Maria Brbić

Syed Asad Rizvi, Nazreen Pallikkavaliyaveetil, David Zhang et al.

Foundation models have achieved remarkable success across many domains, relying on pretraining over vast amounts of data. Graph-structured data often lacks the same scale as unstructured data, making the development of graph foundation models challenging. In this work, we propose Foundation-Informed Message Passing (FIMP), a Graph Neural Network (GNN) message-passing framework that leverages pretrained non-textual foundation models in graph-based tasks. We show that the self-attention layers of foundation models can effectively be repurposed on graphs to perform cross-node attention-based message-passing. Our model is evaluated on a real-world image network dataset and two biological applications (single-cell RNA sequencing data and fMRI brain activity recordings) in both finetuned and zero-shot settings. FIMP outperforms strong baselines, demonstrating that it can effectively leverage state-of-the-art foundation models in graph tasks.

Artyom Gadetsky, Maria Brbic

We present HUME, a simple model-agnostic framework for inferring human labeling of a given dataset without any external supervision. The key insight behind our approach is that classes defined by many human labelings are linearly separable regardless of the representation space used to represent a dataset. HUME utilizes this insight to guide the search over all possible labelings of a dataset to discover an underlying human labeling. We show that the proposed optimization objective is strikingly well-correlated with the ground truth labeling of the dataset. In effect, we only train linear classifiers on top of pretrained representations that remain fixed during training, making our framework compatible with any large pretrained and self-supervised model. Despite its simplicity, HUME outperforms a supervised linear classifier on top of self-supervised representations on the STL-10 dataset by a large margin and achieves comparable performance on the CIFAR-10 dataset. Compared to the existing unsupervised baselines, HUME achieves state-of-the-art performance on four benchmark image classification datasets including the large-scale ImageNet-1000 dataset. Altogether, our work provides a fundamentally new view to tackle unsupervised learning by searching for consistent labelings between different representation spaces.

Ramon Viñas Torné, Sílvia Fàbregas Salazar, Soyon Park et al.

Inferring the structure of directed acyclic graphs (DAGs) from data is a central challenge in causal discovery, particularly in modern high-dimensional settings where large-scale interventional data are increasingly available. While interventional data can improve identifiability, existing methods remain limited by soft acyclicity constraints, leading to optimization over invalid cyclic graphs, numerical instability, and reduced scalability. We introduce PACER (Perturbation-driven Acyclic Causal Edge Recovery), a scalable framework for causal discovery that guarantees acyclicity by construction. PACER parameterizes a distribution over DAGs through a joint model of variable permutations and edge probabilities, enabling direct optimization over valid causal structures without surrogate penalties. The framework supports a unified likelihood-based treatment of observational and interventional data, flexible conditional density models, and the incorporation of structural prior knowledge. For linear-Gaussian mechanisms, we derive closed-form expressions for the expected interventional log-likelihood and its gradients, yielding substantial computational gains. Empirically, PACER matches or exceeds state-of-the-art methods on protein signaling and large-scale genetic perturbation benchmarks, while scaling efficiently to networks with thousands of variables and achieving up to two orders of magnitude speedups over penalty-based differentiable approaches. These results demonstrate that exact and scalable causal discovery from high-dimensional perturbation data is achievable through principled search space design.

Siba Smarak Panigrahi, Jovana Videnović, Maria Brbić

LLM-based reasoning models have enabled the development of agentic systems that act as co-scientists, assisting in multi-step scientific analysis. However, evaluating these systems is challenging, as it requires realistic, end-to-end research scenarios that integrate data analysis, interpretation, and the generation of new insights from the experimental data. To address this limitation, we introduce HeurekaBench, a framework to create benchmarks with exploratory, open-ended research questions for experimental datasets. Each such question is grounded in a scientific study and its corresponding code repository, and is created using a semi-automated pipeline that leverages multiple LLMs to extract insights and generate candidate workflows, which are then verified against reported findings. We instantiate the framework in single-cell biology to obtain sc-HeurekaBench benchmark and use it to compare state-of-the-art single-cell agents. We further showcase the benefits of our benchmark for quantitatively analyzing current design choices in agentic systems. We find that the addition of a critic module can improve ill-formed responses for open-source LLM-based agents by up to 22% and close the gap with their closed-source counterparts. Overall, HeurekaBench sets a path toward rigorous, end-to-end evaluation of scientific agents, grounding benchmark construction in real scientific workflows.

Artyom Gadetsky, Andrei Atanov, Yulun Jiang et al.

