LIVIVO - Search results -

Search results

Result 1 - 10 of total 47

Book ; Online: More for Less

Gao, Andrew Kean

Compact Convolutional Transformers Enable Robust Medical Image Classification with Limited Data

2023

Abstract: Transformers are very powerful tools for a variety of tasks across domains, from text generation to image captioning. However, transformers require substantial amounts of training data, which is often a challenge in biomedical settings, where high ... ...

Abstract	Transformers are very powerful tools for a variety of tasks across domains, from text generation to image captioning. However, transformers require substantial amounts of training data, which is often a challenge in biomedical settings, where high quality labeled data can be challenging or expensive to obtain. This study investigates the efficacy of Compact Convolutional Transformers (CCT) for robust medical image classification with limited data, addressing a key issue faced by conventional Vision Transformers - their requirement for large datasets. A hybrid of transformers and convolutional layers, CCTs demonstrate high accuracy on modestly sized datasets. We employed a benchmark dataset of peripheral blood cell images of eight distinct cell types, each represented by approximately 2,000 low-resolution (28x28x3 pixel) samples. Despite the dataset size being smaller than those typically used with Vision Transformers, we achieved a commendable classification accuracy of 92.49% and a micro-average ROC AUC of 0.9935. The CCT also learned quickly, exceeding 80% validation accuracy after five epochs. Analysis of per-class precision, recall, F1, and ROC showed that performance was strong across cell types. Our findings underscore the robustness of CCTs, indicating their potential as a solution to data scarcity issues prevalent in biomedical imaging. We substantiate the applicability of CCTs in data-constrained areas and encourage further work on CCTs. Comment: 9 pages, 4 figures, 2 tables
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; I.4.9 ; I.2.10
Subject code	006
Publishing date	2023-06-30
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Book ; Online: NLP Meets RNA

Gao, Andrew Kean

Unsupervised Embedding Learning for Ribozymes with Word2Vec

2023

Abstract: Ribozymes, RNA molecules with distinct 3D structures and catalytic activity, have widespread applications in synthetic biology and therapeutics. However, relatively little research has focused on leveraging deep learning to enhance our understanding of ... ...

Abstract	Ribozymes, RNA molecules with distinct 3D structures and catalytic activity, have widespread applications in synthetic biology and therapeutics. However, relatively little research has focused on leveraging deep learning to enhance our understanding of ribozymes. This study implements Word2Vec, an unsupervised learning technique for natural language processing, to learn ribozyme embeddings. Ribo2Vec was trained on over 9,000 diverse ribozymes, learning to map sequences to 128 and 256-dimensional vector spaces. Using Ribo2Vec, sequence embeddings for five classes of ribozymes (hatchet, pistol, hairpin, hovlinc, and twister sister) were calculated. Principal component analysis demonstrated the ability of these embeddings to distinguish between ribozyme classes. Furthermore, a simple SVM classifier trained on ribozyme embeddings showed promising results in accurately classifying ribozyme types. Our results suggest that the embedding vectors contained meaningful information about ribozymes. Interestingly, 256-dimensional embeddings behaved similarly to 128-dimensional embeddings, suggesting that a lower dimension vector space is generally sufficient to capture ribozyme features. This approach demonstrates the potential of Word2Vec for bioinformatics, opening new avenues for ribozyme research. Future research includes using a Transformer-based method to learn RNA embeddings, which can capture long-range interactions between nucleotides.
Keywords	Computer Science - Machine Learning ; Quantitative Biology - Biomolecules ; I.2.7
Subject code	610
Publishing date	2023-07-08
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Book ; Online: Vec2Vec

Gao, Andrew Kean

A Compact Neural Network Approach for Transforming Text Embeddings with High Fidelity

2023

Abstract: Vector embeddings have become ubiquitous tools for many language-related tasks. A leading embedding model is OpenAI's text-ada-002 which can embed approximately 6,000 words into a 1,536-dimensional vector. While powerful, text-ada-002 is not open source ... ...

