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Jian Jiang

Publications and source records attributed to Jian Jiang.

At least 37 records · Page 2Linked to original sources

Machine learning predictions from unpredictable chaos

Chaos is omnipresent in nature, and its understanding provides enormous social and economic benefits. However, the unpredictability of chaotic systems is a textbook concept due to their sensitivity to initial conditions, aperiodic behavior, fractal dimensions, nonlinearity, and strange attractors. In this work, we introduce, for the first time, chaotic learning, a novel multiscale topological paradigm that enables accurate predictions from chaotic systems. We show that seemingly random and unpredictable chaotic dynamics counterintuitively offer unprecedented quantitative predictions. Specifically, we devise multiscale topological Laplacians to embed real-world data into a family of interactive chaotic dynamical systems, modulate their dynamical behaviors, and enable the accurate prediction of the input data. As a proof of concept, we consider 28 datasets from four categories of realistic problems: 10 brain waves, four benchmark protein datasets, 13 single-cell RNA sequencing datasets, and an image dataset, as well as two distinct chaotic dynamical systems, namely the Lorenz and Rossler attractors. We demonstrate chaotic learning predictions of the physical properties from chaos. Our new chaotic learning paradigm profoundly changes the textbook perception of chaos and bridges topology, chaos, and learning for the first time.

nlin.CD↗

Artificial Intelligence Approaches for Anti-Addiction Drug Discovery

Drug addiction is a complex and pervasive global challenge that continues to pose significant public health concerns. Traditional approaches to anti-addiction drug discovery have struggled to deliver effective therapeutics, facing high attrition rates, long development timelines, and inefficiencies in processing large-scale data. Artificial intelligence (AI) has emerged as a transformative solution to address these issues. Using advanced algorithms, AI is revolutionizing drug discovery by enhancing the speed and precision of key processes. This review explores the transformative role of AI in the pipeline for anti-addiction drug discovery, including data collection, target identification, and compound optimization. By highlighting the potential of AI to overcome traditional barriers, this review systematically examines how AI addresses critical gaps in anti-addiction research, emphasizing its potential to revolutionize drug discovery and development, overcome challenges, and advance more effective therapeutic strategies.

q-bio.BM↗

Proteomic Learning of Gamma-Aminobutyric Acid (GABA) Receptor-Mediated Anesthesia

Anesthetics are crucial in surgical procedures and therapeutic interventions, but they come with side effects and varying levels of effectiveness, calling for novel anesthetic agents that offer more precise and controllable effects. Targeting Gamma-aminobutyric acid (GABA) receptors, the primary inhibitory receptors in the central nervous system, could enhance their inhibitory action, potentially reducing side effects while improving the potency of anesthetics. In this study, we introduce a proteomic learning of GABA receptor-mediated anesthesia based on 24 GABA receptor subtypes by considering over 4000 proteins in protein-protein interaction (PPI) networks and over 1.5 millions known binding compounds. We develop a corresponding drug-target interaction network to identify potential lead compounds for novel anesthetic design. To ensure robust proteomic learning predictions, we curated a dataset comprising 136 targets from a pool of 980 targets within the PPI networks. We employed three machine learning algorithms, integrating advanced natural language processing (NLP) models such as pretrained transformer and autoencoder embeddings. Through a comprehensive screening process, we evaluated the side effects and repurposing potential of over 180,000 drug candidates targeting the GABRA5 receptor. Additionally, we assessed the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of these candidates to identify those with near-optimal characteristics. This approach also involved optimizing the structures of existing anesthetics. Our work presents an innovative strategy for the development of new anesthetic drugs, optimization of anesthetic use, and deeper understanding of potential anesthesia-related side effects.

q-bio.BM↗

Observation of liquid-solid transition of nanoconfined water at ambient temperature

