Daily Papers

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

Instruction-guided image editing has achieved remarkable progress, yet current models still face challenges with complex instructions and often require multiple samples to produce a desired result. Reinforcement Learning (RL) offers a promising solution, but its adoption in image editing has been severely hindered by the lack of a high-fidelity, efficient reward signal. In this work, we present a comprehensive methodology to overcome this barrier, centered on the development of a state-of-the-art, specialized reward model. We first introduce EditReward-Bench, a comprehensive benchmark to systematically evaluate reward models on editing quality. Building on this benchmark, we develop EditScore, a series of reward models (7B-72B) for evaluating the quality of instruction-guided image editing. Through meticulous data curation and filtering, EditScore effectively matches the performance of learning proprietary VLMs. Furthermore, coupled with an effective self-ensemble strategy tailored for the generative nature of EditScore, our largest variant even surpasses GPT-5 in the benchmark. We then demonstrate that a high-fidelity reward model is the key to unlocking online RL for image editing. Our experiments show that, while even the largest open-source VLMs fail to provide an effective learning signal, EditScore enables efficient and robust policy optimization. Applying our framework to a strong base model, OmniGen2, results in a final model that shows a substantial and consistent performance uplift. Overall, this work provides the first systematic path from benchmarking to reward modeling to RL training in image editing, showing that a high-fidelity, domain-specialized reward model is the key to unlocking the full potential of RL in this domain.

The Kov\'ats Retention index (RI) is a quantity measured using gas chromatography and commonly used in the identification of chemical structures. Creating libraries of observed RI values is a laborious task, so we explore the use of a deep neural network for predicting RI values from structure for standard semipolar columns. This network generated predictions with a mean absolute error of 15.1 and, in a quantification of the tail of the error distribution, a 95th percentile absolute error of 46.5. Because of the Artificial Intelligence Retention Indices (AIRI) network's accuracy, it was used to predict RI values for the NIST EI-MS spectral libraries. These RI values are used to improve chemical identification methods and the quality of the library. Estimating uncertainty is an important practical need when using prediction models. To quantify the uncertainty of our network for each individual prediction, we used the outputs of an ensemble of 8 networks to calculate a predicted standard deviation for each RI value prediction. This predicted standard deviation was corrected to follow the error between observed and predicted RI values. The Z scores using these predicted standard deviations had a standard deviation of 1.52 and a 95th percentile absolute Z score corresponding to a mean RI value of 42.6.

Uncertainty quantification (UQ) is a critical aspect of artificial intelligence (AI) systems, particularly in high-risk domains such as healthcare, autonomous systems, and financial technology, where decision-making processes must account for uncertainty. This review explores the evolution of uncertainty quantification techniques in AI, distinguishing between aleatoric and epistemic uncertainties, and discusses the mathematical foundations and methods used to quantify these uncertainties. We provide an overview of advanced techniques, including probabilistic methods, ensemble learning, sampling-based approaches, and generative models, while also highlighting hybrid approaches that integrate domain-specific knowledge. Furthermore, we examine the diverse applications of UQ across various fields, emphasizing its impact on decision-making, predictive accuracy, and system robustness. The review also addresses key challenges such as scalability, efficiency, and integration with explainable AI, and outlines future directions for research in this rapidly developing area. Through this comprehensive survey, we aim to provide a deeper understanding of UQ's role in enhancing the reliability, safety, and trustworthiness of AI systems.

Over the last three decades, ensemble forecasts have become an integral part of forecasting the weather. They provide users with more complete information than single forecasts as they permit to estimate the probability of weather events by representing the sources of uncertainties and accounting for the day-to-day variability of error growth in the atmosphere. This paper presents a novel approach to obtain a weather forecast model for ensemble forecasting with machine-learning. AIFS-CRPS is a variant of the Artificial Intelligence Forecasting System (AIFS) developed at ECMWF. Its loss function is based on a proper score, the Continuous Ranked Probability Score (CRPS). For the loss, the almost fair CRPS is introduced because it approximately removes the bias in the score due to finite ensemble size yet avoids a degeneracy of the fair CRPS. The trained model is stochastic and can generate as many exchangeable members as desired and computationally feasible in inference. For medium-range forecasts AIFS-CRPS outperforms the physics-based Integrated Forecasting System (IFS) ensemble for the majority of variables and lead times. For subseasonal forecasts, AIFS-CRPS outperforms the IFS ensemble before calibration and is competitive with the IFS ensemble when forecasts are evaluated as anomalies to remove the influence of model biases.

