluations better capture model capabilities. We show how to overcome challenges associated with probabilistic outputs in a case study on unlearning by introducing (1) a novel loss based on entropy optimization, and (2) adaptive temperature scaling. We demonstrate that our approach significantly enhances unlearning in probabilistic settings on recent benchmarks. Overall, our proposed shift from point estimates to probabilistic evaluations of output distributions represents an important step toward comprehensive evaluations of LLMs. Code available at https://www.cs.cit.tum.de/daml/probabilistic-unlearning/.
Differentially private learners for heterogeneous treatment effects
Venue: Conference ICLR 2025
Year: 2025

Patient data is widely used to estimate heterogeneous treatment effects and thus understand the effectiveness and safety of drugs. Yet, patient data includes highly sensitive information that must be kept private. In this work, we aim to estimate the conditional average treatment effect (CATE) from observational data under differential privacy. Specifically, we present DP-CATE, a novel framework for CATE estimation that is Neyman-orthogonal and further ensures differential privacy of the estimates. Our framework is highly general: it applies to any two-stage CATE meta-learner with a Neyman-orthogonal loss function, and any machine learning model can be used for nuisance estimation. We further provide an extension of our DP-CATE, where we employ RKHS regression to release the complete CATE function while ensuring differential privacy. We demonstrate our DP-CATE across various experiments using synthetic and real-world datasets. To the best of our knowledge, we are the first to provide a framework for CATE estimation that is Neyman-orthogonal and differentially private.
Two Effects, One Trigger: On the Modality Gap, Object Bias, and Information Imbalance in Contrastive Vision-Language Models
Venue: Conference ICLR 2025
Year: 2025

Contrastive vision-language models (VLMs), like CLIP, have gained popularity for their versatile applicability to various downstream tasks. Despite their successes in some tasks, like zero-shot object recognition, they perform surprisingly poor on other tasks, like attribute recognition. Previous work has attributed these challenges to the modality gap, a separation of image and text in the shared representation space, and to a bias towards objects over other factors, such as attributes. In this analysis paper, we investigate both phenomena thoroughly. We evaluated off-the-shelf VLMs and while the gap's influence on performance is typically overshadowed by other factors, we find indications that closing the gap indeed leads to improvements. Moreover, we find that, contrary to intuition, only few embedding dimensions drive the gap and that the embedding spaces are differently organized. To allow for a clean study of object bias, we introduce a definition and a corresponding measure of it. Equipped with this tool, we find that object bias does not lead to worse performance on other concepts, such as attributes per se. However, why do both phenomena, modality gap and object bias, emerge in the first place? To answer this fundamental question and uncover some of the inner workings of contrastive VLMs, we conducted experiments that allowed us to control the amount of shared information between the modalities. These experiments revealed that the driving factor behind both the modality gap and the object bias, is an information imbalance between images and captions, and unveiled an intriguing connection between the modality gap and entropy of the logits.
Attention as a Hypernetwork
Venue: Conference ICLR 2025
Year: 2025

Transformers can under some circumstances generalize to novel problem instances whose constituent parts might have been encountered during training, but whose compositions have not. What mechanisms underlie this ability for compositional generalization? By reformulating multi-head attention as a hypernetwork, we reveal that a composable, low-dimensional latent code specifies key-query specific operations. We find empirically that this latent code is predictive of the subtasks the network performs on unseen task compositions, revealing that latent codes acquired during training are reused to solve unseen problem instances. To further examine the hypothesis that the intrinsic hypernetwork of multi-head attention supports compositional generalization, we ablate whether making the hypernetwork-generated linear value network nonlinear strengthens compositionality. We find that this modification improves compositional generalization on abstract reasoning tasks. In particular, we introduce a symbolic version of the Raven's Progressive Matrices human intelligence test, which gives us precise control over the problem compositions encountered during training and evaluation. We demonstrate on this task how scaling model size and data enables compositional generalization in transformers and gives rise to a functionally structured latent space.
ANaGRAM: A Natural Gradient Relative to Adapted Model for efficient PINNs learning
Venue: Conference ICLR 2025
Year: 2025