Recent advances in large language and vision-language models have enabled zero-shot inference, allowing models to solve new tasks without task-specific training. Various adaptation techniques such as prompt engineering, In-Context Learning (ICL), and supervised fine-tuning can further enhance the model's performance on a downstream task, but they require substantial manual effort to construct effective prompts or labeled examples. In this work, we introduce a joint inference framework for fully unsupervised adaptation, eliminating the need for manual prompt engineering and labeled examples. Unlike zero-shot inference, which makes independent predictions, the joint inference makes predictions simultaneously for all inputs in a given task. Since direct joint inference involves computationally expensive optimization, we develop efficient approximation techniques, leading to two unsupervised adaptation methods: unsupervised fine-tuning and unsupervised ICL. We demonstrate the effectiveness of our methods across diverse tasks and models, including language-only Llama-3.1 on natural language processing tasks, reasoning-oriented Qwen2.5-Math on grade school math problems, vision-language OpenFlamingo on vision tasks, and the API-only access GPT-4o model on massive multi-discipline tasks. Our experiments demonstrate substantial improvements over the standard zero-shot approach, including 39% absolute improvement on the challenging GSM8K math reasoning dataset. Remarkably, despite being fully unsupervised, our framework often performs on par with supervised approaches that rely on ground truth labels.

Yulun Jiang, Yekun Chai, Maria Brbić et al.

The ability to process information from multiple modalities and to reason through it step-by-step remains a critical challenge in advancing artificial intelligence. However, existing reasoning benchmarks focus on text-only reasoning, or employ multimodal questions that can be answered by directly retrieving information from a non-text modality. Thus, complex reasoning remains poorly understood in multimodal domains. Here, we present MARBLE, a challenging multimodal reasoning benchmark that is designed to scrutinize multimodal language models (MLLMs) in their ability to carefully reason step-by-step through complex multimodal problems and environments. MARBLE is composed of two highly challenging tasks, M-Portal and M-Cube, that require the crafting and understanding of multistep plans under spatial, visual, and physical constraints. We find that current MLLMs perform poorly on MARBLE -- all the 12 advanced models obtain near-random performance on M-Portal and 0% accuracy on M-Cube. Only in simplified subtasks some models outperform the random baseline, indicating that complex reasoning is still a challenge for existing MLLMs. Moreover, we show that perception remains a bottleneck, where MLLMs occasionally fail to extract information from the visual inputs. By shedding a light on the limitations of MLLMs, we hope that MARBLE will spur the development of the next generation of models with the ability to reason and plan across many, multimodal reasoning steps.

Shuo Wen, Maria Brbic

In many real-world applications, test data may commonly exhibit categorical shifts, characterized by the emergence of novel classes, as well as distribution shifts arising from feature distributions different from the ones the model was trained on. However, existing methods either discover novel classes in the open-world setting or assume domain shifts without the ability to discover novel classes. In this work, we consider a cross-domain open-world discovery setting, where the goal is to assign samples to seen classes and discover unseen classes under a domain shift. To address this challenging problem, we present CROW, a prototype-based approach that introduces a cluster-then-match strategy enabled by a well-structured representation space of foundation models. In this way, CROW discovers novel classes by robustly matching clusters with previously seen classes, followed by fine-tuning the representation space using an objective designed for cross-domain open-world discovery. Extensive experimental results on image classification benchmark datasets demonstrate that CROW outperforms alternative baselines, achieving an 8% average performance improvement across 75 experimental settings.

Matej Grcić, Artyom Gadetsky, Maria Brbić

In many practical applications, coarse-grained labels are readily available compared to fine-grained labels that reflect subtle differences between classes. However, existing methods cannot leverage coarse labels to infer fine-grained labels in an unsupervised manner. To bridge this gap, we propose FALCON, a method that discovers fine-grained classes from coarsely labeled data without any supervision at the fine-grained level. FALCON simultaneously infers unknown fine-grained classes and underlying relationships between coarse and fine-grained classes. Moreover, FALCON is a modular method that can effectively learn from multiple datasets labeled with different strategies. We evaluate FALCON on eight image classification tasks and a single-cell classification task. FALCON outperforms baselines by a large margin, achieving 22% improvement over the best baseline on the tieredImageNet dataset with over 600 fine-grained classes.

Artyom Gadetsky, Yulun Jiang, Maria Brbic

Foundation vision-language models have enabled remarkable zero-shot transferability of the pre-trained representations to a wide range of downstream tasks. However, to solve a new task, zero-shot transfer still necessitates human guidance to define visual categories that appear in the data. Here, we show that fully unsupervised transfer emerges when searching for the labeling of a dataset that induces maximal margin classifiers in representation spaces of different foundation models. We present TURTLE, a fully unsupervised method that effectively employs this guiding principle to uncover the underlying labeling of a downstream dataset without any supervision and task-specific representation learning. We evaluate TURTLE on a diverse benchmark suite of 26 datasets and show that it achieves new state-of-the-art unsupervised performance. Furthermore, TURTLE, although being fully unsupervised, outperforms zero-shot transfer baselines on a wide range of datasets. In particular, TURTLE matches the average performance of CLIP zero-shot on 26 datasets by employing the same representation space, spanning a wide range of architectures and model sizes. By guiding the search for the underlying labeling using the representation spaces of two foundation models, TURTLE surpasses zero-shot transfer and unsupervised prompt tuning baselines, demonstrating the surprising power and effectiveness of unsupervised transfer.

Ethan Shen, Maria Brbic, Nicholas Monath et al.

