arXiv subjects

Hua Zheng

Publications and source records attributed to Hua Zheng.

At least 55 records · Page 3Linked to original sources

arXiv2024

Comparing pion production in transport simulations of heavy-ion collisions at $270A$ MeV under controlled conditions

Within the TMEP, we present a detailed study of the performance of different transport models in Sn+Sn collisions at $270A$ MeV, and put particular emphasis on the production of pions and $Δ$ resonances, which have been used as probes of the nuclear symmetry energy. We prescribe a common and rather simple physics model, and follow in detail the results of 4 BUU models and 6 QMD models. The nucleonic evolution of the collision and the nucleonic observables in these codes do not completely converge, but the differences among the codes can be understood as being due to several reasons: the basic differences between BUU and QMD models in the representation of the phase-space distributions, computational differences in the mean-field evaluation, and differences in the adopted strategies for the Pauli blocking in the collision integrals. For pionic observables, we find that a higher maximum density leads to an enhanced pion yield and a reduced $π^-/π^+$ yield ratio, while a more effective Pauli blocking generally leads to a slightly suppressed pion yield and an enhanced $π^-/π^+$ yield ratio. We specifically investigate the effect of the Coulomb force, and find that it increases the total $π^-/π^+$ yield ratio but reduces the ratio at high pion energies, although differences in its implementations do not have a dominating role in the differences among the codes. Taking into account only the results of codes that strictly follow the homework specifications, we find a convergence of the codes in the final charged pion yield ratio to a $1σ$ deviation of about $5\%$. However, the uncertainty is expected to be reduced to about $1.6\%$ if the same or similar strategies and ingredients, i.e., an improved Pauli blocking and calculation of the non-linear term in the mean-field potential, are similarly used in all codes.

nucl-th↗

arXiv2023

SiGeo: Sub-One-Shot NAS via Information Theory and Geometry of Loss Landscape

Neural Architecture Search (NAS) has become a widely used tool for automating neural network design. While one-shot NAS methods have successfully reduced computational requirements, they often require extensive training. On the other hand, zero-shot NAS utilizes training-free proxies to evaluate a candidate architecture's test performance but has two limitations: (1) inability to use the information gained as a network improves with training and (2) unreliable performance, particularly in complex domains like RecSys, due to the multi-modal data inputs and complex architecture configurations. To synthesize the benefits of both methods, we introduce a "sub-one-shot" paradigm that serves as a bridge between zero-shot and one-shot NAS. In sub-one-shot NAS, the supernet is trained using only a small subset of the training data, a phase we refer to as "warm-up." Within this framework, we present SiGeo, a proxy founded on a novel theoretical framework that connects the supernet warm-up with the efficacy of the proxy. Extensive experiments have shown that SiGeo, with the benefit of warm-up, consistently outperforms state-of-the-art NAS proxies on various established NAS benchmarks. When a supernet is warmed up, it can achieve comparable performance to weight-sharing one-shot NAS methods, but with a significant reduction ($\sim 60$\%) in computational costs.

cs.LG↗

arXiv2023

Stochastic Biological System-of-Systems Modelling for iPSC Culture

Large-scale manufacturing of induced pluripotent stem cells (iPSCs) is essential for cell therapies and regenerative medicines. Yet, iPSCs form large cell aggregates in suspension bioreactors, resulting in insufficient nutrient supply and extra metabolic waste build-up for the cells located at the core. Since subtle changes in micro-environment can lead to a heterogeneous cell population, a novel Biological System-of-Systems (Bio-SoS) framework is proposed to model cell-to-cell interactions, spatial and metabolic heterogeneity, and cell response to micro-environmental variation. Building on stochastic metabolic reaction network, aggregation kinetics, and reaction-diffusion mechanisms, the Bio-SoS model characterizes causal interdependencies at individual cell, aggregate, and cell population levels. It has a modular design that enables data integration and improves predictions for different monolayer and aggregate culture processes. In addition, a variance decomposition analysis is derived to quantify the impact of factors (i.e., aggregate size) on cell product health and quality heterogeneity.

q-bio.MN↗

arXiv2023

Stochastic Molecular Reaction Queueing Network Modeling for In Vitro Transcription Process