In the recent years, Physics Informed Neural Networks (PINNs) have received strong interest as a method to solve PDE driven systems, in particular for data assimilation purpose. This method is still in its infancy, with many shortcomings and failures that remain not properly understood. In this paper we propose a natural gradient approach to PINNs which contributes to speed-up and improve the accuracy of the training. Based on an in depth analysis of the differential geometric structures of the problem, we come up with two distinct contributions: (i) a new natural gradient algorithm that scales as $\min(P^2S, S^2P)$, where $P$ is the number of parameters, and $S$ the batch size; (ii) a mathematically principled reformulation of the PINNs problem that allows the extension of natural gradient to it, with proved connections to Green's function theory.
MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra
Venue: Conference ICLR 2025
Year: 2025

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.
Following the Human Thread in Social Navigation
Venue: Conference ICLR 2025
Year: 2025

The success of collaboration between humans and robots in shared environments relies on the robot's real-time adaptation to human motion. Specifically, in Social Navigation, the agent should be close enough to assist but ready to back up to let the human move freely, avoiding collisions. Human trajectories emerge as crucial cues in Social Navigation, but they are partially observable from the robot's egocentric view and computationally complex to process. We present the first Social Dynamics Adaptation model (SDA) based on the robot's state-action history to infer the social dynamics. We propose a two-stage Reinforcement Learning framework: the first learns to encode the human trajectories into social dynamics and learns a motion policy conditioned on this encoded information, the current status, and the previous action. Here, the trajectories are fully visible, i.e., assumed as privileged information. In the second stage, the trained policy operates without direct access to trajectories. Instead, the model infers the social dynamics solely from the history of previous actions and statuses in real-time. Tested on the novel Habitat 3.0 platform, SDA sets a novel state-of-the-art (SotA) performance in finding and following humans. The code can be found at https://github.com/L-Scofano/SDA.
Zero-shot Imputation with Foundation Inference Models for Dynamical Systems
Venue: Conference ICLR 2025
Year: 2025

Dynamical systems governed by ordinary differential equations (ODEs) serve as models for a vast number of natural and social phenomena. In this work, we offer a fresh perspective on the classical problem of imputing missing time series data, whose underlying dynamics are assumed to be determined by ODEs. Specifically, we revisit ideas from amortized inference and neural operators, and propose a novel supervised learning framework for zero-shot time series imputation, through parametric functions satisfying some (hidden) ODEs. Our proposal consists of two components. First, a broad probability distribution over the space of ODE solutions, observation times and noise mechanisms, with which we generate a large, synthetic dataset of (hidden) ODE solutions, along with their noisy and sparse observations. Second, a neural recognition model that is trained offline, to map the generated time series onto the spaces of initial conditions and time derivatives of the (hidden) ODE solutions, which we then integrate to impute the missing data. We empirically demonstrate that one and the same (pretrained) recognition model can perform zero-shot imputation across 63 distinct time series with missing values, each sampled from widely different dynamical systems. Likewise, we demonstrate that it can perform zero-shot imputation of missing high-dimensional data in 10 vastly different settings, spanning human motion, air quality, traffic and electricity studies, as well as Navier-Stokes simulations -- without requiring any fine-tuning. What is more, our proposal often outperforms state-of-the-art methods, which are trained on the target datasets. Our pretrained model, repository and tutorials are available online.
LLMs Can Plan Only If We Tell Them
Venue: Conference ICLR 2025
Year: 2025

Large language models (LLMs) have demonstrated significant capabilities in natural language processing and reasoning, yet their effectiveness in autonomous planning has been under debate. While existing studies have utilized LLMs with external feedback mechanisms or in controlled environments for planning, these approaches often involve substantial computational and development resources due to the requirement for careful design and iterative backprompting. Moreover, even the most advanced LLMs like GPT-4 struggle to match human performance on standard planning benchmarks, such as the Blocksworld, without additional support. This paper investigates whether LLMs can independently generate long-horizon plans that rival human baselines. Our novel enhancements to Algorithm-of-Thoughts (AoT), which we dub AoT+, help achieve state-of-the-art results in planning benchmarks out-competing prior methods and human baselines all autonomously.
You Only Prune Once: Designing Calibration-Free Model Compression With Policy Learning
Venue: Conference ICLR 2025
Year: 2025

