Towards Learning Instantiated Logical Rules from Knowledge Graphs

Efficiently inducing high-level interpretable regularities from knowledge graphs (KGs) is an essential yet challenging task that benefits many downstream applications. In this work, we present GPFL, a probabilistic rule learner optimized to mine instantiated first-order logic rules from KGs. Instantiated rules contain constants extracted from KGs. Compared to abstract rules that contain no constants, instantiated rules are capable of explaining and expressing concepts in more details. GPFL utilizes a novel two-stage rule generation mechanism that first generalizes extracted paths into templates that are acyclic abstract rules until a certain degree of template saturation is achieved, then specializes the generated templates into instantiated rules. Unlike existing works that ground every mined instantiated rule for evaluation, GPFL shares groundings between structurally similar rules for collective evaluation. Moreover, we reveal the presence of overfitting rules, their impact on the predictive performance, and the effectiveness of a simple validation method filtering out overfitting rules. Through extensive experiments on public benchmark datasets, we show that GPFL 1.) significantly reduces the runtime on evaluating instantiated rules; 2.) discovers much more quality instantiated rules than existing works; 3.) improves the predictive performance of learned rules by removing overfitting rules via validation; 4.) is competitive on knowledge graph completion task compared to state-of-the-art baselines

The Use of Chinese-language Internet Information about Cancer by Chinese Health Consumers

We investigated the use of Chinese-language Internet information about cancer by Chinese health consumers, and its impact on their cancer care. We applied a grounded theory approach and undertook semi-structured interviews with 20 participants in China to learn their experience of using the Internet for cancer information as a patient or a family member. Thematic analysis of the interview data identified three key themes: (1) information needs evolve during the treatment journey; (2) Traditional Chinese Medicine (TCM) and adverse effects of treatment are the topics of greatest interest; and (3) most participants have encountered Internet health information with questionable quality. These findings suggest that although Internet has great potential to empower Chinese cancer patients and their family through cancer care journey, the information quality issues, cultural considerations and current health care paradigm constrain this potential. Further research is needed to address these issues in improving cancer care in China

Building Rule Hierarchies for Efficient Logical Rule Learning from Knowledge Graphs

Many systems have been developed in recent years to mine logical rules from large-scale Knowledge Graphs (KGs), on the grounds that representing regularities as rules enables both the interpretable inference of new facts, and the explanation of known facts. Among these systems, the walk-based methods that generate the instantiated rules containing constants by abstracting sampled paths in KGs demonstrate strong predictive performance and expressivity. However, due to the large volume of possible rules, these systems do not scale well where computational resources are often wasted on generating and evaluating unpromising rules. In this work, we address such scalability issues by proposing new methods for pruning unpromising rules using rule hierarchies. The approach consists of two phases. Firstly, since rule hierarchies are not readily available in walk-based methods, we have built a Rule Hierarchy Framework (RHF), which leverages a collection of subsumption frameworks to build a proper rule hierarchy from a set of learned rules. And secondly, we adapt RHF to an existing rule learner where we design and implement two methods for Hierarchical Pruning (HPMs), which utilize the generated hierarchies to remove irrelevant and redundant rules. Through experiments over four public benchmark datasets, we show that the application of HPMs is effective in removing unpromising rules, which leads to significant reductions in the runtime as well as in the number of learned rules, without compromising the predictive performance

Learning Logical Rules from Knowledge Graphs

Ph.D. (Integrated) ThesisExpressing and extracting regularities in multi-relational data, where data points are interrelated and heterogeneous, requires well-designed knowledge representation. Knowledge Graphs (KGs), as a graph-based representation of multi-relational data, have seen a rapidly growing presence in industry and academia, where many real-world applications and academic research are either enabled or augmented through the incorporation of KGs. However, due to the way KGs are constructed, they are inherently noisy and incomplete. In this thesis, we focus on developing logic-based graph reasoning systems that utilize logical rules to infer missing facts for the completion of KGs. Unlike most rule learners that primarily mine abstract rules that contain no constants, we are particularly interested in learning instantiated rules that contain constants due to their ability to represent meaningful patterns and correlations that can not be expressed by abstract rules. The inclusion of instantiated rules often leads to exponential growth in the search space. Therefore, it is necessary to develop optimization strategies to balance between scalability and expressivity. To such an end, we propose GPFL, a probabilistic rule learning system optimized to mine instantiated rules through the implementation of a novel two-stage rule generation mechanism. Through experiments, we demonstrate that GPFL not only performs competitively on knowledge graph completion but is also much more efficient then existing methods at mining instantiated rules. With GPFL, we also reveal overfitting instantiated rules and provide detailed analyses about their impact on system performance. Then, we propose RHF, a generic framework for constructing rule hierarchies from a given set of rules. We demonstrate through experiments that with RHF and the hierarchical pruning techniques enabled by it, significant reductions in runtime and rule size are observed due to the pruning of unpromising rules. Eventually, to test the practicability of rule learning systems, we develop Ranta, a novel drug repurposing system that relies on logical rules as features to make interpretable inferences. Ranta outperforms existing methods by a large margin in predictive performance and can make reasonable repurposing suggestions with interpretable evidence

The archaeal ATPase PINA interacts with the helicase Hjm via its carboxyl terminal KH domain remodeling and processing replication fork and Holliday junction.

