Makoto Takamoto

Makoto Takamoto, Timothy Praditia, Raphael Leiteritz et al.

Machine learning-based modeling of physical systems has experienced increased interest in recent years. Despite some impressive progress, there is still a lack of benchmarks for Scientific ML that are easy to use but still challenging and representative of a wide range of problems. We introduce PDEBench, a benchmark suite of time-dependent simulation tasks based on Partial Differential Equations (PDEs). PDEBench comprises both code and data to benchmark the performance of novel machine learning models against both classical numerical simulations and machine learning baselines. Our proposed set of benchmark problems contribute the following unique features: (1) A much wider range of PDEs compared to existing benchmarks, ranging from relatively common examples to more realistic and difficult problems; (2) much larger ready-to-use datasets compared to prior work, comprising multiple simulation runs across a larger number of initial and boundary conditions and PDE parameters; (3) more extensible source codes with user-friendly APIs for data generation and baseline results with popular machine learning models (FNO, U-Net, PINN, Gradient-Based Inverse Method). PDEBench allows researchers to extend the benchmark freely for their own purposes using a standardized API and to compare the performance of new models to existing baseline methods. We also propose new evaluation metrics with the aim to provide a more holistic understanding of learning methods in the context of Scientific ML. With those metrics we identify tasks which are challenging for recent ML methods and propose these tasks as future challenges for the community. The code is available at https://github.com/pdebench/PDEBench.

Makoto Takamoto, Francesco Alesiani, Mathias Niepert

Scientific Machine Learning (SciML) is concerned with the development of learned emulators of physical systems governed by partial differential equations (PDE). In application domains such as weather forecasting, molecular dynamics, and inverse design, ML-based surrogate models are increasingly used to augment or replace inefficient and often non-differentiable numerical simulation algorithms. While a number of ML-based methods for approximating the solutions of PDEs have been proposed in recent years, they typically do not adapt to the parameters of the PDEs, making it difficult to generalize to PDE parameters not seen during training. We propose a Channel Attention mechanism guided by PDE Parameter Embeddings (CAPE) component for neural surrogate models and a simple yet effective curriculum learning strategy. The CAPE module can be combined with neural PDE solvers allowing them to adapt to unseen PDE parameters. The curriculum learning strategy provides a seamless transition between teacher-forcing and fully auto-regressive training. We compare CAPE in conjunction with the curriculum learning strategy using a popular PDE benchmark and obtain consistent and significant improvements over the baseline models. The experiments also show several advantages of CAPE, such as its increased ability to generalize to unseen PDE parameters without large increases inference time and parameter count.

Makoto Takamoto, Viktor Zaverkin, Mathias Niepert

Machine learning plays an increasingly important role in computational chemistry and materials science, complementing computationally intensive ab initio and first-principles methods. Despite their utility, machine-learning models often lack generalization capability and robustness during atomistic simulations, yielding unphysical energy and force predictions that hinder their real-world applications. We address this challenge by introducing a physics-informed, weakly supervised approach for training machine-learned interatomic potentials (MLIPs). We introduce two novel loss functions, extrapolating the potential energy via a Taylor expansion and using the concept of conservative forces. Our approach improves the accuracy of MLIPs applied to training tasks with sparse training data sets and reduces the need for pre-training computationally demanding models with large data sets. Particularly, we perform extensive experiments demonstrating reduced energy and force errors -- often lower by a factor of two -- for various baseline models and benchmark data sets. Moreover, we demonstrate improved robustness during MD simulations of the MLIP models trained with the proposed weakly supervised loss. Finally, our approach improves the fine-tuning of foundation models on sparse, highly accurate ab initio data. An implementation of our method and scripts for executing experiments are available at https://github.com/nec-research/PICPS-ML4Sci.

Daniel Musekamp, Marimuthu Kalimuthu, David Holzmüller et al.

Solving partial differential equations (PDEs) is a fundamental problem in science and engineering. While neural PDE solvers can be more efficient than established numerical solvers, they often require large amounts of training data that is costly to obtain. Active learning (AL) could help surrogate models reach the same accuracy with smaller training sets by querying classical solvers with more informative initial conditions and PDE parameters. While AL is more common in other domains, it has yet to be studied extensively for neural PDE solvers. To bridge this gap, we introduce AL4PDE, a modular and extensible active learning benchmark. It provides multiple parametric PDEs and state-of-the-art surrogate models for the solver-in-the-loop setting, enabling the evaluation of existing and the development of new AL methods for neural PDE solving. We use the benchmark to evaluate batch active learning algorithms such as uncertainty- and feature-based methods. We show that AL reduces the average error by up to 71% compared to random sampling and significantly reduces worst-case errors. Moreover, AL generates similar datasets across repeated runs, with consistent distributions over the PDE parameters and initial conditions. The acquired datasets are reusable, providing benefits for surrogate models not involved in the data generation.