To facilitate a rapid response to pandemic threats, this paper focuses on developing a mechanistic simulation model for in vitro transcription (IVT) process, a crucial step in mRNA vaccine manufacturing. To enhance production and support industry 4.0, this model is proposed to improve the prediction and analysis of IVT enzymatic reaction network. It incorporates a novel stochastic molecular reaction queueing network with a regulatory kinetic model characterizing the effect of bioprocess state variables on reaction rates. The empirical study demonstrates that the proposed model has a promising performance under different production conditions and it could offer potential improvements in mRNA product quality and yield.

q-bio.MN↗

arXiv2023

Structure-Function Dynamics Hybrid Modeling: RNA Degradation

RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery, manufacturing, and delivery mechanisms. However, it is computationally unattainable to support the development of a digital twin for enzymatic reaction network mechanism learning, and end-to-end bioprocess design and control. Thus, we create a hybrid ("mechanistic + machine learning") model characterizing the interdependence of RNA structure and functional dynamics from atomistic to macroscopic levels. To assess the proposed modeling strategy, in this paper, we consider RNA degradation which is a critical process in cellular biology that affects gene expression. The empirical study on RNA lifetime prediction demonstrates the promising performance of the proposed multi-scale bioprocess hybrid modeling strategy.

q-bio.MN↗

arXiv2023

Transformer-based Text Classification on Unified Bangla Multi-class Emotion Corpus

In this research, we propose a complete set of approaches for identifying and extracting emotions from Bangla texts. We provide a Bangla emotion classifier for six classes: anger, disgust, fear, joy, sadness, and surprise, from Bangla words using transformer-based models, which exhibit phenomenal results in recent days, especially for high-resource languages. The Unified Bangla Multi-class Emotion Corpus (UBMEC) is used to assess the performance of our models. UBMEC is created by combining two previously released manually labeled datasets of Bangla comments on six emotion classes with fresh manually labeled Bangla comments created by us. The corpus dataset and code we used in this work are publicly available.

cs.CL↗

arXiv2023

Pair production as a probe for the dynamics of nuclear fission and $α$ decay

Electron-positron pairs can be produced via the Schwinger mechanism in the presence of strong electric fields. In particular, the fields involved in $α$ decay and nuclear fission are strong enough to produce them. The energy of the $e^+e^-$ pair is related to the relative distance and velocity of the daughter nuclei. Thus, the energy distribution of the produced pairs can give information about the dynamics of the fission and $α$ decay processes. A neck model of nuclear fission is used to illustrate how the pairs can be used as a probe of the dynamics.

nucl-th↗

arXiv2023

Universal Energy Dependence of Measured Temperatures for Baryons Produced in Heavy-ion Collisions

From the data on baryon production in heavy-ion collisions it is shown that a set of measurable functions exist, one for each baryon type, that depend exponentially on transverse momenta up to the maximum values detected for all collision energies ranging from the low end of RHIC BES to the high end of CERN LHC. The implied temperatures satisfy a scaling law in collision energy with a universal exponent for all baryon types which is the novel discovery. A self-similar thermal source is implied. Furthermore, it is shown how the scaling behavior depends on centralities. Those features in the data are related to simple properties of light and strange quarks by use of the recombination model. Prediction of $ϕ$ meson production is made and then verified by existing data.

hep-ph↗

arXiv2022

Compressed domain vibration detection and classification for distributed acoustic sensing

Distributed acoustic sensing (DAS) is a novel enabling technology that can turn existing fibre optic networks to distributed acoustic sensors. However, it faces the challenges of transmitting, storing, and processing massive streams of data which are orders of magnitude larger than that collected from point sensors. The gap between intensive data generated by DAS and modern computing system with limited reading/writing speed and storage capacity imposes restrictions on many applications. Compressive sensing (CS) is a revolutionary signal acquisition method that allows a signal to be acquired and reconstructed with significantly fewer samples than that required by Nyquist-Shannon theorem. Though the data size is greatly reduced in the sampling stage, the reconstruction of the compressed data is however time and computation consuming. To address this challenge, we propose to map the feature extractor from Nyquist-domain to compressed-domain and therefore vibration detection and classification can be directly implemented in compressed-domain. The measured results show that our framework can be used to reduce the transmitted data size by 70% while achieves 99.4% true positive rate (TPR) and 0.04% false positive rate (TPR) along 5 km sensing fibre and 95.05% classification accuracy on a 5-class classification task.

