OpenRaiser/Intern-Atlas huggingface dataset:
Simple, Good, Fast: Self-Supervised World Models Free of Baggage
Venue: Conference ICLR 2025
Year: 2025

What are the essential components of world models? How far do we get with world models that are not employing RNNs, transformers, discrete representations, and image reconstructions? This paper introduces SGF, a Simple, Good, and Fast world model that uses self-supervised representation learning, captures short-time dependencies through frame and action stacking, and enhances robustness against model errors through data augmentation. We extensively discuss SGF's connections to established world models, evaluate the building blocks in ablation studies, and demonstrate good performance through quantitative comparisons on the Atari 100k benchmark.
NatureLM-audio: an Audio-Language Foundation Model for Bioacoustics
Venue: Conference ICLR 2025
Year: 2025

Large language models (LLMs) prompted with text and audio have achieved state-of-the-art performance across various auditory tasks, including speech, music, and general audio, showing emergent abilities on unseen tasks. However, their potential has yet to be fully demonstrated in bioacoustics tasks, such as detecting animal vocalizations in large recordings, classifying rare and endangered species, and labeling context and behavior -- tasks that are crucial for conservation, biodiversity monitoring, and animal behavior studies. In this work, we present NatureLM-audio, the first audio-language foundation model specifically designed for bioacoustics. Our training dataset consists of carefully curated text-audio pairs spanning bioacoustics, speech, and music, designed to address the field's limited availability of annotated data. We demonstrate successful transfer of learned representations from music and speech to bioacoustics, and our model shows promising generalization to unseen taxa and tasks. We evaluate NatureLM-audio on a novel benchmark (BEANS-Zero) and it sets a new state of the art on several bioacoustics tasks, including zero-shot classification of unseen species. To advance bioacoustics research, we release our model weights, benchmark data, and open-source the code for training and benchmark data generation and model training.
BigDocs: An Open Dataset for Training Multimodal Models on Document and Code Tasks
Venue: Conference ICLR 2025
Year: 2025

Multimodal AI has the potential to significantly enhance document-understanding tasks, such as processing receipts, understanding workflows, extracting data from documents, and summarizing reports. Code generation tasks that require long-structured outputs can also be enhanced by multimodality. Despite this, their use in commercial applications is often limited due to limited access to training data and restrictive licensing, which hinders open access. To address these limitations, we introduce BigDocs-7.5M, a high-quality, open-access dataset comprising 7.5 million multimodal documents across 30 tasks. We use an efficient data curation process to ensure our data is high-quality and license-permissive. Our process emphasizes accountability, responsibility, and transparency through filtering rules, traceable metadata, and careful content analysis. Additionally, we introduce BigDocs-Bench, a benchmark suite with 10 novel tasks where we create datasets that reflect real-world use cases involving reasoning over Graphical User Interfaces (GUI) and code generation from images. Our experiments show that training with BigDocs-Bench improves average performance up to 25.8% over closed-source GPT-4o in document reasoning and structured output tasks such as Screenshot2HTML or Image2Latex generation. Finally, human evaluations showed a preference for outputs from models trained on BigDocs over GPT-4o. This suggests that BigDocs can help both academics and the open-source community utilize and improve AI tools to enhance multimodal capabilities and document reasoning. The project is hosted at https://bigdocs.github.io .
ELBOing Stein: Variational Bayes with Stein Mixture Inference
Venue: Conference ICLR 2025
Year: 2025

Stein variational gradient descent (SVGD) [Liu and Wang, 2016] performs approximate Bayesian inference by representing the posterior with a set of particles. However, SVGD suffers from variance collapse, i.e. poor predictions due to underestimating uncertainty [Ba et al., 2021], even for moderately-dimensional models such as small Bayesian neural networks (BNNs). To address this issue, we generalize SVGD by letting each particle parameterize a component distribution in a mixture model. Our method, Stein Mixture Inference (SMI), optimizes a lower bound to the evidence (ELBO) and introduces user-specified guides parameterized by particles. SMI extends the Nonlinear SVGD framework [Wang and Liu, 2019] to the case of variational Bayes. SMI effectively avoids variance collapse, judging by a previously described test developed for this purpose, and performs well on standard data sets. In addition, SMI requires considerably fewer particles than SVGD to accurately estimate uncertainty for small BNNs. The synergistic combination of NSVGD, ELBO optimization and user-specified guides establishes a promising approach towards variational Bayesian inference in the case of tall and wide data.
BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments
Venue: Conference ICLR 2025
Year: 2025