The ever-increasing size of large language models (LLMs) presents significant challenges for deployment due to their heavy computational and memory requirements. Current model pruning techniques attempt to alleviate these issues by relying heavily on external calibration datasets to determine which parameters to prune or compress, thus limiting their flexibility and scalability across different compression ratios. Moreover, these methods often cause severe performance degradation, particularly in downstream tasks, when subjected to higher compression rates. In this paper, we propose PruneNet, a novel model compression method that addresses these limitations by reformulating model pruning as a policy learning process. PruneNet decouples the pruning process from the model architecture, eliminating the need for calibration datasets. It learns a stochastic pruning policy to assess parameter importance solely based on intrinsic model properties while preserving the spectral structure to minimize information loss. PruneNet can compress the LLaMA-2-7B model in just 15 minutes, achieving over 80% retention of its zero-shot performance with a 30% compression ratio, outperforming existing methods that retain only 75% performance. Furthermore, on complex multitask language understanding tasks, PruneNet demonstrates its robustness by preserving up to 80% performance of the original model, proving itself a superior alternative to conventional structured compression techniques.
PRISM: Privacy-Preserving Improved Stochastic Masking for Federated Generative Models
Venue: Conference ICLR 2025
Year: 2025

Despite recent advancements in federated learning (FL), the integration of generative models into FL has been limited due to challenges such as high communication costs and unstable training in heterogeneous data environments. To address these issues, we propose PRISM, a FL framework tailored for generative models that ensures (i) stable performance in heterogeneous data distributions and (ii) resource efficiency in terms of communication cost and final model size. The key of our method is to search for an optimal stochastic binary mask for a random network rather than updating the model weights, identifying a sparse subnetwork with high generative performance; i.e., a ``strong lottery ticket''. By communicating binary masks in a stochastic manner, PRISM minimizes communication overhead. This approach, combined with the utilization of maximum mean discrepancy (MMD) loss and a mask-aware dynamic moving average aggregation method (MADA) on the server side, facilitates stable and strong generative capabilities by mitigating local divergence in FL scenarios. Moreover, thanks to its sparsifying characteristic, PRISM yields a lightweight model without extra pruning or quantization, making it ideal for environments such as edge devices. Experiments on MNIST, FMNIST, CelebA, and CIFAR10 demonstrate that PRISM outperforms existing methods, while maintaining privacy with minimal communication costs. PRISM is the first to successfully generate images under challenging non-IID and privacy-preserving FL environments on complex datasets, where previous methods have struggled.
Budgeted Online Continual Learning by Adaptive Layer Freezing and Frequency-based Sampling
Venue: Conference ICLR 2025
Year: 2025

The majority of online continual learning (CL) advocates single-epoch training and imposes restrictions on the size of replay memory. However, single-epoch training would incur a different amount of computations per CL algorithm, and the additional storage cost to store logit or model in addition to replay memory is largely ignored in calculating the storage budget. Arguing different computational and storage budgets hinder fair comparison among CL algorithms in practice, we propose to use floating point operations (FLOPs) and total memory size in Byte as a metric for computational and memory budgets, respectively, to compare and develop CL algorithms in the same 'total resource budget.' To improve a CL method in a limited total budget, we propose adaptive layer freezing that does not update the layers for less informative batches to reduce computational costs with a negligible loss of accuracy. In addition, we propose a memory retrieval method that allows the model to learn the same amount of knowledge as using random retrieval in fewer iterations. Empirical validations on the CIFAR-10/100, CLEAR-10/100, and ImageNet-1K datasets demonstrate that the proposed approach outperforms the state-of-the-art methods within the same total budget
Distributional Associations vs In-Context Reasoning: A Study of Feed-forward and Attention Layers
Venue: Conference ICLR 2025
Year: 2025

Large language models have been successful at tasks involving basic forms of in-context reasoning, such as generating coherent language, as well as storing vast amounts of knowledge. At the core of the Transformer architecture behind such models are feed-forward and attention layers, which are often associated to knowledge and reasoning, respectively. In this paper, we study this distinction empirically and theoretically in a controlled synthetic setting where certain next-token predictions involve both distributional and in-context information. We find that feed-forward layers tend to learn simple distributional associations such as bigrams, while attention layers focus on in-context reasoning. Our theoretical analysis identifies the noise in the gradients as a key factor behind this discrepancy. Finally, we illustrate how similar disparities emerge in pre-trained models through ablations on the Pythia model family on simple reasoning tasks.