Code and Data for 'Fabrication and testing of lensed fiber optic probes for distance sensing using common path low coherence interferometry' by Radu Stancu (21165068)

“…Distance Sensing</p><p dir="ltr">Code and data to demonstrate extracting distance sensing data from A-scans and to generate Fig. 8 using the algorithm described in Fig. 7. Functions to generate distance measurements are in 'distance_sensing_utilities.py' and an example of how to use this on data in the 'data' folder is in 'distance_sensing_example.py', which generates Fig 8. …”

<b>A Single-cell Transcriptomic Sequencing Dataset of Early Female and Male Chicken (</b><b><i>Gallus gallus</i></b><b>) Embryos</b> by Zhi Cao (20682218)

“…To correct for potential batch effects, the Harmony algorithm was applied. For clustering, the FindClusters function was used with a resolution of 0.4, followed by dimensionality reduction and visualization using uniform manifold approximation and projection (UMAP) and t-distributed stochastic neighbor embedding. …”

Brain-in-the-Loop Learning for Intelligent Vehicle Decision-Making by Xiaofei Zhang (16483224)

“…In this paper, we utilize functional near-infrared spectroscopy (fNIRS) signals as real-time human risk-perception feedback to establish a brain-in-the-loop (BiTL) trained artificial intelligence algorithm for decision-making. …”

Integration of mitochondrial gene expression and immune landscape in acute kidney injury prediction by Xiaoping Xia (449582)

“…Immune infiltration was assessed using the xCell algorithm to explore the relationship between MRS and immune cell dynamics in AKI. …”

Table 1_Analysis and validation of biomarkers and immune cell infiltration profiles in unstable coronary atherosclerotic plaques using bioinformatics and machine learning.xlsx by Pengyue Jin (11657894)

“…Sequentially, we performed principal component analysis (PCA), differential gene expression analysis, enrichment analysis, weighted gene co-expression network analysis (WGCNA), utilized a machine learning algorithm to screen key genes, conducted receiver operating characteristic (ROC) curve analysis and nomogram model to assess biomarker diagnostic efficacy, validated the biomarkers, and analyzed immune cell infiltration.…”

Comparison of Five Classification Models by Qiran Wang (22051883)

“…The K-Nearest Neighbors (KNN) algorithm assigns class labels based on the majority vote of the nearest neighbors in the feature space, making it simple yet effective for small-scale datasets. …”

Optimal Network Membership Estimation under Severe Degree Heterogeneity by Zheng Tracy Ke (8293395)

“…To obtain a rate-optimal method, we modify an existing spectral algorithm, Mixed-SCORE, by adding a pre-PCA normalization step. …”

Mechanomics Code - JVT by Carlo Vittorio Cannistraci (5854046)

“…The functions were tested respectively in: MATLAB 2018a or youger, Python 3.9.4, R 4.0.3.…”

Table 1_Kefir and healthy aging: revealing thematic gaps through AI-assisted screening and semantic evidence mapping.docx by Francesco Chiani (2661328)

“…To overcome this fragmentation, we applied an integrative approach that combines a cutting-edge AI-assisted algorithm for evidence screening with a Python-based semantic clustering pipeline. …”

Table 2_Kefir and healthy aging: revealing thematic gaps through AI-assisted screening and semantic evidence mapping.docx by Francesco Chiani (2661328)

“…To overcome this fragmentation, we applied an integrative approach that combines a cutting-edge AI-assisted algorithm for evidence screening with a Python-based semantic clustering pipeline. …”

Table 3_Kefir and healthy aging: revealing thematic gaps through AI-assisted screening and semantic evidence mapping.xlsx by Francesco Chiani (2661328)

“…To overcome this fragmentation, we applied an integrative approach that combines a cutting-edge AI-assisted algorithm for evidence screening with a Python-based semantic clustering pipeline. …”

Table 4_Kefir and healthy aging: revealing thematic gaps through AI-assisted screening and semantic evidence mapping.docx by Francesco Chiani (2661328)

“…To overcome this fragmentation, we applied an integrative approach that combines a cutting-edge AI-assisted algorithm for evidence screening with a Python-based semantic clustering pipeline. …”

Seamless integration of legacy robotic systems into a self-driving laboratory via NIMO: a case study on liquid handler automation by Ryo Tamura (1957942)

“…We developed NIMO (formerly NIMS-OS, NIMS Orchestration System), an OS explicitly designed to integrate multiple artificial intelligence (AI) algorithms with diverse exploratory objectives. NIMO provides a framework for integrating AI into robotic experimental systems that are controlled by other OS platforms based on both Python and non-Python languages. …”

Predictive Analysis of Mushroom Toxicity Based Exclusively on Their Natural Habitat. by Enrico Bertozzi (22461709)

“…The analysis was conducted in a Jupyter Notebook environment, using Python and libraries such as Scikit-learn and Pandas. …”

Table 1_Prognostic and immunological implications of cathepsin Z overexpression in prostate cancer.docx by Junyue Tao (13817719)

“…Immunohistochemical staining and multiplex immunofluorescence staining were performed to evaluate the expression and spatial distribution of CTSZ and immune-related markers in PCa tissues. Functional studies were conducted through a series of experiments, including CCK-8 assay, colony formation, wound healing, and Transwell migration assays. ssGSEA and CIBERSORT algorithms immune infiltration evaluation, and GISTIC2.0 and MutSigCV for tumor mutation burden. …”

Table1_Enhanced classification and severity prediction of major depressive disorder using acoustic features and machine learning.pdf by Lijuan Liang (4277053)

“…We used the Covarep open-source algorithm to extract a total of 1200 high-level statistical functions for each sample. …”

Table 1_Exploring the impact of deubiquitination on melanoma prognosis through single-cell RNA sequencing.docx by Su Peng (5648456)

“…Cell types were annotated based on known marker genes, and the AUCell algorithm assessed the enrichment of deubiquitination-related genes. …”

Data Sheet 1_Exploring the impact of deubiquitination on melanoma prognosis through single-cell RNA sequencing.zip by Su Peng (5648456)

“…Cell types were annotated based on known marker genes, and the AUCell algorithm assessed the enrichment of deubiquitination-related genes. …”

GameOfLife Prediction Dataset by David Towers (12857447)

“…Excluding 0, the lower numbers also get increasingly unlikely, though more likely than higher numbers, we wanted to prevent gaps and therefore limited to 25 contiguous classes</p><p dir="ltr">NumPy (.npy) files can be opened through the NumPy Python library, using the `numpy.load()` function by inputting the path to the file into the function as a parameter. …”

Code and data for evaluating oil spill amount from text-form incident information by Yiming Liu (18823387)

“…These are separately stored in the folders “description” and “posts”.</p><h2>Algorithms for Evaluating Release Amount (RA)</h2><p dir="ltr">The algorithms are split into the following three notebooks based on their functions:</p><ol><li><b>"1_RA_extraction.ipynb"</b>:</li><li><ul><li>Identifies oil spill-related incidents from raw incident data.…”