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.
PharmacoMatch: Efficient 3D Pharmacophore Screening via Neural Subgraph Matching
Venue: Conference ICLR 2025
Year: 2025

The increasing size of screening libraries poses a significant challenge for the development of virtual screening methods for drug discovery, necessitating a re-evaluation of traditional approaches in the era of big data. Although 3D pharmacophore screening remains a prevalent technique, its application to very large datasets is limited by the computational cost associated with matching query pharmacophores to database molecules. In this study, we introduce PharmacoMatch, a novel contrastive learning approach based on neural subgraph matching. Our method reinterprets pharmacophore screening as an approximate subgraph matching problem and enables efficient querying of conformational databases by encoding query-target relationships in the embedding space. We conduct comprehensive investigations of the learned representations and evaluate PharmacoMatch as pre-screening tool in a zero-shot setting. We demonstrate significantly shorter runtimes and comparable performance metrics to existing solutions, providing a promising speed-up for screening very large datasets.
On the Byzantine-Resilience of Distillation-Based Federated Learning
Venue: Conference ICLR 2025
Year: 2025

Federated Learning (FL) algorithms using Knowledge Distillation (KD) have received increasing attention due to their favorable properties with respect to privacy, non-i.i.d. data and communication cost. These methods depart from transmitting model parameters and instead communicate information about a learning task by sharing predictions on a public dataset. In this work, we study the performance of such approaches in the byzantine setting, where a subset of the clients act in an adversarial manner aiming to disrupt the learning process. We show that KD-based FL algorithms are remarkably resilient and analyze how byzantine clients can influence the learning process. Based on these insights, we introduce two new byzantine attacks and demonstrate their ability to break existing byzantine-resilient methods. Additionally, we propose a novel defence method which enhances the byzantine resilience of KD-based FL algorithms. Finally, we provide a general framework to obfuscate attacks, making them significantly harder to detect, thereby improving their effectiveness. Our findings serve as an important building block in the analysis of byzantine FL, contributing through the development of new attacks and new defence mechanisms, further advancing the robustness of KD-based FL algorithms.
DCT-CryptoNets: Scaling Private Inference in the Frequency Domain
Venue: Conference ICLR 2025
Year: 2025

The convergence of fully homomorphic encryption (FHE) and machine learning offers unprecedented opportunities for private inference of sensitive data. FHE enables computation directly on encrypted data, safeguarding the entire machine learning pipeline, including data and model confidentiality. However, existing FHE-based implementations for deep neural networks face significant challenges in computational cost, latency, and scalability, limiting their practical deployment. This paper introduces DCT-CryptoNets, a novel approach that operates directly in the frequency-domain to reduce the burden of computationally expensive non-linear activations and homomorphic bootstrap operations during private inference. It does so by utilizing the discrete cosine transform (DCT), commonly employed in JPEG encoding, which has inherent compatibility with remote computing services where images are generally stored and transmitted in this encoded format. DCT-CryptoNets demonstrates a substantial latency reductions of up to 5.3$\times$ compared to prior work on benchmark image classification tasks. Notably, it demonstrates inference on the ImageNet dataset within 2.5 hours (down from 12.5 hours on equivalent 96-thread compute resources). Furthermore, by learning perceptually salient low-frequency information DCT-CryptoNets improves the reliability of encrypted predictions compared to RGB-based networks by reducing error accumulating homomorphic bootstrap operations. DCT-CryptoNets also demonstrates superior scalability to RGB-based networks by further reducing computational cost as image size increases. This study demonstrates a promising avenue for achieving efficient and practical private inference of deep learning models on high resolution images seen in real-world applications.
Learning Spatial-Semantic Features for Robust Video Object Segmentation
Venue: Conference ICLR 2025
Year: 2025

Tracking and segmenting multiple similar objects with distinct or complex parts in long-term videos is particularly challenging due to the ambiguity in identifying target components and the confusion caused by occlusion, background clutter, and changes in appearance or environment over time. In this paper, we propose a robust video object segmentation framework that learns spatial-semantic features and discriminative object queries to address the above issues. Specifically, we construct a spatial-semantic block comprising a semantic embedding component and a spatial dependency modeling part for associating global semantic features and local spatial features, providing a comprehensive target representation. In addition, we develop a masked cross-attention module to generate object queries that focus on the most discriminative parts of target objects during query propagation, alleviating noise accumulation to ensure effective long-term query propagation. Extensive experimental results show that the proposed method achieves state-of-the-art performance on benchmark data sets, including the DAVIS2017 test (\textbf{87.8\%}), YoutubeVOS 2019 (\textbf{88.1\%}), MOSE val (\textbf{74.0\%}), and LVOS test (\textbf{73.0\%}), and demonstrate the effectiveness and generalization capacity of our model. The source code and trained models are released at \href{https://github.com/yahooo-m/S3}{https://github.com/yahooo-m/S3}.
Conformal Language Model Reasoning with Coherent Factuality
Venue: Conference ICLR 2025
Year: 2025