In many domains, relationships between categories are encoded in the knowledge graph. Recently, promising results have been achieved by incorporating knowledge graph as side information in hard classification tasks with severely limited data. However, prior models consist of highly complex architectures with many sub-components that all seem to impact performance. In this paper, we present a comprehensive empirical study on graph embedded few-shot learning. We introduce a graph regularization approach that allows a deeper understanding of the impact of incorporating graph information between labels. Our proposed regularization is widely applicable and model-agnostic, and boosts the performance of any few-shot learning model, including fine-tuning, metric-based, and optimization-based meta-learning. Our approach improves the performance of strong base learners by up to 2% on Mini-ImageNet and 6.7% on ImageNet-FS, outperforming state-of-the-art graph embedded methods. Additional analyses reveal that graph regularizing models result in a lower loss for more difficult tasks, such as those with fewer shots and less informative support examples.

Kaidi Cao, Maria Brbic, Jure Leskovec

A fundamental limitation of applying semi-supervised learning in real-world settings is the assumption that unlabeled test data contains only classes previously encountered in the labeled training data. However, this assumption rarely holds for data in-the-wild, where instances belonging to novel classes may appear at testing time. Here, we introduce a novel open-world semi-supervised learning setting that formalizes the notion that novel classes may appear in the unlabeled test data. In this novel setting, the goal is to solve the class distribution mismatch between labeled and unlabeled data, where at the test time every input instance either needs to be classified into one of the existing classes or a new unseen class needs to be initialized. To tackle this challenging problem, we propose ORCA, an end-to-end deep learning approach that introduces uncertainty adaptive margin mechanism to circumvent the bias towards seen classes caused by learning discriminative features for seen classes faster than for the novel classes. In this way, ORCA reduces the gap between intra-class variance of seen with respect to novel classes. Experiments on image classification datasets and a single-cell annotation dataset demonstrate that ORCA consistently outperforms alternative baselines, achieving 25% improvement on seen and 96% improvement on novel classes of the ImageNet dataset.

Kaidi Cao, Maria Brbic, Jure Leskovec

Developing algorithms that are able to generalize to a novel task given only a few labeled examples represents a fundamental challenge in closing the gap between machine- and human-level performance. The core of human cognition lies in the structured, reusable concepts that help us to rapidly adapt to new tasks and provide reasoning behind our decisions. However, existing meta-learning methods learn complex representations across prior labeled tasks without imposing any structure on the learned representations. Here we propose COMET, a meta-learning method that improves generalization ability by learning to learn along human-interpretable concept dimensions. Instead of learning a joint unstructured metric space, COMET learns mappings of high-level concepts into semi-structured metric spaces, and effectively combines the outputs of independent concept learners. We evaluate our model on few-shot tasks from diverse domains, including fine-grained image classification, document categorization and cell type annotation on a novel dataset from a biological domain developed in our work. COMET significantly outperforms strong meta-learning baselines, achieving 6-15% relative improvement on the most challenging 1-shot learning tasks, while unlike existing methods providing interpretations behind the model's predictions.

Maria Brbić, Ivica Kopriva

In many applications, high-dimensional data points can be well represented by low-dimensional subspaces. To identify the subspaces, it is important to capture a global and local structure of the data which is achieved by imposing low-rank and sparseness constraints on the data representation matrix. In low-rank sparse subspace clustering (LRSSC), nuclear and $\ell_1$ norms are used to measure rank and sparsity. However, the use of nuclear and $\ell_1$ norms leads to an overpenalized problem and only approximates the original problem. In this paper, we propose two $\ell_0$ quasi-norm based regularizations. First, the paper presents regularization based on multivariate generalization of minimax-concave penalty (GMC-LRSSC), which contains the global minimizers of $\ell_0$ quasi-norm regularized objective. Afterward, we introduce the Schatten-0 ($S_0$) and $\ell_0$ regularized objective and approximate the proximal map of the joint solution using a proximal average method ($S_0/\ell_0$-LRSSC). The resulting nonconvex optimization problems are solved using alternating direction method of multipliers with established convergence conditions of both algorithms. Results obtained on synthetic and four real-world datasets show the effectiveness of GMC-LRSSC and $S_0/\ell_0$-LRSSC when compared to state-of-the-art methods.

Maria Brbic, Ivica Kopriva

Most existing approaches address multi-view subspace clustering problem by constructing the affinity matrix on each view separately and afterwards propose how to extend spectral clustering algorithm to handle multi-view data. This paper presents an approach to multi-view subspace clustering that learns a joint subspace representation by constructing affinity matrix shared among all views. Relying on the importance of both low-rank and sparsity constraints in the construction of the affinity matrix, we introduce the objective that balances between the agreement across different views, while at the same time encourages sparsity and low-rankness of the solution. Related low-rank and sparsity constrained optimization problem is for each view solved using the alternating direction method of multipliers. Furthermore, we extend our approach to cluster data drawn from nonlinear subspaces by solving the corresponding problem in a reproducing kernel Hilbert space. The proposed algorithm outperforms state-of-the-art multi-view subspace clustering algorithms on one synthetic and four real-world datasets.