Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and formidable challenges for researchers striving to keep abreast of the latest advancements. One significant challenge is navigating the vast corpus of literature to extract vital gene-related information, a time-consuming and cumbersome task. To enhance the efficiency of this process, it is crucial to address several key challenges: (1) the overwhelming volume of literature, (2) the complexity of gene functions, and (3) the automated integration and generation. In response, we propose GeneSUM, a two-stage automated gene summary extractor utilizing a large language model (LLM). Our approach retrieves and eliminates redundancy of target gene literature and then fine-tunes the LLM to refine and streamline the summarization process. We conducted extensive experiments to validate the efficacy of our proposed framework. The results demonstrate that LLM significantly enhances the integration of gene-specific information, allowing more efficient decision-making in ongoing research.

The analysis of streaming data is one of the biggest challenges posed by the expansion of digital healthcare and bioinformatics. A data stream is a sequence of data that arrives over time. Familiar examples are stock prices, sensor data from mobile devices, personal data from monitoring platforms and many more. The field of machine learning and data mining offers various frameworks for discovering patterns, hidden information, and learning the functional dependencies in complex data. Most methods in machine learning require a good choice of characteristic features to learn functions or compute the posterior probabilities.

In these notes, we wish to provide an introduction to the signature method, focusing on its basic theoretical properties and recent numerical applications. The notes are split into two parts. The first part focuses on the definition and fundamental properties of the signature of a path, or the path signature. We have aimed for a minimalistic approach, assuming only familiarity with classical real analysis and integration theory, and supplementing theory with straightforward examples. We have chosen to focus in detail on the principle properties of the signature which we believe are fundamental to understanding its role in applications. We also present an informal discussion on some of its deeper properties and briefly mention the role of the signature in rough paths theory, which we hope could serve as a light introduction to rough paths for the interested reader. The second part of these notes discusses practical applications of the path signature to the area of machine learning. The signature approach represents a non-parametric way for extraction of characteristic features from data. The data are converted into a multi-dimensional path by means of various embedding algorithms and then processed for computation of individual terms of the signature which summarise certain information contained in the data. The signature thus transforms raw data into a set of features which are used in machine learning tasks. We will review current progress in applications of signatures to machine learning problems.