Language models are increasingly being used in important decision pipelines, so ensuring the correctness of their outputs is crucial. Recent work has proposed evaluating the "factuality" of claims decomposed from a language model generation and applying conformal prediction techniques to filter out those claims that are not factual. This can be effective for tasks such as information retrieval, where constituent claims may be evaluated in isolation for factuality, but is not appropriate for reasoning tasks, as steps of a logical argument can be evaluated for correctness only within the context of the claims that precede them. To capture this, we define "coherent factuality" and develop a conformal-prediction-based method to guarantee coherent factuality for language model outputs. Our approach applies split conformal prediction to subgraphs within a "deducibility" graph" that represents the steps of a reasoning problem. We evaluate our method on mathematical reasoning problems from the MATH and FELM datasets and find that our algorithm consistently produces correct and substantiated orderings of claims, achieving coherent factuality across target coverage levels. Moreover, we achieve 90% factuality on our stricter definition while retaining 80% or more of the original claims, highlighting the utility of our deducibility-graph-guided approach.
GNNs Getting ComFy: Community and Feature Similarity Guided Rewiring
Venue: Conference ICLR 2025
Year: 2025

Maximizing the spectral gap through graph rewiring has been proposed to enhance the performance of message-passing graph neural networks (GNNs) by addressing over-squashing. However, as we show, minimizing the spectral gap can also improve generalization. To explain this, we analyze how rewiring can benefit GNNs within the context of stochastic block models. Since spectral gap optimization primarily influences community strength, it improves performance when the community structure aligns with node labels. Building on this insight, we propose three distinct rewiring strategies that explicitly target community structure, node labels, and their alignment: (a) community structure-based rewiring (ComMa), a more computationally efficient alternative to spectral gap optimization that achieves similar goals; (b) feature similarity-based rewiring (FeaSt), which focuses on maximizing global homophily; and (c) a hybrid approach (ComFy), which enhances local feature similarity while preserving community structure to optimize label-community alignment. Extensive experiments confirm the effectiveness of these strategies and support our theoretical insights.
Procedural Knowledge in Pretraining Drives Reasoning in Large Language Models
Venue: Conference ICLR 2025
Year: 2025

The capabilities and limitations of Large Language Models have been sketched out in great detail in recent years, providing an intriguing yet conflicting picture. On the one hand, LLMs demonstrate a general ability to solve problems. On the other hand, they show surprising reasoning gaps when compared to humans, casting doubt on the robustness of their generalisation strategies. The sheer volume of data used in the design of LLMs has precluded us from applying the method traditionally used to measure generalisation: train-test set separation. To overcome this, we study what kind of generalisation strategies LLMs employ when performing reasoning tasks by investigating the pretraining data they rely on. For two models of different sizes (7B and 35B) and 2.5B of their pretraining tokens, we identify what documents influence the model outputs for three simple mathematical reasoning tasks and contrast this to the data that are influential for answering factual questions. We find that, while the models rely on mostly distinct sets of data for each factual question, a document often has a similar influence across different reasoning questions within the same task, indicating the presence of procedural knowledge. We further find that the answers to factual questions often show up in the most influential data. However, for reasoning questions the answers usually do not show up as highly influential, nor do the answers to the intermediate reasoning steps. When we characterise the top ranked documents for the reasoning questions qualitatively, we confirm that the influential documents often contain procedural knowledge, like demonstrating how to obtain a solution using formulae or code. Our findings indicate that the approach to reasoning the models use is unlike retrieval, and more like a generalisable strategy that synthesises procedural knowledge from documents doing a similar form of reasoning.
On the Benefits of Memory for Modeling Time-Dependent PDEs
Venue: Conference ICLR 2025
Year: 2025

