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Outline: Workflows Overview; Common Workflow Language (CWL), Example of a CWL; BEE Overview; Machine Learning Components; Machine Learning Scientific Workflow using CWL → A new test case for BEE; Discussion: Benefits and Caveats of current ML workflow; Conclusion.
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-fold improvement in substrate preference and 16-fold improvement in ethyltransferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.
Applications of linguistic principles to potential problems of human and machine communication in space settings are discussed. Variations in language among speakers of different backgrounds and change in language forms resulting from new experiences or reduced contact with other groups need to be considered in the design of intelligent machine systems.
We motivate and introduce a query language PrQL designed for inspecting machine representations of proofs. PrQL natively supports hiproofs which express proof structure using hierarchical nested labelled trees. The core language presented in this paper is locally structured (first-order), with queries built using recursion and patterns over proof structure and rule names. We define the syntax and semantics of locally structured queries, demonstrate their power, and sketch some implementation experiments.
With the advancements made to date in the field of artificial intelligence (AI), significant potential exists to utilize AI capabilities for nuclear power plant (NPP) applications. AI can replicate human decision making and it is usually faster and more accurate than humans. For implementations that impact critical NPP applications (e.g., safety-related or non-safety systems that potentially affect overall plant risk), a deeper safety analysis of the AI methods is necessary. AI applied to NPP operations could resemble the use of digital I&C (DI&C) because such applications involve digital computer hardware and custom-designed software that input plant data, execute complex software algorithms, and output the results to a system or licensed human operator to potentially provoke an action. For AI methods to be compliant with current safety requirements for DI&C, AI compatibility must be evaluated, and AI-related gaps may exist that prevent the prompt deployment of AI in NPPs. This effort aims to evaluate how example AI technologies align with the DI&C safety framework, and discusses how they could be analyzed, modeled, tested, and validated in a manner similar to typical DI&C technologies. Because AI is a broad field that encompasses areas such as machine learning (ML), natural language processing, and computer vision, this research focused on a subset of methods categorized as the computer vision ML (CVML) methods. This report explores two CVML use cases, gauge reading and fire watch, considered relevant to the DI&C standards, as they could play a safety-critical role. For the gauge reading use case, a CVML-enabled technology that can read gauges at oblique angles is utilized. For the fire watch use case, a CVML-enabled technology is utilized that migrates fire watch from a manual (human) approach to automated fire detection. These use cases are mainly intended to give context to the CVML system discussion. This effort assumes the worst-case scenario, with the CVML system being used to replace a safety-related or risk-significant system, thus requiring evaluation. Evaluating CVML against most of the relevant safety requirements for DI&C yielded several CVML-specific considerations due to the uniqueness of its characteristics in comparison with typical DI&C systems. For example, CVML models often employ commonly used (open-source) datasets, and it is not always possible to determine the level of overlap among open-source datasets. Therefore, the independence of the developed CVML models when demonstrating diversity is questionable, therefore creating vulnerability to common cause failure (CCF). The design verification process is also impacted since the data overlap could result in overestimation of the software validation and verification (V&V) performance results. Section 2 of this report evaluates a list of the identified CVML-specific characteristics and discusses the resulting considerations and potential solutions in the context of each referenced requirement. A summation is provided in Section 3. This report is not to be used as a guideline. It was developed to identify and consider issues in the implementation of ML technologies used to augment activities that may have a bearing on plant operation. The report draws parallels to the use of DI&C technologies, for which many standards are available to guide their use in nuclear plant operation. It considers the technologies and some of the potential implications of their use in safety-related applications but is not intended to address regulatory or licensing related issues.
Current approaches for risk analysis of software vulnerabilities using manual assessment and numeric scoring do not complete fast enough to keep pace with the maintenance work rate to patch and mitigate the vulnerabilities. This paper proposes a new approach to modeling software vulnerability risk in the context of the network environment and firewall configuration. In the approach, vulnerability features are automatically matched up with networking, target asset, and adversary features to determine whether adversaries can exploit a vulnerability. The ability of adversaries to reach a vulnerability is modeled by automatically identifying the network services associated with vulnerabilities through a pipeline of machine learning and natural language processing and automatically analyzing network reachability. Our results show that the pipeline can identify network services accurately. We also find that only a small number of vulnerabilities pose real risks to a system. However, if left unmitigated, adversarial reach to vulnerabilities may extend to nullify the effect of firewall countermeasures.