The reasoning capabilities of advanced large language models (LLMs) like o1 have revolutionized artificial intelligence applications. Nevertheless, evaluating and optimizing complex reasoning processes remain significant challenges due to diverse policy distributions and the inherent limitations of human effort and accuracy. In this paper, we present AURORA, a novel automated framework for training universal process reward models (PRMs) using ensemble prompting and reverse verification. The framework employs a two-phase approach: First, it uses diverse prompting strategies and ensemble methods to perform automated annotation and evaluation of processes, ensuring robust assessments for reward learning. Second, it leverages practical reference answers for reverse verification, enhancing the model's ability to validate outputs and improving training accuracy. To assess the framework's performance, we extend beyond the existing ProcessBench benchmark by introducing UniversalBench, which evaluates reward predictions across full trajectories under diverse policy distribtion with long Chain-of-Thought (CoT) outputs. Experimental results demonstrate that AURORA enhances process evaluation accuracy, improves PRMs' accuracy for diverse policy distributions and long-CoT responses. The project will be open-sourced at https://auroraprm.github.io/. The Universal-PRM-7B is available at https://huggingface.co/infly/Universal-PRM-7B.

In breast cancer imaging, there has been a trend to directly predict pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) from histological images based on deep learning (DL). However, it has been a commonly known problem that the constructed DL-based models numerically have better performances in internal validation than in external validation. The primary reason for this situation lies in that the distribution of the external data for validation is different from the distribution of the training data for the construction of the predictive model. In this paper, we aim to alleviate this situation with a more intrinsic approach. We propose an experts' cognition-driven ensemble deep learning (ECDEDL) approach for external validation of predicting pCR to NAC from histological images in breast cancer. The proposed ECDEDL, which takes the cognition of both pathology and artificial intelligence experts into consideration to improve the generalization of the predictive model to the external validation, more intrinsically approximates the working paradigm of a human being which will refer to his various working experiences to make decisions. The proposed ECDEDL approach was validated with 695 WSIs collected from the same center as the primary dataset to develop the predictive model and perform the internal validation, and 340 WSIs collected from other three centers as the external dataset to perform the external validation. In external validation, the proposed ECDEDL approach improves the AUCs of pCR prediction from 61.52(59.80-63.26) to 67.75(66.74-68.80) and the Accuracies of pCR prediction from 56.09(49.39-62.79) to 71.01(69.44-72.58). The proposed ECDEDL was quite effective for external validation, numerically more approximating the internal validation.

Probabilistic forecasting is crucial to decision-making under uncertainty about future weather. The dominant approach is to use an ensemble of forecasts to represent and quantify uncertainty in operational numerical weather prediction. However, generating ensembles is computationally costly. In this paper, we propose to generate ensemble forecasts at scale by leveraging recent advances in generative artificial intelligence. Our approach learns a data-driven probabilistic diffusion model from the 5-member ensemble GEFS reforecast dataset. The model can then be sampled efficiently to produce realistic weather forecasts, conditioned on a few members of the operational GEFS forecasting system. The generated ensembles have similar predictive skill as the full GEFS 31-member ensemble, evaluated against ERA5 reanalysis, and emulate well the statistics of large physics-based ensembles. We also apply the same methodology to developing a diffusion model for generative post-processing: the model directly learns to correct biases present in the emulated forecasting system by leveraging reanalysis data as labels during training. Ensembles from this generative post-processing model show greater reliability and accuracy, particularly in extreme event classification. In general, they are more reliable and forecast the probability of extreme weather more accurately than the GEFS operational ensemble. Our models achieve these results at less than 1/10th of the computational cost incurred by the operational GEFS system.