Damped sinusoidal oscillations are widely observed in many physical systems, and their analysis provides access to underlying physical properties. However, parameter estimation becomes difficult when the signal decays rapidly, multiple components are superposed, and observational noise is present. In this study, we develop an autoencoder-based method that uses the latent space to estimate the frequency, phase, decay time, and amplitude of each component in noisy multi-component damped sinusoidal signals. We investigate multi-component cases under Gaussian-distribution training and further examine the effect of the training-data distribution through comparisons between Gaussian and uniform training. The performance is evaluated through waveform reconstruction and parameter-estimation accuracy. We find that the proposed method can estimate the parameters with high accuracy even in challenging setups, such as those involving a subdominant component or nearly opposite-phase components, while remaining reasonably robust when the training distribution is less informative. This demonstrates its potential as a tool for analyzing short-duration, noisy signals.

While impressive, most of these tasks can be easily performed by an intelligent human.

Graph Neural Networks (GNNs) have proven to be highly effective in various graph learning tasks. A key characteristic of GNNs is their use of a fixed number of message-passing steps for all nodes in the graph, regardless of each node's diverse computational needs and characteristics. Through empirical real-world data analysis, we demonstrate that the optimal number of message-passing layers varies for nodes with different characteristics. This finding is further supported by experiments conducted on synthetic datasets. To address this, we propose Adaptive Depth Message Passing GNN (ADMP-GNN), a novel framework that dynamically adjusts the number of message passing layers for each node, resulting in improved performance. This approach applies to any model that follows the message passing scheme. We evaluate ADMP-GNN on the node classification task and observe performance improvements over baseline GNN models.

Large language models (LLMs) have enabled powerful advances in natural language understanding and generation. Yet their application to complex, real-world scientific workflows remain limited by challenges in memory, planning, and tool integration. Here, we introduce SciBORG (Scientific Bespoke Artificial Intelligence Agents Optimized for Research Goals), a modular agentic framework that allows LLM-based agents to autonomously plan, reason, and achieve robust and reliable domain-specific task execution. Agents are constructed dynamically from source code documentation and augmented with finite-state automata (FSA) memory, enabling persistent state tracking and context-aware decision-making. This approach eliminates the need for manual prompt engineering and allows for robust, scalable deployment across diverse applications via maintaining context across extended workflows and to recover from tool or execution failures. We validate SciBORG through integration with both physical and virtual hardware, such as microwave synthesizers for executing user-specified reactions, with context-aware decision making and demonstrate its use in autonomous multi-step bioassay retrieval from the PubChem database utilizing multi-step planning, reasoning, agent-to-agent communication and coordination for execution of exploratory tasks. Systematic benchmarking shows that SciBORG agents achieve reliable execution, adaptive planning, and interpretable state transitions. Our results show that memory and state awareness are critical enablers of agentic planning and reliability, offering a generalizable foundation for deploying AI agents in complex environments.

In qualitative research, data transcription is often labor-intensive and time-consuming. To expedite this process, a workflow utilizing artificial intelligence (AI) was developed. This workflow not only enhances transcription speed but also addresses the issue of AI-generated transcripts often lacking compatibility with standard content analysis software. Within this workflow, automatic speech recognition is employed to create initial transcripts from audio recordings, which are then formatted to be compatible with content analysis software such as ATLAS.ti or MAXQDA. Empirical data from a study of 12 interviews suggests that this workflow can reduce transcription time by up to 46.2%. Furthermore, by using widely used standard software, this process is suitable for both students and researchers while also being adaptable to a variety of learning, teaching, and research environments. It is also particularly beneficial for non-native speakers. In addition, the workflow is GDPR-compliant and facilitates local, offline transcript generation, which is crucial when dealing with sensitive data.

It has been 100 years since statistical process control (SPC) or statistical process monitoring (SPM) was first introduced for production processes and later applied to service, healthcare, and other industries. The techniques applied to SPM applications are mostly statistically oriented. Recent advances in Artificial Intelligence (AI) have reinvigorated the imagination of adopting AI for SPM applications. This manuscript begins with a concise review of the historical development of the statistically based SPM methods. Next, this manuscript explores AI and Machine Learning (ML) algorithms and methods applied in various SPM applications, addressing quality characteristics of univariate, multivariate, profile, and image. These AI methods can be classified into the following categories: classification, pattern recognition, time series applications, and generative AI. Specifically, different kinds of neural networks, such as artificial neural networks (ANN), convolutional neural networks (CNN), recurrent neural networks (RNN), and generative adversarial networks (GAN), are among the most implemented AI methods impacting SPM. Finally, this manuscript outlines a couple of future directions that harness the potential of the Large Multimodal Model (LMM) for advancing SPM research and applications in complex systems. The ultimate objective is to transform statistical process monitoring (SPM) into smart process control (SMPC), where corrective actions are autonomously implemented to either prevent quality issues or restore process performance.