Data-driven techniques have emerged as a promising alternative to traditional numerical methods for solving PDEs. For time-dependent PDEs, many approaches are Markovian -- the evolution of the trained system only depends on the current state, and not the past states. In this work, we investigate the benefits of using memory for modeling time-dependent PDEs: that is, when past states are explicitly used to predict the future. Motivated by the Mori-Zwanzig theory of model reduction, we theoretically exhibit examples of simple (even linear) PDEs, in which a solution that uses memory is arbitrarily better than a Markovian solution. Additionally, we introduce Memory Neural Operator (MemNO), a neural operator architecture that combines recent state space models (specifically, S4) and Fourier Neural Operators (FNOs) to effectively model memory. We empirically demonstrate that when the PDEs are supplied in low resolution or contain observation noise at train and test time, MemNO significantly outperforms the baselines without memory -- with up to 6x reduction in test error. Furthermore, we show that this benefit is particularly pronounced when the PDE solutions have significant high-frequency Fourier modes (e.g., low-viscosity fluid dynamics) and we construct a challenging benchmark dataset consisting of such PDEs.
Oscillatory State-Space Models
Venue: Conference ICLR 2025
Year: 2025

We propose Linear Oscillatory State-Space models (LinOSS) for efficiently learning on long sequences. Inspired by cortical dynamics of biological neural networks, we base our proposed LinOSS model on a system of forced harmonic oscillators. A stable discretization, integrated over time using fast associative parallel scans, yields the proposed state-space model. We prove that LinOSS produces stable dynamics only requiring nonnegative diagonal state matrix. This is in stark contrast to many previous state-space models relying heavily on restrictive parameterizations. Moreover, we rigorously show that LinOSS is universal, i.e., it can approximate any continuous and causal operator mapping between time-varying functions, to desired accuracy. In addition, we show that an implicit-explicit discretization of LinOSS perfectly conserves the symmetry of time reversibility of the underlying dynamics. Together, these properties enable efficient modeling of long-range interactions, while ensuring stable and accurate long-horizon forecasting. Finally, our empirical results, spanning a wide range of time-series tasks from mid-range to very long-range classification and regression, as well as long-horizon forecasting, demonstrate that our proposed LinOSS model consistently outperforms state-of-the-art sequence models. Notably, LinOSS outperforms Mamba and LRU by nearly 2x on a sequence modeling task with sequences of length 50k.
Ensembling Diffusion Models via Adaptive Feature Aggregation
Venue: Conference ICLR 2025
Year: 2025

The success of the text-guided diffusion model has inspired the development and release of numerous powerful diffusion models within the open-source community. These models are typically fine-tuned on various expert datasets, showcasing diverse denoising capabilities. Leveraging multiple high-quality models to produce stronger generation ability is valuable, but has not been extensively studied. Existing methods primarily adopt parameter merging strategies to produce a new static model. However, they overlook the fact that the divergent denoising capabilities of the models may dynamically change across different states, such as when experiencing different prompts, initial noises, denoising steps, and spatial locations. In this paper, we propose a novel ensembling method, Adaptive Feature Aggregation (AFA), which dynamically adjusts the contributions of multiple models at the feature level according to various states (i.e., prompts, initial noises, denoising steps, and spatial locations), thereby keeping the advantages of multiple diffusion models, while suppressing their disadvantages. Specifically, we design a lightweight Spatial-Aware Block-Wise (SABW) feature aggregator that adaptive aggregates the block-wise intermediate features from multiple U-Net denoisers into a unified one. The core idea lies in dynamically producing an individual attention map for each model's features by comprehensively considering various states. It is worth noting that only SABW is trainable with about 50 million parameters, while other models are frozen. Both the quantitative and qualitative experiments demonstrate the effectiveness of our proposed Adaptive Feature Aggregation method.
Divide and Translate: Compositional First-Order Logic Translation and Verification for Complex Logical Reasoning
Venue: Conference ICLR 2025
Year: 2025

Complex logical reasoning tasks require a long sequence of reasoning, which a large language model (LLM) with chain-of-thought prompting still falls short. To alleviate this issue, neurosymbolic approaches incorporate a symbolic solver. Specifically, an LLM only translates a natural language problem into a satisfiability (SAT) problem that consists of first-order logic formulas, and a sound symbolic solver returns a mathematically correct solution. However, we discover that LLMs have difficulties to capture complex logical semantics hidden in the natural language during translation. To resolve this limitation, we propose a Compositional First-Order Logic Translation. An LLM first parses a natural language sentence into newly defined logical dependency structures that consist of an atomic subsentence and its dependents, then sequentially translate the parsed subsentences. Since multiple logical dependency structures and sequential translations are possible for a single sentence, we also introduce two Verification algorithms to ensure more reliable results. We utilize an SAT solver to rigorously compare semantics of generated first-order logic formulas and select the most probable one. We evaluate the proposed method, dubbed CLOVER, on seven logical reasoning benchmarks and show that it outperforms the previous neurosymbolic approaches and achieves new state-of-the-art results.