9 research outputs found
An Ontology-Based Artificial Intelligence Model for Medicine Side-Effect Prediction: Taking Traditional Chinese Medicine as An Example
In this work, an ontology-based model for AI-assisted medicine side-effect
(SE) prediction is developed, where three main components, including the drug
model, the treatment model, and the AI-assisted prediction model, of proposed
model are presented. To validate the proposed model, an ANN structure is
established and trained by two hundred and forty-two TCM prescriptions. These
data are gathered and classified from the most famous ancient TCM book and more
than one thousand SE reports, in which two ontology-based attributions, hot and
cold, are introduced to evaluate whether the prescription will cause SE or not.
The results preliminarily reveal that it is a relationship between the
ontology-based attributions and the corresponding predicted indicator that can
be learnt by AI for predicting the SE, which suggests the proposed model has a
potential in AI-assisted SE prediction. However, it should be noted that, the
proposed model highly depends on the sufficient clinic data, and hereby, much
deeper exploration is important for enhancing the accuracy of the prediction
White-box Compiler Fuzzing Empowered by Large Language Models
Compiler correctness is crucial, as miscompilation falsifying the program
behaviors can lead to serious consequences. In the literature, fuzzing has been
extensively studied to uncover compiler defects. However, compiler fuzzing
remains challenging: Existing arts focus on black- and grey-box fuzzing, which
generates tests without sufficient understanding of internal compiler
behaviors. As such, they often fail to construct programs to exercise
conditions of intricate optimizations. Meanwhile, traditional white-box
techniques are computationally inapplicable to the giant codebase of compilers.
Recent advances demonstrate that Large Language Models (LLMs) excel in code
generation/understanding tasks and have achieved state-of-the-art performance
in black-box fuzzing. Nonetheless, prompting LLMs with compiler source-code
information remains a missing piece of research in compiler testing.
To this end, we propose WhiteFox, the first white-box compiler fuzzer using
LLMs with source-code information to test compiler optimization. WhiteFox
adopts a dual-model framework: (i) an analysis LLM examines the low-level
optimization source code and produces requirements on the high-level test
programs that can trigger the optimization; (ii) a generation LLM produces test
programs based on the summarized requirements. Additionally,
optimization-triggering tests are used as feedback to further enhance the test
generation on the fly. Our evaluation on four popular compilers shows that
WhiteFox can generate high-quality tests to exercise deep optimizations
requiring intricate conditions, practicing up to 80 more optimizations than
state-of-the-art fuzzers. To date, WhiteFox has found in total 96 bugs, with 80
confirmed as previously unknown and 51 already fixed. Beyond compiler testing,
WhiteFox can also be adapted for white-box fuzzing of other complex, real-world
software systems in general
Corrigendum: Phenotype-based drug screening: An in vivo strategy to classify and identify the chemical compounds modulating zebrafish M-cell regeneration
An Ontology-Based Artificial Intelligence Model for Medicine Side-Effect Prediction: Taking Traditional Chinese Medicine as an Example
Meta-Aerogels: Auxetic Shape-Memory Polyurethane Aerogels
Shape-memory poly(isocyanurate-urethane) (PIR-PUR) aerogels are low-density monolithic nanoporous solids that remember and return to their permanent shape through a heating actuation step. Herein, through structural design at the macro scale, the shape-memory response is augmented with an auxetic effect manifested by a negative Poisson\u27s ratio of approximately -0.8 at 15% compressive strain. Thus, auxetic shape-memory PIR-PUR monoliths experience volume contraction upon compression at a temperature above the glass transition temperature of the base polymer (Tg ≈ 30 °C), and they can be stowed indefinitely in that temporary shape by cooling below Tg. By heating back above Tg, the compressed/shrunk form expands back to their original shape/size. This technology is relevant to a broad range of industries spanning the commercial, aeronautical, and aerospace sectors. The materials are referred to as meta-aerogels, and their potential applications include minimally invasive medical devices, soft robotics, and situations where volume is at a premium, as for example for storage of deployable space structures and planetary habitats during transport to the point of service
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Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of 110 tumors and 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, and acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, and gender. Proteomic and phosphoproteomic data illuminated biology downstream of copy number aberrations, somatic mutations, and fusions and identified therapeutic vulnerabilities associated with driver events involving KRAS, EGFR, and ALK. Immune subtyping revealed a complex landscape, reinforced the association of STK11 with immune-cold behavior, and underscored a potential immunosuppressive role of neutrophil degranulation. Smoking-associated LUADs showed correlation with other environmental exposure signatures and a field effect in NATs. Matched NATs allowed identification of differentially expressed proteins with potential diagnostic and therapeutic utility. This proteogenomics dataset represents a unique public resource for researchers and clinicians seeking to better understand and treat lung adenocarcinomas
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Proteogenomic and metabolomic characterization of human glioblastoma
Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment