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Text mining has been shown to be an auxiliary but key driver for modeling, data harmonization, and interpretation in bio-medicine. Scientific literature holds a wealth of information and embodies cumulative knowledge and remains the core basis on which mechanistic pathways, molecular databases, and models are built and refined. Text mining provides the necessary tools to automatically harness the potential of text. In this study, we show the potential of large-scale text mining for deriving novel insights, with a focus on the growing field of microbiome. We first collected the complete set of abstracts relevant to the microbiome from PubMed and used our text mining and intelligence platform Taxila for analysis. We drive the usefulness of text mining using two case studies. First, we analyze the geographical distribution of research and study locations for the field of microbiome by extracting geo mentions from text. Using this analysis, we were able to draw useful insights on the state of research in microbiome w. r.t geographical distributions and economic drivers. Next, to understand the relationships between diseases, microbiome, and food which are central to the field, we construct semantic relationship networks between these different concepts central to the field of microbiome. We show how such networks can be useful to derive useful insight with no prior knowledge encoded. [ABSTRACT FROM AUTHOR]

In this paper, we study an automatic hypothesis generation (HG) problem, which refers to the discovery of meaningful implicit connections between scientific terms, including but not limited to diseases, chemicals, drugs, and genes extracted from databases of biomedical publications. Most prior studies of this problem focused on the use of static information of terms and largely ignored the temporal dynamics of scientific term relations. Even when the dynamics were considered in a few recent studies, they learned the representations for the scientific terms, rather than focusing on the term-pair relations. Since the HG problem is to predict term-pair connections, it is not enough to know with whom the terms are connected, it is more important to know how the connections have been formed (in a dynamic process). We formulate this HG problem as a future connectivity prediction in a dynamic attributed graph. The key is to capture the temporal evolution of node-pair (term-pair) relations. We propose an inductive edge (node-pair) embedding method named T-PAIR, utilizing both the graphical structure and node attribute to encode the temporal node-pair relationship. We demonstrate the efficiency of the proposed model on three real-world datasets, which are three graphs constructed from Pubmed papers published until 2019 in Neurology, Immunotherapy, and Virology, respectively. Evaluations were conducted on predicting future term-pair relations between millions of seen terms (in the transductive setting), as well as on the relations involving unseen terms (in the inductive setting). Experiment results and case study analyses show the effectiveness of the proposed model. [ABSTRACT FROM AUTHOR]

Abstract Statistical model checking techniques have been shown to be effective for approximate model checking on large stochastic systems, where explicit representation of the state space is impractical. Importantly, these techniques ensure the validity of results with statistical guarantees on errors. There is an increasing interest in these classes of algorithms in computational systems biology since analysis using traditional model checking techniques does not scale well. In this context, we present two improvements to existing statistical model checking algorithms. Firstly, we construct an algorithm which removes the need of the user to define the indifference region, a critical parameter in previous sequential hypothesis testing algorithms. Secondly, we extend the algorithm to account for the case when there may be a limit on the computational resources that can be spent on verifying a property; i.e, if the original algorithm is not able to make a decision even after consuming the available amount of resources, we resort to a p-value based approach to make a decision. We demonstrate the improvements achieved by our algorithms in comparison to current algorithms first with a straightforward yet representative example, followed by a real biological model on cell fate of gustatory neurons with microRNAs.

Dynamic Bayesian Networks (DBNs) can serve as succinct probabilistic dynamic models of biochemical networks [CHECK END OF SENTENCE]. To analyze these models, one must compute the probability distribution over system states at a given time point. Doing this exactly is infeasible for large models; hence one must use approximate algorithms. The Factored Frontier algorithm (FF) is one such algorithm [CHECK END OF SENTENCE]. However FF as well as the earlier Boyen-Koller (BK) algorithm [CHECK END OF SENTENCE] can incur large errors. To address this, we present a new approximate algorithm called the Hybrid Factored Frontier (HFF) algorithm. At each time slice, in addition to maintaining probability distributions over local states—as FF does—HFF explicitly maintains the probabilities of a number of global states called spikes. When the number of spikes is 0, we get FF and with all global states as spikes, we get the exact inference algorithm. We show that by increasing the number of spikes one can reduce errors while the additional computational effort required is only quadratic in the number of spikes. We validated the performance of HFF on large DBN models of biopathways. Each pathway has more than 30 species and the corresponding DBN has more than 3,000 nodes. Comparisons with FF and BK show that HFF is a useful and powerful approximate inferencing algorithm for DBNs. [ABSTRACT FROM PUBLISHER]