eess.SP↗

arXiv2022

Sequential Importance Sampling for Hybrid Model Bayesian Inference to Support Bioprocess Mechanism Learning and Robust Control

Driven by the critical needs of biomanufacturing 4.0, we introduce a probabilistic knowledge graph hybrid model characterizing the risk- and science-based understanding of bioprocess mechanisms. It can faithfully capture the important properties, including nonlinear reactions, partially observed state, and nonstationary dynamics. Given very limited real process observations, we derive a posterior distribution quantifying model estimation uncertainty. To avoid the evaluation of intractable likelihoods, Approximate Bayesian Computation sampling with Sequential Monte Carlo (ABC-SMC) is utilized to approximate the posterior distribution. Under high stochastic and model uncertainties, it is computationally expensive to match output trajectories. Therefore, we create a linear Gaussian dynamic Bayesian network (LG-DBN) auxiliary likelihood-based ABC-SMC approach. Through matching the summary statistics driven through LG-DBN likelihood that can capture critical interactions and variations, the proposed algorithm can accelerate hybrid model inference, support process monitoring, and facilitate mechanism learning and robust control.

stat.ML↗

arXiv2022

Variance Reduction based Experience Replay for Policy Optimization

For reinforcement learning on complex stochastic systems where many factors dynamically impact the output trajectories, it is desirable to effectively leverage the information from historical samples collected in previous iterations to accelerate policy optimization. Classical experience replay allows agents to remember by reusing historical observations. However, the uniform reuse strategy that treats all observations equally overlooks the relative importance of different samples. To overcome this limitation, we propose a general variance reduction based experience replay (VRER) framework that can selectively reuse the most relevant samples to improve policy gradient estimation. This selective mechanism can adaptively put more weight on past samples that are more likely to be generated by the current target distribution. Our theoretical and empirical studies show that the proposed VRER can accelerate the learning of optimal policy and enhance the performance of state-of-the-art policy optimization approaches.

stat.ML↗

arXiv2022

Policy Optimization in Dynamic Bayesian Network Hybrid Models of Biomanufacturing Processes

Biopharmaceutical manufacturing is a rapidly growing industry with impact in virtually all branches of medicines. Biomanufacturing processes require close monitoring and control, in the presence of complex bioprocess dynamics with many interdependent factors, as well as extremely limited data due to the high cost of experiments as well as the novelty of personalized bio-drugs. We develop a novel model-based reinforcement learning framework that can achieve human-level control in low-data environments. The model uses a dynamic Bayesian network to capture causal interdependencies between factors and predict how the effects of different inputs propagate through the pathways of the bioprocess mechanisms. This enables the design of process control policies that are both interpretable and robust against model risk. We present a computationally efficient, provably convergence stochastic gradient method for optimizing such policies. Validation is conducted on a realistic application with a multi-dimensional, continuous state variable.

cs.AI↗

arXiv2022

Variance Reduction based Partial Trajectory Reuse to Accelerate Policy Gradient Optimization

Built on our previous study on green simulation assisted policy gradient (GS-PG) focusing on trajectory-based reuse, in this paper, we consider infinite-horizon Markov Decision Processes and create a new importance sampling based policy gradient optimization approach to support dynamic decision making. The existing GS-PG method was designed to learn from complete episodes or process trajectories, which limits its applicability to low-data situations and flexible online process control. To overcome this limitation, the proposed approach can selectively reuse the most related partial trajectories, i.e., the reuse unit is based on per-step or per-decision historical observations. In specific, we create a mixture likelihood ratio (MLR) based policy gradient optimization that can leverage the information from historical state-action transitions generated under different behavioral policies. The proposed variance reduction experience replay (VRER) approach can intelligently select and reuse most relevant transition observations, improve the policy gradient estimation, and accelerate the learning of optimal policy. Our empirical study demonstrates that it can improve optimization convergence and enhance the performance of state-of-the-art policy optimization approaches such as actor-critic method and proximal policy optimizations.

cs.LG↗

arXiv2022

Is "My Favorite New Movie" My Favorite Movie? Probing the Understanding of Recursive Noun Phrases