Seungone Kim, Dongkeun Yoon, Kiril Gashteovski et al.

With the advancement of AI capabilities, AI reviewers are beginning to be deployed in scientific peer review, yet their capability and credibility remain in question: many scientists simply view them as probabilistic systems without the expertise to evaluate research, while other researchers are more optimistic about their readiness without concrete evidence. Understanding what AI reviewers do well, where they fall short, and what challenges remain is essential. However, existing evaluations of AI reviewers have focused on whether their verdicts match human verdicts (e.g., score alignment, acceptance prediction), which is insufficient to characterize their capabilities and limits. In this paper, we close this gap through a large-scale expert annotation study, in which 45 domain scientists in Physical, Biological, and Health Sciences spent 469 hours rating 2,960 individual criticisms (each targeting one specific aspect of a paper) from human-written and AI-generated reviews of 82 Nature-family papers on correctness, significance, and sufficiency of evidence. On a composite of all three dimensions, a reviewing agent powered by GPT-5.2 scores above each paper's top-rated human reviewer (60.0% vs. 48.2%, p = 0.009), while all three AI reviewers (including Gemini 3.0 Pro and Claude Opus 4.5) exceed the lowest-rated human across every dimension. AI reviewers' accurate criticisms are also more often rated significant and well-evidenced, and surface a distinct 26% of issues no human raises. However, AI reviewers overlap far more than humans do (21% vs. 3% for cross-reviewer pairs), and exhibit 16 recurring weaknesses humans do not share, such as limited subfield knowledge, lack of long context management over multiple files, and overly critical stance on minor issues. Overall, our results position current AI reviewers as complements to, not substitutes for, human reviewers.

Henrik Christiansen, Takashi Maruyama, Federico Errica et al.

We present an end-to-end differentiable molecular simulation framework (DIMOS) for molecular dynamics and Monte Carlo simulations. DIMOS easily integrates machine-learning-based interatomic potentials and implements classical force fields including an efficient implementation of particle-mesh Ewald. Thanks to its modularity, both classical and machine-learning-based approaches can be easily combined into a hybrid description of the system (ML/MM). By supporting key molecular dynamics features such as efficient neighborlists and constraint algorithms for larger time steps, the framework makes steps in bridging the gap between hand-optimized simulation engines and the flexibility of a \verb|PyTorch| implementation. We show that due to improved linear instead of quadratic scaling as function of system size DIMOS is able to obtain speed-up factors of up to $170\times$ for classical force field simulations against another fully differentiable simulation framework. The advantage of differentiability is demonstrated by an end-to-end optimization of the proposal distribution in a Markov Chain Monte Carlo simulation based on Hamiltonian Monte Carlo (HMC). Using these optimized simulation parameters a $3\times$ acceleration is observed in comparison to ad-hoc chosen simulation parameters. The code is available at https://github.com/nec-research/DIMOS.

Makoto Takamoto, Daniel Oñoro-Rubio, Wiem Ben Rim et al.

Knowledge graph embedding (KGE) models encode the structural information of knowledge graphs to predicting new links. Effective training of these models requires distinguishing between positive and negative samples with high precision. Although prior research has shown that improving the quality of negative samples can significantly enhance model accuracy, identifying high-quality negative samples remains a challenging problem. This paper theoretically investigates the condition under which negative samples lead to optimal KG embedding and identifies a sufficient condition for an effective negative sample distribution. Based on this theoretical foundation, we propose \textbf{E}mbedding \textbf{MU}tation (\textsc{EMU}), a novel framework that \emph{generates} negative samples satisfying this condition, in contrast to conventional methods that focus on \emph{identifying} challenging negative samples within the training data. Importantly, the simplicity of \textsc{EMU} ensures seamless integration with existing KGE models and negative sampling methods. To evaluate its efficacy, we conducted comprehensive experiments across multiple datasets. The results consistently demonstrate significant improvements in link prediction performance across various KGE models and negative sampling methods. Notably, \textsc{EMU} enables performance improvements comparable to those achieved by models with embedding dimension five times larger. An implementation of the method and experiments are available at https://github.com/nec-research/EMU-KG.