PINA is a novel ATPase and DNA helicase highly conserved in Archaea, the third domain of life. The PINA from Sulfolobus islandicus (SisPINA) forms a hexameric ring in crystal and solution. The protein is able to promote Holliday junction (HJ) migration and physically and functionally interacts with Hjc, the HJ specific endonuclease. Here, we show that SisPINA has direct physical interaction with Hjm (Hel308a), a helicase presumably targeting replication forks. In vitro biochemical analysis revealed that Hjm, Hjc, and SisPINA are able to coordinate HJ migration and cleavage in a concerted way. Deletion of the carboxyl 13 amino acid residues impaired the interaction between SisPINA and Hjm. Crystal structure analysis showed that the carboxyl 70 amino acid residues fold into a type II KH domain which, in other proteins, functions in binding RNA or ssDNA. The KH domain not only mediates the interactions of PINA with Hjm and Hjc but also regulates the hexameric assembly of PINA. Our results collectively suggest that SisPINA, Hjm and Hjc work together to function in replication fork regression, HJ formation and HJ cleavage

Merger-induced star formation in low-metallicity dwarf galaxy NGC 4809/4810

The physical mechanisms driving starbursts in dwarf galaxies are unclear, and the effects of mergers on star formation in these galaxies are still uncertain. We explore how the merger process affects star formation in metal-poor dwarf galaxies by analyzing high-spatial-resolution ($\sim$ 70 pc) integral field spectrograph observations of ionized gas. We use archival data from the Very Large Telescope/Multi Unit Spectroscopic Explorer to map the spatial distribution of strong emission lines (e.g., $\rm H\beta$, $\rm H\alpha$, $\rm [OIII]\lambda5007$, $\rm [NII]\lambda6583$, etc) in the nearby merging star-forming dwarf galaxy system NGC 4809/4810. We identify approximately 112 star-forming knots scattered among the two galaxies, where the gas-phase metallicity distribution is inhomogeneous and mixing with metal-poor and metal-rich ionized gas. Star-forming knots at the interacting region show lower metallicity, the highest star formation rates (SFRs) and SFR to resolved main-sequence-relation (rMSR) ratios. Ionized gas exhibits an obvious northeast-southwest velocity gradient in NGC 4809, while seemingly mixed in NGC 4810. High virial parameters and the stellar mass-size relation of HII regions indicate that these regions are dominated by direct radiation pressure from massive stars/clusters and persistently expanding. We find two different stellar mass surface density-stellar age relations in NGC 4809 and NGC 4810, and the stellar ages of NGC 4810 are systematically younger than in NGC 4809. Our study suggests that the merging stage of two dwarf galaxies can induce starburst activities at the interaction areas, despite the metal-deficient environment. Considering the high specific SFRs and different stellar ages, we propose that the interaction initially triggered star formation in NGC 4809 and then drove star formation in NGC 4810.Comment: 13 pages, 12 figures; accepted for publication in A&

Online dosimetric evaluation of larynx SBRT: A pilot study to assess the necessity of adaptive replanning

PURPOSE: We have initiated a multi-institutional phase I trial of 5-fraction stereotactic body radiotherapy (SBRT) for Stage III-IVa laryngeal cancer. We conducted this pilot dosimetric study to confirm potential utility of online adaptive replanning to preserve treatment quality. METHODS: We evaluated ten cases: five patients enrolled onto the current trial and five patients enrolled onto a separate phase I SBRT trial for early-stage glottic larynx cancer. Baseline SBRT treatment plans were generated per protocol. Daily cone-beam CT (CBCT) or diagnostic CT images were acquired prior to each treatment fraction. Simulation CT images and target volumes were deformably registered to daily volumetric images, the original SBRT plan was copied to the deformed images and contours, delivered dose distributions were re-calculated on the deformed CT images. All of these were performed on a commercial treatment planning system. In-house software was developed to propagate the delivered dose distribution back to reference CT images using the deformation information exported from the treatment planning system. Dosimetric differences were evaluated via dose-volume histograms. RESULTS: We could evaluate dose within 10 minutes in all cases. Prescribed coverage to gross tumor volume (GTV) and clinical target volume (CTV) was uniformly preserved; however, intended prescription dose coverage of planning treatment volume (PTV) was lost in 53% of daily treatments (mean: 93.9%, range: 83.9-97.9%). Maximum bystander point dose limits to arytenoids, parotids, and spinal cord remained respected in all cases, although variances in carotid artery doses were observed in a minority of cases. CONCLUSIONS: Although GTV and CTV SBRT dose coverage is preserved with in-room three-dimensional image guidance, PTV coverage can vary significantly from intended plans and dose to critical structures may exceed tolerances. Online adaptive treatment re-planning is potentially necessary and clinically applicable to fully preserve treatment quality. Confirmatory trial accrual and analysis remains ongoing