Recursive noun phrases (NPs) have interesting semantic properties. For example, "my favorite new movie" is not necessarily my favorite movie, whereas "my new favorite movie" is. This is common sense to humans, yet it is unknown whether language models have such knowledge. We introduce the Recursive Noun Phrase Challenge (RNPC), a dataset of three textual inference tasks involving textual entailment and event plausibility comparison, precisely targeting the understanding of recursive NPs. When evaluated on RNPC, state-of-the-art Transformer models only perform around chance. Still, we show that such knowledge is learnable with appropriate data. We further probe the models for relevant linguistic features that can be learned from our tasks, including modifier semantic category and modifier scope. Finally, models trained on RNPC achieve strong zero-shot performance on an extrinsic Harm Detection evaluation task, showing the usefulness of the understanding of recursive NPs in downstream applications.

cs.CL↗

arXiv2022

Opportunities of Hybrid Model-based Reinforcement Learning for Cell Therapy Manufacturing Process Control

Driven by the key challenges of cell therapy manufacturing, including high complexity, high uncertainty, and very limited process observations, we propose a hybrid model-based reinforcement learning (RL) to efficiently guide process control. We first create a probabilistic knowledge graph (KG) hybrid model characterizing the risk- and science-based understanding of biomanufacturing process mechanisms and quantifying inherent stochasticity, e.g., batch-to-batch variation. It can capture the key features, including nonlinear reactions, nonstationary dynamics, and partially observed state. This hybrid model can leverage existing mechanistic models and facilitate learning from heterogeneous process data. A computational sampling approach is used to generate posterior samples quantifying model uncertainty. Then, we introduce hybrid model-based Bayesian RL, accounting for both inherent stochasticity and model uncertainty, to guide optimal, robust, and interpretable dynamic decision making. Cell therapy manufacturing examples are used to empirically demonstrate that the proposed framework can outperform the classical deterministic mechanistic model assisted process optimization.

eess.SY↗

arXiv2021

Reinforcement Learning Assisted Oxygen Therapy for COVID-19 Patients Under Intensive Care

Patients with severe Coronavirus disease 19 (COVID-19) typically require supplemental oxygen as an essential treatment. We developed a machine learning algorithm, based on a deep Reinforcement Learning (RL), for continuous management of oxygen flow rate for critical ill patients under intensive care, which can identify the optimal personalized oxygen flow rate with strong potentials to reduce mortality rate relative to the current clinical practice. Basically, we modeled the oxygen flow trajectory of COVID-19 patients and their health outcomes as a Markov decision process. Based on individual patient characteristics and health status, a reinforcement learning based oxygen control policy is learned and real-time recommends the oxygen flow rate to reduce the mortality rate. We assessed the performance of proposed methods through cross validation by using a retrospective cohort of 1,372 critically ill patients with COVID-19 from New York University Langone Health ambulatory care with electronic health records from April 2020 to January 2021. The mean mortality rate under the RL algorithm is lower than standard of care by 2.57% (95% CI: 2.08- 3.06) reduction (P<0.001) from 7.94% under the standard of care to 5.37 % under our algorithm and the averaged recommended oxygen flow rate is 1.28 L/min (95% CI: 1.14-1.42) lower than the rate actually delivered to patients. Thus, the RL algorithm could potentially lead to better intensive care treatment that can reduce mortality rate, while saving the oxygen scarce resources. It can reduce the oxygen shortage issue and improve public health during the COVID-19 pandemic.

cs.LG↗

arXiv2021

Spin Quantization in Heavy Ion Collision

We analyzed recent experimental data on the disassembly of $^{28}$Si into 7$α$ in terms of a hybrid $α$-cluster model. We calculated the probability of breaking into several $α$-like fragments for high $l$-spin values for identical and non-identical spin zero nuclei. Resonant energies were found for each $l$-value and compared to the data and other theoretical models. Toroidal-like structures were revealed in coordinate and momentum space when averaging over many events at high $l$. The transition from quantum to classical mechanics is highlighted.

nucl-th↗

arXiv2021

Coulomb field correction due to virtual $e^+e^-$ production in heavy ion collisions

The correction to the Coulomb energy due to virtual production of $e^+e^-$ pairs, which is on the order of one percent of the Coulomb energy at nuclear scales is discussed. The effects of including a pair-production term in the semi-empirical mass formula and the correction to the Coulomb barrier for a handful of nuclear collisions using the Bass and Coulomb potentials are studied. With an eye toward future work using Constrained Molecular Dynamics (CoMD) model, we also calculate the correction to the Coulomb energy and force between protons after folding with a Gaussian spatial distribution.

nucl-th↗