Statistical model checking techniques have been shown to be effective for approximate model checking on large stochastic systems, where explicit representation of the state space is impractical. Importantly, these techniques ensure the validity of results with statistical guarantees on errors. There is an increasing interest in these classes of algorithms in computational systems biology since analysis using traditional model checking techniques does not scale well. In this context, we present two improvements to existing statistical model checking algorithms. Firstly, we construct an algorithm which removes the need of the user to define the indifference region, a critical parameter in previous sequential hypothesis testing algorithms. Secondly, we extend the algorithm to account for the case when there may be a limit on the computational resources that can be spent on verifying a property; i.e, if the original algorithm is not able to make a decision even after consuming the available amount of resources, we resort to a p-value based approach to make a decision. We demonstrate the improvements achieved by our algorithms in comparison to current algorithms first with a straightforward yet representative example, followed by a real biological model on cell fate of gustatory neurons with microRNAs. [ABSTRACT FROM AUTHOR]

Background: Maintaining good communication and engagement between people with dementia and their caregivers is a major challenge in dementia care. Cognitive stimulation is a psychosocial intervention that supports communication and engagement, and several digital applications for cognitive stimulation have been developed. Personalization is an important factor for obtaining sustainable benefits, but the time and effort required to personalize and optimize applications often makes them difficult for routine use by nonspecialist caregivers and families. Although artificial intelligence (AI) has great potential to support automation of the personalization process, its use is largely unexplored because of the lack of suitable data from which to develop and train machine learning models., Objective: This pilot study aims to evaluate a digital application called Aikomi in Japanese care homes for its potential to (1) create and deliver personalized cognitive stimulation programs to promote communication and engagement between people with dementia and usual care staff and (2) capture meaningful personalized data suitable for the development of AI systems., Methods: A modular technology platform was developed and used to create personalized programs for 15 people with dementia living in 4 residential care facilities in Japan with the cooperation of a family member or care staff. A single intervention with the program was conducted with the person with dementia together with a care staff member, and for some participants, smell stimulation was provided using selected smell sticks in conjunction with the digital program. All sessions were recorded using a video camera, and the combined personalized data obtained by the platform were analyzed., Results: Most people with dementia (10/15, 67%) showed high levels of engagement (>40 on Engagement of a Person with Dementia Scale), and there were no incidences of negative reactions toward the programs. Care staff reported that some participants showed extended concentration and spontaneous communication while using Aikomi, which was not their usual behavior. Smell stimulation promoted engagement for some participants even when they were unable to identify the smell. No changes in well-being were observed following the intervention according to the Mental Function Impairment Scale. The level of response to each type of content in the stimulation program varied greatly according to the person with dementia, and personalized data captured by the Aikomi platform enabled understanding of correlations between stimulation content and responses for each participant., Conclusions: This study suggests that the Aikomi digital application is acceptable for use by persons with dementia and care staff and may have the potential to promote communication and engagement. The platform captures personalized data, which can provide suitable input for machine learning. Further investigation of Aikomi will be conducted to develop AI systems and create personalized digital cognitive stimulation applications that can be easily used by nonspecialist caregivers., (©Nick Hird, Tohmi Osaki, Samik Ghosh, Sucheendra K Palaniappan, Kiyoshi Maeda. Originally published in JMIR Formative Research (https://formative.jmir.org), 16.01.2024.)