Nanoconfined water plays an indispensable role in various phenomena in biology, chemistry, and engineering. It exhibits many abnormal properties compared to bulk water, especially under strong confinement. However, the origin of those anomalies is still elusive due to the lack of structural information on hydrogen-bonding networks. Considering the inhomogeneity of the nanocavity and the tiny amount of water molecules, conventional optical spectroscopies and nuclear magnetic resonance (NMR) fail to realize the structure analysis of nanoconfined water. Here, we addressed this issue by combining scanning probe microscopy (SPM) with advanced quantum sensing(QS) based on an atomic-size quantum sensor like nitrogen-vacancy (NV) center in diamond, which can apply the nanoscale-NMR for characterizing both the dynamics and structure of confined water at ambient conditions. We built a two-dimensional (2D) nanoconfined water system with a hexagonal-boron nitride (hBN) flake and a hydrophilic diamond surface. By using the SPM tip to measure the confinement size precisely, we observed a critical confinement size of ~2 nm, below which the water diffusion was significantly suppressed and the hydrogen-bonding network of water showed an ordered structure. Meanwhile, molecular dynamics (MD) simulation revealed a solid-like water contact layer on the diamond surface under strong confinement, which also reproduced the measured nanoscale-NMR spectra and confirmed the liquid-solid phase transition observed in the experiments. Notably, with this new SPM-QS platform, our results showed a promising way to elucidate the abnormal properties of nanoconfined water in future applications.

cond-mat.mes-hall↗

CP-DETR: Concept Prompt Guide DETR Toward Stronger Universal Object Detection

Recent research on universal object detection aims to introduce language in a SoTA closed-set detector and then generalize the open-set concepts by constructing large-scale (text-region) datasets for training. However, these methods face two main challenges: (i) how to efficiently use the prior information in the prompts to genericise objects and (ii) how to reduce alignment bias in the downstream tasks, both leading to sub-optimal performance in some scenarios beyond pre-training. To address these challenges, we propose a strong universal detection foundation model called CP-DETR, which is competitive in almost all scenarios, with only one pre-training weight. Specifically, we design an efficient prompt visual hybrid encoder that enhances the information interaction between prompt and visual through scale-by-scale and multi-scale fusion modules. Then, the hybrid encoder is facilitated to fully utilize the prompted information by prompt multi-label loss and auxiliary detection head. In addition to text prompts, we have designed two practical concept prompt generation methods, visual prompt and optimized prompt, to extract abstract concepts through concrete visual examples and stably reduce alignment bias in downstream tasks. With these effective designs, CP-DETR demonstrates superior universal detection performance in a broad spectrum of scenarios. For example, our Swin-T backbone model achieves 47.6 zero-shot AP on LVIS, and the Swin-L backbone model achieves 32.2 zero-shot AP on ODinW35. Furthermore, our visual prompt generation method achieves 68.4 AP on COCO val by interactive detection, and the optimized prompt achieves 73.1 fully-shot AP on ODinW13.

cs.CV↗

A Neural-Network-Based Mapping and Optimization Framework for High-Precision Coarse-Grained Simulation

The accuracy and efficiency of a coarse-grained (CG) force field are pivotal for high-precision molecular simulations of large systems with complex molecules. We present an automated mapping and optimization framework for molecular simulation (AMOFMS), which is designed to streamline and improve the force field optimization process. It features a neural-network-based mapping function, DSGPM-TP (Deep Supervised Graph Partitioning Model with Type Prediction). This model can accurately and efficiently convert atomistic structures to CG mappings, reducing the need for manual intervention. By integrating bottom-up and top-down methodologies, AMOFMS allows users to freely combine these approaches or use them independently as optimization targets. Moreover, users can select and combine different optimizers to meet their specific mission. With its parallel optimizer, AMOFMS significantly accelerates the optimization process, reducing the time required to achieve optimal results. Successful applications of AMOFMS include parameter optimizations for systems such as POPC and PEO, demonstrating its robustness and effectiveness. Overall, AMOFMS provides a general and flexible framework for the automated development of high-precision CG force fields.