Abstract	Vector embeddings have become ubiquitous tools for many language-related tasks. A leading embedding model is OpenAI's text-ada-002 which can embed approximately 6,000 words into a 1,536-dimensional vector. While powerful, text-ada-002 is not open source and is only available via API. We trained a simple neural network to convert open-source 768-dimensional MPNet embeddings into text-ada-002 embeddings. We compiled a subset of 50,000 online food reviews. We calculated MPNet and text-ada-002 embeddings for each review and trained a simple neural network to for 75 epochs. The neural network was designed to predict the corresponding text-ada-002 embedding for a given MPNET embedding. Our model achieved an average cosine similarity of 0.932 on 10,000 unseen reviews in our held-out test dataset. We manually assessed the quality of our predicted embeddings for vector search over text-ada-002-embedded reviews. While not as good as real text-ada-002 embeddings, predicted embeddings were able to retrieve highly relevant reviews. Our final model, Vec2Vec, is lightweight (<80 MB) and fast. Future steps include training a neural network with a more sophisticated architecture and a larger dataset of paired embeddings to achieve greater performance. The ability to convert between and align embedding spaces may be helpful for interoperability, limiting dependence on proprietary models, protecting data privacy, reducing costs, and offline operations. Comment: 14 pages, 6 figures, 5 tables
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence ; Computer Science - Information Retrieval ; Computer Science - Machine Learning ; I.2.7 ; D.2.12
Subject code	410
Publishing date	2023-06-22
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Book ; Online: On the Origin of LLMs

Gao, Sarah / Gao, Andrew Kean

An Evolutionary Tree and Graph for 15,821 Large Language Models

2023

Abstract: Since late 2022, Large Language Models (LLMs) have become very prominent with LLMs like ChatGPT and Bard receiving millions of users. Hundreds of new LLMs are announced each week, many of which are deposited to Hugging Face, a repository of machine ... ...

Abstract	Since late 2022, Large Language Models (LLMs) have become very prominent with LLMs like ChatGPT and Bard receiving millions of users. Hundreds of new LLMs are announced each week, many of which are deposited to Hugging Face, a repository of machine learning models and datasets. To date, nearly 16,000 Text Generation models have been uploaded to the site. Given the huge influx of LLMs, it is of interest to know which LLM backbones, settings, training methods, and families are popular or trending. However, there is no comprehensive index of LLMs available. We take advantage of the relatively systematic nomenclature of Hugging Face LLMs to perform hierarchical clustering and identify communities amongst LLMs using n-grams and term frequency-inverse document frequency. Our methods successfully identify families of LLMs and accurately cluster LLMs into meaningful subgroups. We present a public web application to navigate and explore Constellation, our atlas of 15,821 LLMs. Constellation rapidly generates a variety of visualizations, namely dendrograms, graphs, word clouds, and scatter plots. Constellation is available at the following link: https://constellation.sites.stanford.edu/. Comment: 14 pages, 6 figures, 1 table
Keywords	Computer Science - Digital Libraries ; Computer Science - Computation and Language ; I.2.1 ; H.5.0
Publishing date	2023-07-19
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Machine-learning-based virtual screening to repurpose drugs for treatment of Candida albicans infection.

Gao, Andrew / Kouznetsova, Valentina L / Tsigelny, Igor F

Mycoses

2022 Volume 65, Issue 8, Page(s) 794–805

Abstract: Background: Approximately 30% of Candida genus isolates are resistant to all currently available antifungal drugs and it is highly important to develop new treatments. Additionally, many current drugs are toxic and cause unwanted side effects. 1,3-beta- ... ...

Abstract	Background: Approximately 30% of Candida genus isolates are resistant to all currently available antifungal drugs and it is highly important to develop new treatments. Additionally, many current drugs are toxic and cause unwanted side effects. 1,3-beta-glucan synthase is an essential enzyme that builds the cell walls of Candida. Objectives: Targeting CaFKS1, a subunit of the synthase, could be used to fight Candida. Methods: In the present study, a machine-learning model based on chemical descriptors was trained to recognise drugs that inhibit CaFKS1. The model attained 96.72% accuracy for classifying between active and inactive drug compounds. Descriptors for FDA-approved and other drugs were calculated, and the model was used to predict the potential activity of these drugs against CaFKS1. Results: Several drugs, including goserelin and icatibant, were detected as active with high confidence. Many of the drugs, interestingly, were gonadotrophin-releasing hormone (GnRH) antagonists or agonists. A literature search found that five of the predicted drugs inhibit Candida experimentally. Conclusions: This study yields promising drugs to be repurposed to combat Candida albicans infection. Future steps include testing the drugs on fungal cells in vitro.
MeSH term(s)	Antifungal Agents/pharmacology ; Antifungal Agents/therapeutic use ; Candida ; Candida albicans ; Candidiasis/drug therapy ; Candidiasis/microbiology ; Humans ; Machine Learning ; Microbial Sensitivity Tests
Chemical Substances	Antifungal Agents
Language	English
Publishing date	2022-06-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	392487-7
ISSN	1439-0507 ; 0933-7407
ISSN (online)	1439-0507
ISSN	0933-7407
DOI	10.1111/myc.13475
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Ud II Zs.176: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾

Article ; Online: Computation by Convective Logic Gates and Thermal Communication.

