arXiv subjects

Jiatong Xu

Publications and source records attributed to Jiatong Xu.

4 recordsLinked to original sources

arXiv2026

MIRCID: Inferred Hub-miRNAs Drive Cross-Task Improvements in Drug Mechanistic Modeling

Drug mechanism-of-action (MoA) modeling commonly relies on perturbational transcriptomes, but matched microRNA (miRNA) measurements are often unavailable. Inferred regulatory features offer a scalable way to reuse these data. Here, we present MIRCID, a framework comparing gene expression with inferred transcription factor (TF) activity and miRNA expression across pathway classification and similarity-based MoA retrieval. HubmiRNet infers 414 pan-cancer hub miRNAs (HubmiRs) from 977 L1000 landmark genes, achieving a Pearson correlation coefficient of 87.72\%; its 1,298-output variant also outperformed SiCmiR on the full-miRNA task (71.21\% versus 67.30\%). In the evaluated comparisons, miRNA augmentation provided more consistent gains than TF activity. Generic embedding controls showed model-dependent utility, while complementarity analyses identified a distinct, partially linearly recoverable representation that retained gene-derived structure. Illustrative rescue cases linked improved classification to biologically plausible miRNA patterns in samples with weak transcriptional signatures. These findings support inferred HubmiRs as a biologically informed recoding of transcriptomic data for perturbational drug modeling, while leaving recovery of measured perturbational miRNA responses to further validation.

cs.LG↗

arXiv2025

Laser-Induced Heating in Diamonds: Influence of Substrate Thermal Conductivity and Interfacial Polymer Layers

Diamonds hosting color centers possess intrinsically high thermal conductivity; therefore, laser-induced heating has often received little attention. However, when placed on substrates with low thermal conductivity, localized heating of diamonds under laser excitation can become significant, and the presence of an interfacial polymer layer between substrate and diamond further amplifies this effect. Yet, the relationship between substrate thermal conductivity, polymer thickness, and laser heating remains to be established. Here, a systematic investigation is presented on laser-induced heating of silicon-vacancy diamond on substrates with varying thermal conductivity and interfacial polymer thickness. Results reveal that even at a low excitation power of 737~$μ$W/$μ$m$^2$, thin amorphous holey carbon -- the lowest-conductivity substrate ($\sim$0.2~W~m$^{-1}$~K$^{-1}$) studied -- exhibits substantial heating, while glass ($\sim$1.4~W~m$^{-1}$~K$^{-1}$) and polydimethylsiloxane (PDMS, $\sim$0.35~W~m$^{-1}$~K$^{-1}$) show noticeable heating only above 2.95~mW/$μ$m$^2$. For polymer interlayers, a thickness of just 2.2~$μ$m induces significant heating at 2.95~mW/$μ$m$^2$ and above, highlighting strong influence of both substrate and polymer thickness on local heating response. Experimental findings are further validated using COMSOL Multiphysics simulations with a steady-state 3D heat transfer model. These results provide practical guidance for substrate selection and sample preparation, enabling optimization of conditions for optical thermometry and quantum sensing applications.

cond-mat.mtrl-sci↗

arXiv2023

Demonstration of a Facile and Efficient Strategy for Yield Stress Determination in Large Amplitude Oscillatory Shear: Algebraic Stress Bifurcation

The large amplitude oscillatory shear (LAOS) has been extensively studied for understanding the rheological responses of yield stress fluids. However, the employed methodology for determining the yield stress remains uncertain albeit the fact that many classical or plausible methods exist in the literature. Along these lines, herein, based on Fourier transform (FT) rheology, stress decomposition, and stress bifurcation, a new straightforward method termed as algebraic stress bifurcation was developed. More specifically, the main goal was to determine the yield stress and investigate the solid-liquid transition of fluids in LAOS. A simple and efficient mathematical framework was established and verified by the KVHB, Saramito, Giesekus models, and FT rheology. The main strength of this approach is that only the data from the stress/strain sweep are required instead of Lissajous curves. Alternative curves based on the first harmonic were constructed to demonstrate the non-critical role of both higher harmonics and phenomenological Lissajous curves in determining yield stress. The determined start and end yield points in the solid-liquid transition were compared with the already existing methods. Furthermore, the resulting solid-liquid transition region was analyzed by FT rheology, stress decomposition, and sequence of the physical process to obtain information on nonlinearity and intracycle/intercycle yielding. Our work provides fruitful insights for explaining and reducing the complexities of the stress bifurcation technique by using an easy-to-understand and implement format. Therefore, a concise theoretical framework was introduced for understanding the concept of yield stress, the intercycle yielding process, and the rational choice of yield stress measurement techniques.

physics.flu-dyn↗

arXiv2023

New insights into tackling large amplitude oscillatory shear (LAOS): an analytic LAOS approach (aLAOS)

Large amplitude oscillatory shear (LAOS) has been widely applied for performing rheological analysis of complex fluids, and the Fourier transform (FT) rheology is considered one of the mainstays in LAOS since FT is an essential mathematic tool that is applied in numerous fields of signal analysis. However, the challenge of understanding FT, diverse mathematical frameworks, and complicated data processing render existing LAOS methods hard to be effectively used. As a result, their accessibility and implementation are limited in practice. Thus, the development of novel LAOS methods remains an unmet need. In this context, a newly analytic LAOS (aLAOS) approach was deduced here to tackle LAOS by the reverse use of the methodology of the FT rheology. More specifically, the rheological signals and measures can be precisely reconstructed based on the established equations involving Fourier coefficients instead of processing numerous discrete points of the Lissajous curves. Furthermore, considering the acquired results from the LAOS tests on the various typical yield stress fluids, it was demonstrated that the aLAOS could unify the mainstream LAOS methods into one Fourier coefficient-based framework and visually distinguish the contribution of arbitrary higher harmonics. Consequently, the proposed approach is arising as a promising candidate for the convenient treatment of LAOS, which could also highly promote the multi-field applications of LAOS.

physics.flu-dyn↗