Viktor Zaverkin, Francesco Alesiani, Takashi Maruyama et al.

The ability to perform fast and accurate atomistic simulations is crucial for advancing the chemical sciences. By learning from high-quality data, machine-learned interatomic potentials achieve accuracy on par with ab initio and first-principles methods at a fraction of their computational cost. The success of machine-learned interatomic potentials arises from integrating inductive biases such as equivariance to group actions on an atomic system, e.g., equivariance to rotations and reflections. In particular, the field has notably advanced with the emergence of equivariant message passing. Most of these models represent an atomic system using spherical tensors, tensor products of which require complicated numerical coefficients and can be computationally demanding. Cartesian tensors offer a promising alternative, though state-of-the-art methods lack flexibility in message-passing mechanisms, restricting their architectures and expressive power. This work explores higher-rank irreducible Cartesian tensors to address these limitations. We integrate irreducible Cartesian tensor products into message-passing neural networks and prove the equivariance and traceless property of the resulting layers. Through empirical evaluations on various benchmark data sets, we consistently observe on-par or better performance than that of state-of-the-art spherical and Cartesian models.

Bhushan Kotnis, Kiril Gashteovski, Daniel Oñoro Rubio et al.

Open Information Extraction (OpenIE) is the task of extracting (subject, predicate, object) triples from natural language sentences. Current OpenIE systems extract all triple slots independently. In contrast, we explore the hypothesis that it may be beneficial to extract triple slots iteratively: first extract easy slots, followed by the difficult ones by conditioning on the easy slots, and therefore achieve a better overall extraction. Based on this hypothesis, we propose a neural OpenIE system, milIE, that operates in an iterative fashion. Due to the iterative nature, the system is also modular -- it is possible to seamlessly integrate rule based extraction systems with a neural end-to-end system, thereby allowing rule based systems to supply extraction slots which milIE can leverage for extracting the remaining slots. We confirm our hypothesis empirically: milIE outperforms SOTA systems on multiple languages ranging from Chinese to Arabic. Additionally, we are the first to provide an OpenIE test dataset for Arabic and Galician.

Makoto Takamoto, Yusuke Morishita

It is well-known that training of generative adversarial networks (GANs) requires huge iterations before the generator's providing good-quality samples. Although there are several studies to tackle this problem, there is still no universal solution. In this paper, we investigated the effect of sample mixing methods, that is, Mixup, CutMix, and newly proposed Smoothed Regional Mix (SRMix), to alleviate this problem. The sample-mixing methods are known to enhance the accuracy and robustness in the wide range of classification problems, and can naturally be applicable to GANs because the role of the discriminator can be interpreted as the classification between real and fake samples. We also proposed a new formalism applying the sample-mixing methods to GANs with the saturated losses which do not have a clear "label" of real and fake. We performed a vast amount of numerical experiments using LSUN and CelebA datasets. The results showed that Mixup and SRMix improved the quality of the generated images in terms of FID in most cases, in particular, SRMix showed the best improvement in most cases. Our analysis indicates that the mixed-samples can provide different properties from the vanilla fake samples, and the mixing pattern strongly affects the decision of the discriminators. The generated images of Mixup have good high-level feature but low-level feature is not so impressible. On the other hand, CutMix showed the opposite tendency. Our SRMix showed the middle tendency, that is, showed good high and low level features. We believe that our finding provides a new perspective to accelerate the GANs convergence and improve the quality of generated samples.

Makoto Takamoto, Yusuke Morishita, Hitoshi Imaoka

Compressing deep neural network (DNN) models becomes a very important and necessary technique for real-world applications, such as deploying those models on mobile devices. Knowledge distillation is one of the most popular methods for model compression, and many studies have been made on developing this technique. However, those studies mainly focused on classification problems, and very few attempts have been made on regression problems, although there are many application of DNNs on regression problems. In this paper, we propose a new formalism of knowledge distillation for regression problems. First, we propose a new loss function, teacher outlier rejection loss, which rejects outliers in training samples using teacher model predictions. Second, we consider a multi-task network with two outputs: one estimates training labels which is in general contaminated by noisy labels; And the other estimates teacher model's output which is expected to modify the noise labels following the memorization effects. By considering the multi-task network, training of the feature extraction of student models becomes more effective, and it allows us to obtain a better student model than one trained from scratch. We performed comprehensive evaluation with one simple toy model: sinusoidal function, and two open datasets: MPIIGaze, and Multi-PIE. Our results show consistent improvement in accuracy regardless of the annotation error level in the datasets.