Bartlett, Stuart / Gao, Andrew K / Yung, Yuk L

Artificial life

2022 Volume 28, Issue 1, Page(s) 96–107

Abstract: We demonstrate a novel computational architecture based on fluid convection logic gates and heat flux-mediated information flows. Our previous work demonstrated that Boolean logic operations can be performed by thermally driven convection flows. In this ... ...

Abstract	We demonstrate a novel computational architecture based on fluid convection logic gates and heat flux-mediated information flows. Our previous work demonstrated that Boolean logic operations can be performed by thermally driven convection flows. In this work, we use numerical simulations to demonstrate a different , but universal Boolean logic operation (NOR), performed by simpler convective gates. The gates in the present work do not rely on obstacle flows or periodic boundary conditions, a significant improvement in terms of experimental realizability. Conductive heat transfer links can be used to connect the convective gates, and we demonstrate this with the example of binary half addition. These simulated circuits could be constructed in an experimental setting with modern, 2-dimensional fluidics equipment, such as a thin layer of fluid between acrylic plates. The presented approach thus introduces a new realm of unconventional, thermal fluid-based computation.
MeSH term(s)	Communication ; Logic
Language	English
Publishing date	2022-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2024100-8
ISSN	1530-9185 ; 1064-5462
ISSN (online)	1530-9185
ISSN	1064-5462
DOI	10.1162/artl_a_00358
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Methylation Profiling Identifies Stability of Isocitrate Dehydrogenase Mutation Over Time.

Voisin, Mathew R / Gui, Chloe / Patil, Vikas / Gao, Andrew F / Zadeh, Gelareh

The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques

2023 , Page(s) 1–7

Abstract: Objective: Isocitrate dehydrogenase (IDH) mutation status is a key diagnostic and prognostic feature of gliomas. It is thought to occur early in glioma tumorigenesis and remain stable over time. However, there are reports documenting a loss of IDH ... ...

Abstract	Objective: Isocitrate dehydrogenase (IDH) mutation status is a key diagnostic and prognostic feature of gliomas. It is thought to occur early in glioma tumorigenesis and remain stable over time. However, there are reports documenting a loss of IDH mutation status in a subset of patients with glioma recurrence. Here, we identified patients with a documented loss of IDH mutation status longitudinally and performed multi-platform analysis in order to determine if IDH mutations are stable throughout glioma evolution. Methods: We retrospectively identified patients from our institution from 2009 to 2018 with immunohistochemistry (IHC)-recorded IDH mutation status changes longitudinally. Archived formalin-fixed paraffin-embedded and frozen tissue samples from these patients were collected from our institution's tumour bank. Samples were analysed using methylation profiling, copy number variation, Sanger sequencing, droplet digital PCR (ddPCR) and IHC. Results: We reviewed 1491 archived glioma samples including 78 patients with multiple IDH mutant tumour samples collected longitudinally. In all instances of documented loss of IDH mutation status, multi-platform profiling identified a mixture of low tumour cell content and non-neoplastic tissue including perilesional, reactive or inflammatory cells. Conclusions: All patients with a documented loss of IDH mutation status longitudinally were resolved through multi-platform analysis. These findings support the hypothesis that IDH mutations occur early in gliomagenesis and in the absence of copy number changes at the IDH loci and are stable throughout tumour treatment and evolution. Our study highlights the importance of accurate surgical sampling and the role of DNA methylome profiling in diagnostically uncertain cases for integrated pathological and molecular diagnosis.
Language	English
Publishing date	2023-07-12
Publishing country	England
Document type	Journal Article
ZDB-ID	197622-9
ISSN	0317-1671
ISSN	0317-1671
DOI	10.1017/cjn.2023.253
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1203: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Bovine leukemia virus relation to human breast cancer: Meta-analysis.

