Uncertainty-Aware Adaptation of Large Language Models for Protein-Protein Interaction Analysis
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97 MATHEMATICS AND COMPUTING↗
Engineering topics
Park, Gilchan
Publications and source records attributed to Park, Gilchan.
Quantum error mitigations for quantum approximate optimization algorithms on IBM quantum processors
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97 MATHEMATICS AND COMPUTING↗
Pathway-based analyses of gene expression profiles at low doses of ionizing radiation
Radiation exposure poses a significant threat to human health. Emerging research indicates that even low-dose radiation once believed to be safe, may have harmful effects. This perception has spurred a growing interest in investigating the potential risks associated with low-dose radiation exposure across various scenarios. To comprehensively explore the health consequences of low-dose radiation, our study employs a robust statistical framework that examines whether specific groups of genes, belonging to known pathways, exhibit coordinated expression patterns that align with the radiation levels. Notably, our findings reveal the existence of intricate yet consistent signatures that reflect the molecular response to radiation exposure, distinguishing between low-dose and high-dose radiation. Moreover, we leverage a pathway-constrained variational autoencoder to capture the nonlinear interactions within gene expression data. By comparing these two analytical approaches, our study aims to gain valuable insights into the impact of low-dose radiation on gene expression patterns, identify pathways that are differentially affected, and harness the potential of machine learning to uncover hidden activity within biological networks. This comparative analysis contributes to a deeper understanding of the molecular consequences of low-dose radiation exposure.
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
Density estimation via measure transport: Outlook for applications in the biological sciences
Abstract One among several advantages of measure transport methods is that they allow or a unified framework for processing and analysis of data distributed according to a wide class of probability measures. Within this context, we present results from computational studies aimed at assessing the potential of measure transport techniques, specifically, the use of triangular transport maps, as part of a workflow intended to support research in the biological sciences. Scenarios characterized by the availability of limited amount of sample data, which are common in domains such as radiation biology, are of particular interest. We find that when estimating a distribution density function given limited amount of sample data, adaptive transport maps are advantageous. In particular, statistics gathered from computing series of adaptive transport maps, trained on a series of randomly chosen subsets of the set of available data samples, leads to uncovering information hidden in the data. As a result, in the radiation biology application considered here, this approach provides a tool for generating hypotheses about gene relationships and their dynamics under radiation exposure.
gene expression data↗
Parallel hybrid quantum-classical machine learning for kernelized time-series classification
Supervised time-series classification garners widespread interest because of its applicability throughout a broad application domain including finance, astronomy, biosensors, and many others. Here, in this work, we tackle this problem with hybrid quantum-classical machine learning, deducing pairwise temporal relationships between time-series instances using a timeseries Hamiltonian kernel (TSHK). A TSHK is constructed with a sum of inner products generated by quantum states evolved using a parameterized time evolution operator. This sum is then optimally weighted using techniques derived from multiple kernel learning. Because we treat the kernel weighting step as a differentiable convex optimization problem, our method can be regarded as an end-to-end learnable hybrid quantum-classical-convex neural network, or QCC-net, whose output is a data set-generalized kernel function suitable for use in any kernelized machine learning technique such as the support vector machine (SVM). Using our TSHK as input to a SVM, we classify univariate and multivariate time-series using quantum circuit simulators and demonstrate the efficient parallel deployment of the algorithm to 127-qubit superconducting quantum processors using quantum multi-programming.
97 MATHEMATICS AND COMPUTING↗
Quantum multi-programming for Grover’s search
Quantum multi-programming is a method utilizing contemporary noisy intermediate-scale quantum computers by executing multiple quantum circuits concurrently. Despite early research on it, the research remains on quantum gates or small-size quantum algorithms without correlation. In this paper, we propose a quantum multi-programming (QMP algorithm for Grover's search. Our algorithm decomposes Grover's algorithm by the partial diffusion operator and executes the decomposed circuits in parallel by QMP. We proved that this new algorithm increases the rotation angle of the Grover operator which, as a result, increases the success probability. The new algorithm is implemented on IBM quantum computers and compared with the canonical Grover's algorithm and other variations of Grover's algorithms. So, the empirical tests validate that our new algorithm outperforms other variations of Grover's algorithms as well as the canonical Grover's algorithm.
97 MATHEMATICS AND COMPUTING↗
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.
60 APPLIED LIFE SCIENCES↗
Figure Descriptive Text Extraction Using Ontological Representation
Abstract Experimental research publications provide figure form resources including graphs, charts, and any type of images to effectively support and convey methods and results. To describe figures, authors add captions, which are often incomplete, and more descriptions reside in body text. This work presents a method to extract figure descriptive text from the body of scientific articles. We adopted ontological semantics to aid concept recognition of figure-related information, which generates human- and machine-readable knowledge representations from sentences. Our results show that conceptual models bring an improvement in figure descriptive sentence classification over word-based approaches.
97 MATHEMATICS AND COMPUTING↗
Provenance infrastructure for multimodal x-ray experiments and reproducible analysis
Exploring relationships between material structures and desired properties for material discovery and synthesis requires mining machine-readable databases and linking experimental data with sufficiently rich annotations. There are vast gaps both in these data sources and in the connections between them. We present a provenance-based data management and analysis framework that enables capturing, persisting, and reanalyzing experimental data from the BNL National Synchrotron Light Source II (NSLS-II). Our system leverages NSLS-II Bluesky for experimental data acquisition, captures analysis parameters, and enriches the search space with results from the scientific literature. We describe in detail the challenges and benefits of data-driven approaches when comparing computational and experimental data, such as the multiple possible scenarios of interest in often ill-posed inverse problems and missing data. Our infrastructure utilizes the NSLS-II event model and includes discovery mechanisms across multiple beamlines. A text and data mining module using natural language processing classification techniques extracts relevant information from the literature that is added to data sources. We describe a provenance acquisition and analysis rerun workflow based on a directed acyclic graph that keeps track of process and data provenance and allows to replay analysis.
97 MATHEMATICS AND COMPUTING↗
Scientific Literature Mining for Experiment Information in Materials Design
Scientific literature is a plethora of documents written in natural language, where the agglomeration of well-cogitated knowledge is inextricably intertwined. The large-scale knowledge source might have the great potential to derive valuable information when text mined and untangled. Typically, scientists obtain preliminary knowledge from research papers prior to beginning a new experiment. Researchers manually harvest experimental information, which is labor-intensive and error prone. To reduce manual effort and human errors, this project aims to build a system for data collection from literature that supplements other data sources so users can look up needed information while preparing experiments or analyzing results.
97 MATHEMATICS AND COMPUTING↗