physics.comp-ph↗

Field Test of Quantum Key Distribution with High Key Creation Efficiency

Quantumkey distribution (QKD) promises unconditional security for communication. However, the random choices of the measurement basis in QKD usually result in low key creation efficiency. This drawback is overcome in the differential-phase-shift QKD, provided that each photon can be prepared in a large number of time bins with a proper waveform. In this work we develop a miniature 1550-nm single-photon source to generate narrowband single photon in 50 time bins with a nearly optimal waveform for achieving unity key creation efficiency. By utilizing these single photons in the field test, we demonstrate the differential-phase-shift QKD with a key creation efficiency of 97%. Our work shows that the practical QKD can benefit from the narrowband single photons with controllable waveforms.

quant-ph↗

Synergistic integration of physical embedding and machine learning enabling precise and reliable force field

The machine learning force field has achieved significant strides in accurately reproducing the potential energy surface with quantum chemical accuracy. However, it still faces significant challenges, e.g., extrapolating to uncharted chemical spaces, interpreting long-range electrostatics, and mapping complex macroscopic properties. To address these issues, we advocate for a synergistic integration of physical principles and machine learning techniques within the framework of a physically informed neural network (PINN). This innovative approach involves the incorporation of physical constraints directly into the parameters of the neural network, coupled with the implementation of a global optimization strategy. We choose the AMOEBA+ force field as the physics-based model for embedding, and then train and test it using the diethylene glycol dimethyl ether (DEGDME) dataset as a case study. The results reveal a significant breakthrough in constructing a precise and noise-robust machine learning force field. Utilizing two training sets with hundreds of samples, our model exhibits remarkable generalization and DFT accuracy in describing molecular interactions and enables a precise prediction of the macroscopic properties such as diffusion coefficient with minimal cost. This work provides a crucial insight into establishing a fundamental framework of PINN.

physics.chem-ph↗

Efficient Machine Learning Force Field for Large-Scale Molecular Simulations of Organic Systems

To address the computational challenges of ab initio molecular dynamics and the accuracy limitations of empirical force fields, the introduction of machine learning force fields has proven effective in various systems including metals and inorganic materials. However, in large-scale organic systems, the application of machine learning force fields is often hindered by impediments such as the complexity of long-range intermolecular interactions and molecular conformations, as well as the instability in long-time molecular simulations. Therefore, we propose a universal multiscale higher-order equivariant model combined with active learning techniques, efficiently capturing the complex long-range intermolecular interactions and molecular conformations. Compared to existing equivariant models, our model achieves the highest predictive accuracy, and magnitude-level improvements in computational speed and memory efficiency. In addition, a bond length stretching method is designed to improve the stability of long-time molecular simulations. Utilizing only 901 samples from a dataset with 120 atoms, our model successfully extends high precision to systems with hundreds of thousands of atoms. These achievements guarantee high predictive accuracy, fast simulation speed, minimal memory consumption, and robust simulation stability, satisfying the requirements for high-precision and long-time molecular simulations in large-scale organic systems.

cond-mat.soft↗

Exploration of visual prompt in Grounded pre-trained open-set detection

Text prompts are crucial for generalizing pre-trained open-set object detection models to new categories. However, current methods for text prompts are limited as they require manual feedback when generalizing to new categories, which restricts their ability to model complex scenes, often leading to incorrect detection results. To address this limitation, we propose a novel visual prompt method that learns new category knowledge from a few labeled images, which generalizes the pre-trained detection model to the new category. To allow visual prompts to represent new categories adequately, we propose a statistical-based prompt construction module that is not limited by predefined vocabulary lengths, thus allowing more vectors to be used when representing categories. We further utilize the category dictionaries in the pre-training dataset to design task-specific similarity dictionaries, which make visual prompts more discriminative. We evaluate the method on the ODinW dataset and show that it outperforms existing prompt learning methods and performs more consistently in combinatorial inference.

cs.CV↗

Machine Learning Study of the Extended Drug-target Interaction Network informed by Pain Related Voltage-Gated Sodium Channels

Pain is a significant global health issue, and the current treatment options for pain management have limitations in terms of effectiveness, side effects, and potential for addiction. There is a pressing need for improved pain treatments and the development of new drugs. Voltage-gated sodium channels, particularly Nav1.3, Nav1.7, Nav1.8, and Nav1.9, play a crucial role in neuronal excitability and are predominantly expressed in the peripheral nervous system. Targeting these channels may provide a means to treat pain while minimizing central and cardiac adverse effects. In this study, we construct protein-protein interaction (PPI) networks based on pain-related sodium channels and develop a corresponding drug-target interaction (DTI) network to identify potential lead compounds for pain management. To ensure reliable machine learning predictions, we carefully select 111 inhibitor datasets from a pool of over 1,000 targets in the PPI network. We employ three distinct machine learning algorithms combined with advanced natural language processing (NLP)-based embeddings, specifically pre-trained transformer and autoencoder representations. Through a systematic screening process, we evaluate the side effects and repurposing potential of over 150,000 drug candidates targeting Nav1.7 and Nav1.8 sodium channels. Additionally, we assess the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of these candidates to identify leads with near-optimal characteristics. Our strategy provides an innovative platform for the pharmacological development of pain treatments, offering the potential for improved efficacy and reduced side effects.

q-bio.BM↗

A Kapitza Pendulum for Ultracold Atoms

We report on the experimental realization of a Kapitza pendulum for ultracold atoms. Using time-periodic attractive and repulsive Gaussian potentials, we create an effective trap for ultracold neutral atoms in a regime where the time average of the potential is equal to zero. We analyze the role of experimental imperfections, the stability of the trapped atomic cloud, and the magnitude of the effective potential. We find good agreement with the high-frequency expansion of the underlying system dynamics. Our experimental approach opens up new possibilities to study Floquet systems of neutral atoms.

cond-mat.quant-gas↗

Machine-learning Repurposing of DrugBank Compounds for Opioid Use Disorder

Opioid use disorder (OUD) is a chronic and relapsing condition that involves the continued and compulsive use of opioids despite harmful consequences. The development of medications with improved efficacy and safety profiles for OUD treatment is urgently needed. Drug repurposing is a promising option for drug discovery due to its reduced cost and expedited approval procedures. Computational approaches based on machine learning enable the rapid screening of DrugBank compounds, identifying those with the potential to be repurposed for OUD treatment. We collected inhibitor data for four major opioid receptors and used advanced machine learning predictors of binding affinity that fuse the gradient boosting decision tree algorithm with two natural language processing (NLP)-based molecular fingerprints and one traditional 2D fingerprint. Using these predictors, we systematically analyzed the binding affinities of DrugBank compounds on four opioid receptors. Based on our machine learning predictions, we were able to discriminate DrugBank compounds with various binding affinity thresholds and selectivities for different receptors. The prediction results were further analyzed for ADMET (absorption, distribution, metabolism, excretion, and toxicity), which provided guidance on repurposing DrugBank compounds for the inhibition of selected opioid receptors. The pharmacological effects of these compounds for OUD treatment need to be tested in further experimental studies and clinical trials. Our machine learning studies provide a valuable platform for drug discovery in the context of OUD treatment.

q-bio.BM↗

Machine-learning Analysis of Opioid Use Disorder Informed by MOR, DOR, KOR, NOR and ZOR-Based Interactome Networks

Opioid use disorder (OUD) continuously poses major public health challenges and social implications worldwide with dramatic rise of opioid dependence leading to potential abuse. Despite that a few pharmacological agents have been approved for OUD treatment, the efficacy of said agents for OUD requires further improvement in order to provide safer and more effective pharmacological and psychosocial treatments. Preferable therapeutic treatments of OUD rely on the advances in understanding the neurobiological mechanism of opioid dependence. Proteins including mu, delta, kappa, nociceptin, and zeta opioid receptors are the direct targets of opioids. Each receptor has a large protein-protein interaction (PPI) network, that behaves differently when subjected to various treatments, thus increasing the complexity in the drug development process for an effective opioid addiction treatment. The report below analyzes the work by presenting a PPI-network informed machine-learning study of OUD. We have examined more than 500 proteins in the five opioid receptor networks and subsequently collected 74 inhibitor datasets. Machine learning models were constructed by pairing gradient boosting decision tree (GBDT) algorithm with two advanced natural language processing (NLP)-based molecular fingerprints. With these models, we systematically carried out evaluations of screening and repurposing potential of drug candidates for four opioid receptors. In addition, absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties were also considered in the screening of potential drug candidates. Our study can be a valuable and promising tool of pharmacological development for OUD treatments.