Multimodal models are expected to be a critical component to future advances in artificial intelligence. Here, this field is starting to grow rapidly with a surge of new design elements motivated by the success of foundation models in natural language processing (NLP) and vision. It is widely hoped that further extending the foundation models to multiple modalities (e.g., text, image, video, sensor, time series, graph, etc.) will ultimately lead to generalist multimodal models, i.e. one model across different data modalities and tasks. However, there is little research that systematically analyzes recent multimodal models (particularly the ones that work beyond text and vision) with respect to the underling architecture proposed. Therefore, this work provides a fresh perspective on generalist multimodal models (GMMs) via a novel architecture and training configuration specific taxonomy. This includes factors such as Unifiability, Modularity, and Adaptability that are pertinent and essential to the wide adoption and application of GMMs. The review further highlights key challenges and prospects for the field and guide the researchers into the new advancements.
The development of a materials synthesis route is usually based on heuristics and experience. A possible new approach would be to apply data-driven approaches to learn the patterns of synthesis from past experience and use them to predict the syntheses of novel materials. However, this route is impeded by the lack of a large-scale database of synthesis formulations. In this work, we applied advanced machine learning and natural language processing techniques to construct a dataset of 35,675 solution-based synthesis procedures extracted from the scientific literature. Each procedure contains essential synthesis information including the precursors and target materials, their quantities, and the synthesis actions and corresponding attributes. Every procedure is also augmented with the reaction formula. Through this work, we are making freely available the first large dataset of solution-based inorganic materials synthesis procedures.
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The Workflow Orchestration Language Framework (WOLF) is an agentic framework grounded in natural language with an architecture inspired by reinforcement learning (RL)—designed to orchestrate, scale, and accelerate complex workflows. The concept of WOLF was born out of the very successful ASC Tri-lab Multi-Agent Design Assistant (MADA) project, but extends beyond its domain-specific design agents to provide a more general and extensible architecture. WOLF capitalizes on the lessons learned from MADA and is fully aligned with Sutton’s The Bitter Lesson—that the most enduring progress in AI comes from general-purpose methods that scale with computation, rather than narrow techniques built on domain-specific human knowledge. In this spirit, WOLF enables agents to autonomously learn workflows, capture strategies as reusable playbooks, and build a growing corpus of interpretable, auditable “wisdom artifacts.” These artifacts, expressed in natural language, bridge human and machine understanding while preserving adaptability and scalability as computational power continues to expand.
This datastet contains kernels extracted from OpenMP microbenchmarks collected in DataRaceBench. The purpose of this dataset is to serve as training data for machine learning with programming language processing (PLP).
The aim of this literature review is to examine the current state of the art in the area of citation classification. In particular, we investigate the approaches for characterizing citations based on their semantic type. We conduct this literature review as a meta-analysis covering 60 scholarly articles in this domain. Although we included some of the manual pioneering works in this review, more emphasis is placed on the later automated methods, which use Machine Learning and Natural Language Processing (NLP) for analyzing the fine-grained linguistic features in the surrounding text of citations. The sections are organized based on the steps involved in the pipeline for citation classification. Specifically, we explore the existing classification schemes, data sets, pre-processing methods, extraction of contextual and non-contextual features, and the different types of classifiers and evaluation approaches. The review highlights the importance of identifying the citation types for research evaluation, the challenges faced by the researchers in the process, and the existing research gaps in this field.
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 are 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 deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-foldimprovement in substrate preference and 16-fold improvement in ethyl-transferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.
Large Language Models (LLMs) struggle out of the box when answering factually about detailed questions, especially in domains that are sparsely represented in their training data. This causes hallucinations and reduces reliability making it difficult for them to be used in practice. This work shows that using RAG techniques can improve factual accuracy and reliability, allowing for the application of LLMs in specialized areas, even when those areas that aren’t extensively covered in their initial training.
Studies of Latvian morphophonemics, metrics of Arabic poetry, and intersection of regular languages and languages generated by transformational grammars
The main emphasis has been on the programming language for a self organizing computer. An example of programming with the language of finite state machines is presented in a real time processing for weather radars.