Development of an evidence-based mHealth weight management program using a formative research process

BACKGROUND: There is a critical need for weight management programs that are effective, cost efficient, accessible, and acceptable to adults from diverse ethnic and socioeconomic backgrounds. mHealth (delivered via mobile phone and Internet) weight management programs have potential to address this need. To maximize the success and cost-effectiveness of such an mHealth approach it is vital to develop program content based on effective behavior change techniques, proven weight management programs, and closely aligned with participants’ needs. OBJECTIVE: This study aims to develop an evidence-based mHealth weight management program (Horizon) using formative research and a structured content development process. METHODS: The Horizon mHealth weight management program involved the modification of the group-based UK Weight Action Program (WAP) for delivery via short message service (SMS) and the Internet. We used an iterative development process with mixed methods entailing two phases: (1) expert input on evidence of effective programs and behavior change theory; and (2) target population input via focus group (n=20 participants), one-on-one phone interviews (n=5), and a quantitative online survey (n=120). RESULTS: Expert review determined that core components of a successful program should include: (1) self-monitoring of behavior; (2) prompting intention formation; (3) promoting specific goal setting; (4) providing feedback on performance; and (5) promoting review of behavioral goals. Subsequent target group input confirmed that participants liked the concept of an mHealth weight management program and expressed preferences for the program to be personalized, with immediate (prompt) and informative text messages, practical and localized physical activity and dietary information, culturally appropriate language and messages, offer social support (group activities or blogs) and weight tracking functions. Most target users expressed a preference for at least one text message per day. We present the prototype mHealth weight management program (Horizon) that aligns with those inputs. CONCLUSIONS: The Horizon prototype described in this paper could be used as a basis for other mHealth weight management programs. The next priority will be to further develop the program and conduct a full randomized controlled trial of effectiveness

Neural Interactive Collaborative Filtering

In this paper, we study collaborative filtering in an interactive setting, in which the recommender agents iterate between making recommendations and updating the user profile based on the interactive feedback. The most challenging problem in this scenario is how to suggest items when the user profile has not been well established, i.e., recommend for cold-start users or warm-start users with taste drifting. Existing approaches either rely on overly pessimistic linear exploration strategy or adopt meta-learning based algorithms in a full exploitation way. In this work, to quickly catch up with the user's interests, we propose to represent the exploration policy with a neural network and directly learn it from the feedback data. Specifically, the exploration policy is encoded in the weights of multi-channel stacked self-attention neural networks and trained with efficient Q-learning by maximizing users' overall satisfaction in the recommender systems. The key insight is that the satisfied recommendations triggered by the exploration recommendation can be viewed as the exploration bonus (delayed reward) for its contribution on improving the quality of the user profile. Therefore, the proposed exploration policy, to balance between learning the user profile and making accurate recommendations, can be directly optimized by maximizing users' long-term satisfaction with reinforcement learning. Extensive experiments and analysis conducted on three benchmark collaborative filtering datasets have demonstrated the advantage of our method over state-of-the-art methods

Rapid detection of multiple resistance genes to last-resort antibiotics in Enterobacteriaceae pathogens by recombinase polymerase amplification combined with lateral flow dipstick

The worrying emergence of multiple resistance genes to last-resort antibiotics in food animals and human populations throughout the food chain and relevant environments has been increasingly reported worldwide. Enterobacteriaceae pathogens are considered the most common reservoirs of such antibiotic resistance genes (ARGs). Thus, a rapid, efficient and accurate detection method to simultaneously screen and monitor such ARGs in Enterobacteriaceae pathogens has become an urgent need. Our study developed a recombinase polymerase amplification (RPA) assay combined with a lateral flow dipstick (LFD) for simultaneously detecting predominant resistance genes to last-resort antibiotics of Enterobacteriaceae pathogens, including mcr-1, blaNDM-1 and tet(X4). It is allowed to complete the entire process, including crude DNA extraction, amplification as well as reading, within 40 min at 37°C, and the detection limit is 101 copies/μl for mcr-1, blaNDM-1 and tet(X4). Sensitivity analysis showed obvious association of color signals with the template concentrations of mcr-1, blaNDM-1 and tet(X4) genes in Enterobacteriaceae pathogens using a test strip reader (R2 = 0.9881, R2 = 0.9745, and R2 = 0.9807, respectively), allowing for quantitative detection using multiplex RPA-LFD assays. Therefore, the RPA-LFD assay can suitably help to detect multiple resistance genes to last-resort antibiotics in foodborne pathogens and has potential applications in the field