Early screening of potential breakthrough technologies with enhanced interpretability: A patent-specific hierarchical attention network model

Despite the usefulness of machine learning approaches for the early screening of potential breakthrough technologies, their practicality is often hindered by opaque models. To address this, we propose an interpretable machine learning approach to predicting future citation counts from patent texts using a patent-specific hierarchical attention network (PatentHAN) model. Central to this approach are (1) a patent-specific pre-trained language model, capturing the meanings of technical words in patent claims, (2) a hierarchical network structure, enabling detailed analysis at the claim level, and (3) a claim-wise self-attention mechanism, revealing pivotal claims during the screening process. A case study of 35,376 pharmaceutical patents demonstrates the effectiveness of our approach in early screening of potential breakthrough technologies while ensuring interpretability. Furthermore, we conduct additional analyses using different language models and claim types to examine the robustness of the approach. It is expected that the proposed approach will enhance expert-machine collaboration in identifying breakthrough technologies, providing new insight derived from text mining into technological value.

Text-to-Battery Recipe: A language modeling-based protocol for automatic battery recipe extraction and retrieval

Recent studies have increasingly applied natural language processing (NLP) to automatically extract experimental research data from the extensive battery materials literature. Despite the complex process involved in battery manufacturing -- from material synthesis to cell assembly -- there has been no comprehensive study systematically organizing this information. In response, we propose a language modeling-based protocol, Text-to-Battery Recipe (T2BR), for the automatic extraction of end-to-end battery recipes, validated using a case study on batteries containing LiFePO4 cathode material. We report machine learning-based paper filtering models, screening 2,174 relevant papers from the keyword-based search results, and unsupervised topic models to identify 2,876 paragraphs related to cathode synthesis and 2,958 paragraphs related to cell assembly. Then, focusing on the two topics, two deep learning-based named entity recognition models are developed to extract a total of 30 entities -- including precursors, active materials, and synthesis methods -- achieving F1 scores of 88.18% and 94.61%. The accurate extraction of entities enables the systematic generation of 165 end-toend recipes of LiFePO4 batteries. Our protocol and results offer valuable insights into specific trends, such as associations between precursor materials and synthesis methods, or combinations between different precursor materials. We anticipate that our findings will serve as a foundational knowledge base for facilitating battery-recipe information retrieval. The proposed protocol will significantly accelerate the review of battery material literature and catalyze innovations in battery design and development.

MaTableGPT: GPT-based Table Data Extractor from Materials Science Literature

Efficiently extracting data from tables in the scientific literature is pivotal for building large-scale databases. However, the tables reported in materials science papers exist in highly diverse forms; thus, rule-based extractions are an ineffective approach. To overcome this challenge, we present MaTableGPT, which is a GPT-based table data extractor from the materials science literature. MaTableGPT features key strategies of table data representation and table splitting for better GPT comprehension and filtering hallucinated information through follow-up questions. When applied to a vast volume of water splitting catalysis literature, MaTableGPT achieved an extraction accuracy (total F1 score) of up to 96.8%. Through comprehensive evaluations of the GPT usage cost, labeling cost, and extraction accuracy for the learning methods of zero-shot, few-shot and fine-tuning, we present a Pareto-front mapping where the few-shot learning method was found to be the most balanced solution owing to both its high extraction accuracy (total F1 score>95%) and low cost (GPT usage cost of 5.97 US dollars and labeling cost of 10 I/O paired examples). The statistical analyses conducted on the database generated by MaTableGPT revealed valuable insights into the distribution of the overpotential and elemental utilization across the reported catalysts in the water splitting literature.

Design of reliable technology valuation model with calibrated machine learning of patent indicators

Machine learning (ML) has revolutionized the digital transformation of technology valuation by predicting the value of patents with high accuracy. However, the lack of validation regarding the reliability of these models hinders experts from fully trusting the confidence of model predictions. To address this issue, we propose an analytical framework for reliable technology valuation using calibrated ML models, which provide robust confidence levels in model predictions. We extract quantitative patent indicators that represent various technology characteristics as input data, using the patent maintenance period as a proxy for technology values. Multiple ML models are developed to capture the nonlinear relationship between patent indicators and technology value. The reliability and accuracy of these models are evaluated, presenting a Pareto-front map where the expected calibration error, Matthews correlation coefficient and F1-scores are compared. After identifying the best-performing model, we apply SHapley Additive exPlanation (SHAP) analysis to pinpoint the most significant input features by confidence bin. Through a case study, we confirmed that the proposed approach offers a practical guideline for developing reliable and accurate ML-based technology valuation models, with significant implications for both academia and industry.

Scalable Wasserstein Gradient Flow for Generative Modeling through Unbalanced Optimal Transport

Wasserstein Gradient Flow (WGF) describes the gradient dynamics of probability density within the Wasserstein space. WGF provides a promising approach for conducting optimization over the probability distributions. Numerically approximating the continuous WGF requires the time discretization method. The most well-known method for this is the JKO scheme. In this regard, previous WGF models employ the JKO scheme and parametrize transport map for each JKO step. However, this approach results in quadratic training complexity $O(K^2)$ with the number of JKO step $K$. This severely limits the scalability of WGF models. In this paper, we introduce a scalable WGF-based generative model, called Semi-dual JKO (S-JKO). Our model is based on the semi-dual form of the JKO step, derived from the equivalence between the JKO step and the Unbalanced Optimal Transport. Our approach reduces the training complexity to $O(K)$. We demonstrate that our model significantly outperforms existing WGF-based generative models, achieving FID scores of 2.62 on CIFAR-10 and 6.19 on CelebA-HQ-256, which are comparable to state-of-the-art image generative models.