q-bio.BM↗

Neural Weight Search for Scalable Task Incremental Learning

Task incremental learning aims to enable a system to maintain its performance on previously learned tasks while learning new tasks, solving the problem of catastrophic forgetting. One promising approach is to build an individual network or sub-network for future tasks. However, this leads to an ever-growing memory due to saving extra weights for new tasks and how to address this issue has remained an open problem in task incremental learning. In this paper, we introduce a novel Neural Weight Search technique that designs a fixed search space where the optimal combinations of frozen weights can be searched to build new models for novel tasks in an end-to-end manner, resulting in scalable and controllable memory growth. Extensive experiments on two benchmarks, i.e., Split-CIFAR-100 and CUB-to-Sketches, show our method achieves state-of-the-art performance with respect to both average inference accuracy and total memory cost.

cs.CV↗

Improving COVID-19 CT Classification of CNNs by Learning Parameter-Efficient Representation

COVID-19 pandemic continues to spread rapidly over the world and causes a tremendous crisis in global human health and the economy. Its early detection and diagnosis are crucial for controlling the further spread. Many deep learning-based methods have been proposed to assist clinicians in automatic COVID-19 diagnosis based on computed tomography imaging. However, challenges still remain, including low data diversity in existing datasets, and unsatisfied detection resulting from insufficient accuracy and sensitivity of deep learning models. To enhance the data diversity, we design augmentation techniques of incremental levels and apply them to the largest open-access benchmark dataset, COVIDx CT-2A. Meanwhile, similarity regularization (SR) derived from contrastive learning is proposed in this study to enable CNNs to learn more parameter-efficient representations, thus improving the accuracy and sensitivity of CNNs. The results on seven commonly used CNNs demonstrate that CNN performance can be improved stably through applying the designed augmentation and SR techniques. In particular, DenseNet121 with SR achieves an average test accuracy of 99.44% in three trials for three-category classification, including normal, non-COVID-19 pneumonia, and COVID-19 pneumonia. And the achieved precision, sensitivity, and specificity for the COVID-19 pneumonia category are 98.40%, 99.59%, and 99.50%, respectively. These statistics suggest that our method has surpassed the existing state-of-the-art methods on the COVIDx CT-2A dataset.

eess.IV↗

Experimental observation of a dissipative phase transition in a multi-mode many-body quantum system

We characterize the dissipative phase transition in a driven dissipative Bose-Einstein condensate of neutral atoms. Our results generalize the work on dissipative nonlinear Kerr resonators towards many modes and stronger interactions. We measure the effective Liouvillian gap and analyze the microscopic system dynamics, where we identify a non-equilibrium condensation process.

cond-mat.quant-gas↗

MIIDL: a Python package for microbial biomarkers identification powered by interpretable deep learning

Detecting microbial biomarkers used to predict disease phenotypes and clinical outcomes is crucial for disease early-stage screening and diagnosis. Most methods for biomarker identification are linear-based, which is very limited as biological processes are rarely fully linear. The introduction of machine learning to this field tends to bring a promising solution. However, identifying microbial biomarkers in an interpretable, data-driven and robust manner remains challenging. We present MIIDL, a Python package for the identification of microbial biomarkers based on interpretable deep learning. MIIDL innovatively applies convolutional neural networks, a variety of interpretability algorithms and plenty of pre-processing methods to provide a one-stop and robust pipeline for microbial biomarkers identification from high-dimensional and sparse data sets.

q-bio.QM↗