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DiffInfinite: Large Mask-Image Synthesis via Parallel Random Patch Diffusion in Histopathology

Neural Information Processing Systems

We present DiffInfinite, a hierarchical diffusion model that generates arbitrarily large histological images while preserving long-range correlation structural information. Our approach first generates synthetic segmentation masks, subsequently used as conditions for the high-fidelity generative diffusion process.


Autoguided Online Data Curation for Diffusion Model Training

Pais, Valeria, Oala, Luis, Faccio, Daniele, Aversa, Marco

arXiv.org Artificial Intelligence

The costs of generative model compute rekindled promises and hopes for efficient data curation. In this work, we investigate whether recently developed autoguidance and online data selection methods can improve the time and sample efficiency of training generative diffusion models. We integrate joint example selection (JEST) and autoguidance into a unified code base for fast ablation and benchmarking. We evaluate combinations of data curation on a controlled 2-D synthetic data generation task as well as (3x64x64)-D image generation. Our comparisons are made at equal wall-clock time and equal number of samples, explicitly accounting for the overhead of selection. Across experiments, autoguidance consistently improves sample quality and diversity. Early AJEST (applying selection only at the beginning of training) can match or modestly exceed autoguidance alone in data efficiency on both tasks. However, its time overhead and added complexity make autoguidance or uniform random data selection preferable in most situations. These findings suggest that while targeted online selection can yield efficiency gains in early training, robust sample quality improvements are primarily driven by autoguidance. We discuss limitations and scope, and outline when data selection may be beneficial.


EconAgentic in DePIN Markets: A Large Language Model Approach to the Sharing Economy of Decentralized Physical Infrastructure

Liu, Yulin, Schweitzer, Mocca

arXiv.org Artificial Intelligence

The Decentralized Physical Infrastructure (DePIN) market is revolutionizing the sharing economy through token-based economics and smart contracts that govern decentralized operations. By 2024, DePIN projects have exceeded \$10 billion in market capitalization, underscoring their rapid growth. However, the unregulated nature of these markets, coupled with the autonomous deployment of AI agents in smart contracts, introduces risks such as inefficiencies and potential misalignment with human values. To address these concerns, we introduce EconAgentic, a Large Language Model (LLM)-powered framework designed to mitigate these challenges. Our research focuses on three key areas: 1) modeling the dynamic evolution of DePIN markets, 2) evaluating stakeholders' actions and their economic impacts, and 3) analyzing macroeconomic indicators to align market outcomes with societal goals. Through EconAgentic, we simulate how AI agents respond to token incentives, invest in infrastructure, and adapt to market conditions, comparing AI-driven decisions with human heuristic benchmarks. Our results show that EconAgentic provides valuable insights into the efficiency, inclusion, and stability of DePIN markets, contributing to both academic understanding and practical improvements in the design and governance of decentralized, tokenized economies.


In-silico biological discovery with large perturbation models

Miladinovic, Djordje, Höppe, Tobias, Chevalley, Mathieu, Georgiou, Andreas, Stuart, Lachlan, Mehrjou, Arash, Bantscheff, Marcus, Schölkopf, Bernhard, Schwab, Patrick

arXiv.org Artificial Intelligence

Data generated in perturbation experiments link perturbations to the changes they elicit and therefore contain information relevant to numerous biological discovery tasks -- from understanding the relationships between biological entities to developing therapeutics. However, these data encompass diverse perturbations and readouts, and the complex dependence of experimental outcomes on their biological context makes it challenging to integrate insights across experiments. Here, we present the Large Perturbation Model (LPM), a deep-learning model that integrates multiple, heterogeneous perturbation experiments by representing perturbation, readout, and context as disentangled dimensions. LPM outperforms existing methods across multiple biological discovery tasks, including in predicting post-perturbation transcriptomes of unseen experiments, identifying shared molecular mechanisms of action between chemical and genetic perturbations, and facilitating the inference of gene-gene interaction networks.


Multi-megabase scale genome interpretation with genetic language models

Träuble, Frederik, Stuart, Lachlan, Georgiou, Andreas, Notin, Pascal, Mehrjou, Arash, Schwessinger, Ron, Chevalley, Mathieu, Branson, Kim, Schölkopf, Bernhard, van Duijn, Cornelia, Marks, Debora, Schwab, Patrick

arXiv.org Artificial Intelligence

Understanding how molecular changes caused by genetic variation drive disease risk is crucial for deciphering disease mechanisms. However, interpreting genome sequences is challenging because of the vast size of the human genome, and because its consequences manifest across a wide range of cells, tissues and scales -- spanning from molecular to whole organism level. Here, we present Phenformer, a multi-scale genetic language model that learns to generate mechanistic hypotheses as to how differences in genome sequence lead to disease-relevant changes in expression across cell types and tissues directly from DNA sequences of up to 88 million base pairs. Using whole genome sequencing data from more than 150 000 individuals, we show that Phenformer generates mechanistic hypotheses about disease-relevant cell and tissue types that match literature better than existing state-of-the-art methods, while using only sequence data. Furthermore, disease risk predictors enriched by Phenformer show improved prediction performance and generalisation to diverse populations. Accurate multi-megabase scale interpretation of whole genomes without additional experimental data enables both a deeper understanding of molecular mechanisms involved in disease and improved disease risk prediction at the level of individuals.


Measuring the Groundedness of Legal Question-Answering Systems

Trautmann, Dietrich, Ostapuk, Natalia, Grail, Quentin, Pol, Adrian Alan, Bonifazi, Guglielmo, Gao, Shang, Gajek, Martin

arXiv.org Artificial Intelligence

In high-stakes domains like legal question-answering, the accuracy and trustworthiness of generative AI systems are of paramount importance. This work presents a comprehensive benchmark of various methods to assess the groundedness of AI-generated responses, aiming to significantly enhance their reliability. Our experiments include similarity-based metrics and natural language inference models to evaluate whether responses are well-founded in the given contexts. We also explore different prompting strategies for large language models to improve the detection of ungrounded responses. We validated the effectiveness of these methods using a newly created grounding classification corpus, designed specifically for legal queries and corresponding responses from retrieval-augmented prompting, focusing on their alignment with source material. Our results indicate potential in groundedness classification of generated responses, with the best method achieving a macro-F1 score of 0.8. Additionally, we evaluated the methods in terms of their latency to determine their suitability for real-world applications, as this step typically follows the generation process. This capability is essential for processes that may trigger additional manual verification or automated response regeneration. In summary, this study demonstrates the potential of various detection methods to improve the trustworthiness of generative AI in legal settings.


Unlabeled Debiasing in Downstream Tasks via Class-wise Low Variance Regularization

Masoudian, Shahed, Frohmann, Markus, Rekabsaz, Navid, Schedl, Markus

arXiv.org Artificial Intelligence

Language models frequently inherit societal biases from their training data. Numerous techniques have been proposed to mitigate these biases during both the pre-training and fine-tuning stages. However, fine-tuning a pre-trained debiased language model on a downstream task can reintroduce biases into the model. Additionally, existing debiasing methods for downstream tasks either (i) require labels of protected attributes (e.g., age, race, or political views) that are often not available or (ii) rely on indicators of bias, which restricts their applicability to gender debiasing since they rely on gender-specific words. To address this, we introduce a novel debiasing regularization technique based on the class-wise variance of embeddings. Crucially, our method does not require attribute labels and targets any attribute, thus addressing the shortcomings of existing debiasing methods. Our experiments on encoder language models and three datasets demonstrate that our method outperforms existing strong debiasing baselines that rely on target attribute labels while maintaining performance on the target task.