Nanomaterials exhibit distinctive properties governed by parameters such as size, shape, and surface characteristics, which critically influence their applications and interactions across technological, biological, and environmental contexts. Accurate quantification and understanding of these materials are essential for advancing research and innovation. In this regard, deep learning segmentation networks have emerged as powerful tools that enable automated insights and replace subjective methods with precise quantitative analysis. However, their efficacy depends on representative annotated datasets, which are challenging to obtain due to the costly imaging of nanoparticles and the labor-intensive nature of manual annotations. To overcome these limitations, we introduce DiffRenderGAN, a novel generative model designed to produce annotated synthetic data. By integrating a differentiable renderer into a Generative Adversarial Network (GAN) framework, DiffRenderGAN optimizes textural rendering parameters to generate realistic, annotated nanoparticle images from non-annotated real microscopy images. This approach reduces the need for manual intervention and enhances segmentation performance compared to existing synthetic data methods by generating diverse and realistic data. Tested on multiple ion and electron microscopy cases, including titanium dioxide (TiO$_2$), silicon dioxide (SiO$_2$)), and silver nanowires (AgNW), DiffRenderGAN bridges the gap between synthetic and real data, advancing the quantification and understanding of complex nanomaterial systems.

Conventional echo state networks (ESNs) require supervised learning to train the readout layer, using the desired outputs as training data. In this study, we focus on input reconstruction (IR), which refers to training the readout layer to reproduce the input time series in its output. We reformulate the learning algorithm of the ESN readout layer to perform IR using unsupervised learning (UL). By conducting theoretical analysis and numerical experiments, we demonstrate that IR in ESNs can be effectively implemented under realistic conditions without explicitly using the desired outputs as training data; in this way, UL is enabled. Furthermore, we demonstrate that applications relying on IR, such as dynamical system replication and noise filtering, can be reformulated within the UL framework. Our findings establish a theoretically sound and universally applicable IR formulation, along with its related tasks in ESNs. This work paves the way for novel predictions and highlights unresolved theoretical challenges in ESNs, particularly in the context of time-series processing methods and computational models of the brain.

Olfaction -- how molecules are perceived as odors to humans -- remains poorly understood. Recently, the principal odor map (POM) was introduced to digitize the olfactory properties of single compounds. However, smells in real life are not pure single molecules, but complex mixtures of molecules, whose representations remain relatively under-explored. In this work, we introduce POMMix, an extension of the POM to represent mixtures. Our representation builds upon the symmetries of the problem space in a hierarchical manner: (1) graph neural networks for building molecular embeddings, (2) attention mechanisms for aggregating molecular representations into mixture representations, and (3) cosine prediction heads to encode olfactory perceptual distance in the mixture embedding space. POMMix achieves state-of-the-art predictive performance across multiple datasets. We also evaluate the generalizability of the representation on multiple splits when applied to unseen molecules and mixture sizes. Our work advances the effort to digitize olfaction, and highlights the synergy of domain expertise and deep learning in crafting expressive representations in low-data regimes.

Deep learning models for anticipating the products of organic reactions have found many use cases, including validating retrosynthetic pathways and constraining synthesis-based molecular design tools. Despite compelling performance on popular benchmark tasks, strange and erroneous predictions sometimes ensue when using these models in practice. The core issue is that common benchmarks test models in an in-distribution setting, whereas many real-world uses for these models are in out-of-distribution settings and require a greater degree of extrapolation. To better understand how current reaction predictors work in out-of-distribution domains, we report a series of more challenging evaluations of a prototypical SMILES-based deep learning model. First, we illustrate how performance on randomly sampled datasets is overly optimistic compared to performance when generalizing to new patents or new authors. Second, we conduct time splits that evaluate how models perform when tested on reactions published in years after those in their training set, mimicking real-world deployment. Finally, we consider extrapolation across reaction classes to reflect what would be required for the discovery of novel reaction types. This panel of tasks can reveal the capabilities and limitations of today's reaction predictors, acting as a crucial first step in the development of tomorrow's next-generation models capable of reaction discovery.