Analyzing and Improving OT-based Adversarial Networks

Optimal Transport (OT) problem aims to find a transport plan that bridges two distributions while minimizing a given cost function. OT theory has been widely utilized in generative modeling. In the beginning, OT distance has been used as a measure for assessing the distance between data and generated distributions. Recently, OT transport map between data and prior distributions has been utilized as a generative model. These OT-based generative models share a similar adversarial training objective. In this paper, we begin by unifying these OT-based adversarial methods within a single framework. Then, we elucidate the role of each component in training dynamics through a comprehensive analysis of this unified framework. Moreover, we suggest a simple but novel method that improves the previously best-performing OT-based model. Intuitively, our approach conducts a gradual refinement of the generated distribution, progressively aligning it with the data distribution. Our approach achieves a FID score of 2.51 on CIFAR-10, outperforming unified OT-based adversarial approaches.

Learning a Patent-Informed Biomedical Knowledge Graph Reveals Technological Potential of Drug Repositioning Candidates

Drug repositioning-a promising strategy for discovering new therapeutic uses for existing drugs-has been increasingly explored in the computational science literature using biomedical databases. However, the technological potential of drug repositioning candidates has often been overlooked. This study presents a novel protocol to comprehensively analyse various sources such as pharmaceutical patents and biomedical databases, and identify drug repositioning candidates with both technological potential and scientific evidence. To this end, first, we constructed a scientific biomedical knowledge graph (s-BKG) comprising relationships between drugs, diseases, and genes derived from biomedical databases. Our protocol involves identifying drugs that exhibit limited association with the target disease but are closely located in the s-BKG, as potential drug candidates. We constructed a patent-informed biomedical knowledge graph (p-BKG) by adding pharmaceutical patent information. Finally, we developed a graph embedding protocol to ascertain the structure of the p-BKG, thereby calculating the relevance scores of those candidates with target disease-related patents to evaluate their technological potential. Our case study on Alzheimer's disease demonstrates its efficacy and feasibility, while the quantitative outcomes and systematic methods are expected to bridge the gap between computational discoveries and successful market applications in drug repositioning research.

Accelerated materials language processing enabled by GPT

Materials language processing (MLP) is one of the key facilitators of materials science research, as it enables the extraction of structured information from massive materials science literature. Prior works suggested high-performance MLP models for text classification, named entity recognition (NER), and extractive question answering (QA), which require complex model architecture, exhaustive fine-tuning and a large number of human-labelled datasets. In this study, we develop generative pretrained transformer (GPT)-enabled pipelines where the complex architectures of prior MLP models are replaced with strategic designs of prompt engineering. First, we develop a GPT-enabled document classification method for screening relevant documents, achieving comparable accuracy and reliability compared to prior models, with only small dataset. Secondly, for NER task, we design an entity-centric prompts, and learning few-shot of them improved the performance on most of entities in three open datasets. Finally, we develop an GPT-enabled extractive QA model, which provides improved performance and shows the possibility of automatically correcting annotations. While our findings confirm the potential of GPT-enabled MLP models as well as their value in terms of reliability and practicability, our scientific methods and systematic approach are applicable to any materials science domain to accelerate the information extraction of scientific literature.

Understanding the Latent Space of Diffusion Models through the Lens of Riemannian Geometry

Despite the success of diffusion models (DMs), we still lack a thorough understanding of their latent space. To understand the latent space $\mathbf{x}_t \in \mathcal{X}$, we analyze them from a geometrical perspective. Specifically, we utilize the pullback metric to find the local latent basis in $\mathcal{X}$ and their corresponding local tangent basis in $\mathcal{H}$, the intermediate feature maps of DMs. The discovered latent basis enables unsupervised image editing capability through latent space traversal. We investigate the discovered structure from two perspectives. First, we examine how geometric structure evolves over diffusion timesteps. Through analysis, we show that 1) the model focuses on low-frequency components early in the generative process and attunes to high-frequency details later; 2) At early timesteps, different samples share similar tangent spaces; and 3) The simpler datasets that DMs trained on, the more consistent the tangent space for each timestep. Second, we investigate how the geometric structure changes based on text conditioning in Stable Diffusion. The results show that 1) similar prompts yield comparable tangent spaces; and 2) the model depends less on text conditions in later timesteps. To the best of our knowledge, this paper is the first to present image editing through $\mathbf{x}$-space traversal and provide thorough analyses of the latent structure of DMs.

Generative Modeling through the Semi-dual Formulation of Unbalanced Optimal Transport

Optimal Transport (OT) problem investigates a transport map that bridges two distributions while minimizing a given cost function. In this regard, OT between tractable prior distribution and data has been utilized for generative modeling tasks. However, OT-based methods are susceptible to outliers and face optimization challenges during training. In this paper, we propose a novel generative model based on the semi-dual formulation of Unbalanced Optimal Transport (UOT). Unlike OT, UOT relaxes the hard constraint on distribution matching. This approach provides better robustness against outliers, stability during training, and faster convergence. We validate these properties empirically through experiments. Moreover, we study the theoretical upper-bound of divergence between distributions in UOT. Our model outperforms existing OT-based generative models, achieving FID scores of 2.97 on CIFAR-10 and 5.80 on CelebA-HQ-256.