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9 results on '"Ji, Yanmin"'

1. Calibrate to Discriminate: Improve In-Context Learning with Label-Free Comparative Inference

Author

Cheng, Wei, Wang, Tianlu, Ji, Yanmin, Yang, Fan, Tan, Keren, and Zheng, Yiyu

Subjects
Computer Science - Computation and Language, Computer Science - Machine Learning
Abstract

While in-context learning with large language models (LLMs) has shown impressive performance, we have discovered a unique miscalibration behavior where both correct and incorrect predictions are assigned the same level of confidence. We refer to this phenomenon as indiscriminate miscalibration. We found that traditional calibration metrics, such as Expected Calibrated Errors (ECEs), are unable to capture this behavior effectively. To address this issue, we propose new metrics to measure the severity of indiscriminate miscalibration. Additionally, we develop a novel in-context comparative inference method to alleviate miscalibrations and improve classification performance. Through extensive experiments on five datasets, we demonstrate that our proposed method can achieve more accurate and calibrated predictions compared to regular zero-shot and few-shot prompting., Comment: 19 pages

Published
2024

3. Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors

Author

Peng, Qin, Lu, Shaoying, Shi, Yuxin, Pan, Yijia, Limsakul, Praopim, Chernov, Andrei V, Qiu, Juhui, Chai, Xiaoqi, Shi, Yiwen, Wang, Pengzhi, Ji, Yanmin, Li, Yi-Shuan J, Strongin, Alex Y, Verkhusha, Vladislav V, Izpisua Belmonte, Juan Carlos, Ren, Bing, Wang, Yuanliang, Chien, Shu, and Wang, Yingxiao

Subjects
Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Bacterial Proteins, Biosensing Techniques, Chromatin Assembly and Disassembly, Fluorescence Resonance Energy Transfer, Green Fluorescent Proteins, HEK293 Cells, Heterochromatin, Histone Code, Histones, Humans, Luminescent Proteins, Mitosis, Models, Biological, Single-Cell Analysis, histone modifications, chromatin reorganization, FRET biosensors
Abstract

The dramatic reorganization of chromatin during mitosis is perhaps one of the most fundamental of all cell processes. It remains unclear how epigenetic histone modifications, despite their crucial roles in regulating chromatin architectures, are dynamically coordinated with chromatin reorganization in controlling this process. We have developed and characterized biosensors with high sensitivity and specificity based on fluorescence resonance energy transfer (FRET). These biosensors were incorporated into nucleosomes to visualize histone H3 Lys-9 trimethylation (H3K9me3) and histone H3 Ser-10 phosphorylation (H3S10p) simultaneously in the same live cell. We observed an anticorrelated coupling in time between H3K9me3 and H3S10p in a single live cell during mitosis. A transient increase of H3S10p during mitosis is accompanied by a decrease of H3K9me3 that recovers before the restoration of H3S10p upon mitotic exit. We further showed that H3S10p is causatively critical for the decrease of H3K9me3 and the consequent reduction of heterochromatin structure, leading to the subsequent global chromatin reorganization and nuclear envelope dissolution as a cell enters mitosis. These results suggest a tight coupling of H3S10p and H3K9me3 dynamics in the regulation of heterochromatin dissolution before a global chromatin reorganization during mitosis.

Published
2018

6. Dynamic Genetic Control: Manipulating Cell Behaviors Using Heat

Author

Ji, Yanmin

Subjects
Molecular biology, Biomedical engineering, Cre, FKBP/FRB, heat, short exposure, TRPV1
Abstract

Although Chimeric Antigen Receptor (CAR) T cells have been proven to be powerful in eradicating tumors. However, its non-specific activity against normal tissues and cells has been a major problem. Here, utilizing the activation of transient receptor potential cation channel subfamily V member 1 (TRPV1) under heat, the translocation of nuclear factor of activated T-cells (NFAT) triggered by Calcium influx, and the recombination effects of Cre-lox system, we have developed a system to remotely manipulate the expression of proteins in cells under the control of both heat and drugs. The significance of this project is to provide a method to precisely control the activities of CAR T cells within targeted local tissues.

Published
2017

9. Performance evaluation of injectivity for water-alternating-CO2 processes in tight oil formations

Author

Ji Yanmin, Guangqing Zhang, Junmin Gao, Daoyong Yang, Zhang Jiguo, and Chengyao Song

Subjects
Pressure drop, Petroleum engineering, 020209 energy, General Chemical Engineering, Organic Chemistry, Tight oil, Energy Engineering and Power Technology, 02 engineering and technology, Water production, Cycle time, Fuel Technology, 020401 chemical engineering, Oil production, 0202 electrical engineering, electronic engineering, information engineering, Environmental science, Sensitivity (control systems), 0204 chemical engineering
Abstract

Techniques have been developed to experimentally and numerically evaluate fluid injectivity and oil recovery of water-alternating-CO2 processes in tight oil formations. Experimentally, core samples collected from tight formations are utilized to conduct a series of water-alternating-CO2 flooding experiments with different water-alternating-CO2 ratios and slug sizes. The corresponding oil production, pressure drop, gas production and water production are examined throughout the experiments. Subsequently, numerical simulations are performed to history-match the experimental measurements and conduct sensitivity analysis on operational parameters (i.e., water-alternating-CO2 ratio, cycle time, and slug size) as well. Compared to waterflooding, fluid injectivity is found to be significantly improved by injecting CO2 during the water-alternating-CO2 processes in tight formations. There exists a good agreement between the experimental measurements and simulated results, indicating that the mechanisms governing water-alternating-CO2 processes in tight oil formations have been well incorporated. It is shown from sensitivity analysis that fluid injectivity is strongly dependent on slug size, water-alternating-CO2 ratio, and cycle time.

Published
2015

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