Gao, Andrew / Kouznetsova, Valentina L / Tsigelny, Igor F

Microbial pathogenesis

2020 Volume 149, Page(s) 104417

Abstract: Bovine leukemia virus (BLV) is a virus that infects cattle around the world and is very similar to the human T-cell leukemia virus (HTLV), which causes adult T-cell leukemia/lymphoma (ATL). Recently, presence of BLV DNA and protein was demonstrated in ... ...

Abstract	Bovine leukemia virus (BLV) is a virus that infects cattle around the world and is very similar to the human T-cell leukemia virus (HTLV), which causes adult T-cell leukemia/lymphoma (ATL). Recently, presence of BLV DNA and protein was demonstrated in commercial bovine products and in humans. BLV DNA is generally found at higher rates in humans who have or will develop breast cancer, according to research done with subjects from several countries. These findings have led to a hypothesis that BLV transmission plays a role in breast cancer oncogenesis in humans. Here we summarize the current knowledge in the field.
MeSH term(s)	Adult ; Animals ; Breast Neoplasms ; Cattle ; Female ; Humans ; Leukemia Virus, Bovine/genetics
Keywords	covid19
Language	English
Publishing date	2020-07-27
Publishing country	England
Document type	Journal Article ; Meta-Analysis
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2020.104417
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2136: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: A case of disseminated microscopic demyelination with multifocal dystrophic calcification.

Abdollahi, Maryam / Gao, Andrew F / Munoz, David G

Neuropathology : official journal of the Japanese Society of Neuropathology

2020 Volume 40, Issue 3, Page(s) 308–314

Abstract: We present a 47-year-old woman with a 10-year disease course consisting of episodic confusion, aphasia, psychosis, depression, migrainous headaches and seizures. There was mild elevation of protein levels in the cerebrospinal fluid, progressive cerebral ... ...

Abstract	We present a 47-year-old woman with a 10-year disease course consisting of episodic confusion, aphasia, psychosis, depression, migrainous headaches and seizures. There was mild elevation of protein levels in the cerebrospinal fluid, progressive cerebral atrophy, and numerous small T1 hypointensities appearing as central "holes" in the corpus callosum on magnetic resonance imaging. She eventually expired due to status epilepticus and subsequent significant respiratory complications. In the central nervous system, there was generalized brain atrophy, and patchy labeling of blood vessels by antibodies to complement component 4d (C4d) and membrane attack complex. Innumerable small patches with loss of cell bodies (neurons and glial cells in gray matter and glial cells in white matter) and demyelination were scattered throughout the brain and spinal cord. There was no cavitation and the passing axons were mostly preserved. Large solid calcified foci were present predominantly in the pons along with disseminated focal calcification involving neuron cell bodies, neurites, and capillaries. Patchy labeling of glial cells and linear structures suggestive of myelin sheaths with C4d antibodies was observed while immunostains for SV40, tau, β-amyloid, alpha synuclein, p62, and trans-activation response DNA-binding protein 43 kDa were negative. Whole-exome sequencing did not reveal any clinically significant variants. Although the radiological findings are suggestive of Susac's syndrome (a rare condition characterized by encephalopathy, hearing loss, and branch retinal artery occlusion), in the absence of audiovisual manifestations, a definitive diagnosis cannot be rendered and therefore, this case may be representing a new entity. Further reports of similar cases are needed for clarification.
MeSH term(s)	Brain/pathology ; Calcinosis/pathology ; Demyelinating Diseases/pathology ; Fatal Outcome ; Female ; Humans ; Middle Aged ; Neurodegenerative Diseases/pathology
Language	English
Publishing date	2020-03-03
Publishing country	Australia
Document type	Case Reports
ZDB-ID	1483794-8
ISSN	1440-1789 ; 0919-6544
ISSN (online)	1440-1789
ISSN	0919-6544
DOI	10.1111/neup.12642
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 5086: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article: Malignant Mimics of Trigeminal Schwannoma.

Raswoli, Musthafa / Tsang, Derek S / Zadeh, Gelareh / Gao, Andrew F / Shultz, David B

Advances in radiation oncology

2022 Volume 8, Issue 1, Page(s) 101056

Language	English
Publishing date	2022-08-27
Publishing country	United States
Document type	Case Reports
ISSN	2452-1094
ISSN	2452-1094
DOI	10.1016/j.adro.2022.101056
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED