arXiv subjects

Jie Yan

Publications and source records attributed to Jie Yan.

35 records · Page 2Linked to original sources

arXiv2023

Privacy-Preserving Federated Deep Clustering based on GAN

Federated clustering (FC) is an essential extension of centralized clustering designed for the federated setting, wherein the challenge lies in constructing a global similarity measure without the need to share private data. Conventional approaches to FC typically adopt extensions of centralized methods, like K-means and fuzzy c-means. However, these methods are susceptible to non-independent-and-identically-distributed (non-IID) data among clients, leading to suboptimal performance, particularly with high-dimensional data. In this paper, we present a novel approach to address these limitations by proposing a Privacy-Preserving Federated Deep Clustering based on Generative Adversarial Networks (GANs). Each client trains a local generative adversarial network (GAN) locally and uploads the synthetic data to the server. The server applies a deep clustering network on the synthetic data to establish $k$ cluster centroids, which are then downloaded to the clients for cluster assignment. Theoretical analysis demonstrates that the GAN-generated samples, shared among clients, inherently uphold certain privacy guarantees, safeguarding the confidentiality of individual data. Furthermore, extensive experimental evaluations showcase the effectiveness and utility of our proposed method in achieving accurate and privacy-preserving federated clustering.

cs.LG↗

arXiv2023

The Ensemble Approach of Column Generation for Solving Cutting Stock Problems

This paper investigates the column generation (CG) for solving cutting stock problems (CSP). Traditional CG method, which repeatedly solves a restricted master problem (RMP), often suffers from two critical issues in practice -- the loss of solution quality introduced by linear relaxation of both feasible domain and objective and the high time cost of last iterations close to convergence. We empirically find that the first issue is common in ordinary CSPs with linear cutting constraints, while the second issue is especially severe in CSPs with nonlinear cutting constraints that are often generated by approximating chance constraints. We propose an alternative approach, ensembles of multiple column generation processes. In particular, we present two methods -- \mc (multi-column) which return multiple feasible columns in each RMP iteration, and \mt (multi-path) which restarts the RMP iterations from different initialized column sets once the iteration time exceeds a given time limit. The ideas behind are same: leverage the multiple column generation pathes to compensate the loss induced by relaxation, and add earlier sub-optimal columns to accelerate convergence of RMP iterations. Besides, we give theoretical analysis on performance improvement guarantees. Experiments on cutting stock problems demonstrate that compared to traditional CG, our method achieves significant run-time reduction on CSPs with nonlinear constraints, and dramatically improves the ratio of solve-to-optimal on CSPs with linear constraints.

math.OC↗

arXiv2023

Introspective Tips: Large Language Model for In-Context Decision Making

The emergence of large language models (LLMs) has substantially influenced natural language processing, demonstrating exceptional results across various tasks. In this study, we employ ``Introspective Tips" to facilitate LLMs in self-optimizing their decision-making. By introspectively examining trajectories, LLM refines its policy by generating succinct and valuable tips. Our method enhances the agent's performance in both few-shot and zero-shot learning situations by considering three essential scenarios: learning from the agent's past experiences, integrating expert demonstrations, and generalizing across diverse games. Importantly, we accomplish these improvements without fine-tuning the LLM parameters; rather, we adjust the prompt to generalize insights from the three aforementioned situations. Our framework not only supports but also emphasizes the advantage of employing LLM in in-contxt decision-making. Experiments involving over 100 games in TextWorld illustrate the superior performance of our approach.

cs.AI↗

arXiv2023

NoiseTrans: Point Cloud Denoising with Transformers

Point clouds obtained from capture devices or 3D reconstruction techniques are often noisy and interfere with downstream tasks. The paper aims to recover the underlying surface of noisy point clouds. We design a novel model, NoiseTrans, which uses transformer encoder architecture for point cloud denoising. Specifically, we obtain structural similarity of point-based point clouds with the assistance of the transformer's core self-attention mechanism. By expressing the noisy point cloud as a set of unordered vectors, we convert point clouds into point embeddings and employ Transformer to generate clean point clouds. To make the Transformer preserve details when sensing the point cloud, we design the Local Point Attention to prevent the point cloud from being over-smooth. In addition, we also propose sparse encoding, which enables the Transformer to better perceive the structural relationships of the point cloud and improve the denoising performance. Experiments show that our model outperforms state-of-the-art methods in various datasets and noise environments.

cs.CV↗

arXiv2022

Drug repositioning for Alzheimer's disease with transfer learning

Deep Learning and DRUG-seq (Digital RNA with perturbation of genes) have attracted attention in drug discovery. However, the public DRUG-seq dataset is too small to be used for directly training a deep learning neural network from scratch. Inspired by the transfer learning technique, we pretrain a drug efficacy prediction neural network model with the Library of Integrated Network-based Cell-Signature (LINCS) L1000 data and then use human neural cell DRUG-seq data to fine-tune it. After training, the model is used for virtual screening to find potential drugs for Alzheimer's disease (AD) treatment. Finally, we find 27 potential drugs for AD treatment including Irsogladine (PDE4 inhibitor), Tasquinimod (HDAC4 selective inhibitor), Suprofen (dual COX-1/COX-2 inhibitor) et al.

q-bio.QM↗

arXiv2022

Solving the Batch Stochastic Bin Packing Problem in Cloud: A Chance-constrained Optimization Approach

This paper investigates a critical resource allocation problem in the first party cloud: scheduling containers to machines. There are tens of services and each service runs a set of homogeneous containers with dynamic resource usage; containers of a service are scheduled daily in a batch fashion. This problem can be naturally formulated as Stochastic Bin Packing Problem (SBPP). However, traditional SBPP research often focuses on cases of empty machines, whose objective, i.e., to minimize the number of used machines, is not well-defined for the more common reality with nonempty machines. This paper aims to close this gap. First, we define a new objective metric, Used Capacity at Confidence (UCaC), which measures the maximum used resources at a probability and is proved to be consistent for both empty and nonempty machines, and reformulate the SBPP under chance constraints. Second, by modeling the container resource usage distribution in a generative approach, we reveal that UCaC can be approximated with Gaussian, which is verified by trace data of real-world applications. Third, we propose an exact solver by solving the equivalent cutting stock variant as well as two heuristics-based solvers -- UCaC best fit, bi-level heuristics. We experimentally evaluate these solvers on both synthetic datasets and real application traces, demonstrating our methodology's advantage over traditional SBPP optimal solver minimizing the number of used machines, with a low rate of resource violations.

math.OC↗

arXiv2022

Selective clustering ensemble based on kappa and F-score

Clustering ensemble has an impressive performance in improving the accuracy and robustness of partition results and has received much attention in recent years. Selective clustering ensemble (SCE) can further improve the ensemble performance by selecting base partitions or clusters in according to diversity and stability. However, there is a conflict between diversity and stability, and how to make the trade-off between the two is challenging. The key here is how to evaluate the quality of the base partitions and clusters. In this paper, we propose a new evaluation method for partitions and clusters using kappa and F-score, leading to a new SCE method, which uses kappa to select informative base partitions and uses F-score to weight clusters based on stability. The effectiveness and efficiency of the proposed method is empirically validated over real datasets.

cs.LG↗

arXiv2021

A Surrogate Objective Framework for Prediction+Optimization with Soft Constraints

Prediction+optimization is a common real-world paradigm where we have to predict problem parameters before solving the optimization problem. However, the criteria by which the prediction model is trained are often inconsistent with the goal of the downstream optimization problem. Recently, decision-focused prediction approaches, such as SPO+ and direct optimization, have been proposed to fill this gap. However, they cannot directly handle the soft constraints with the $max$ operator required in many real-world objectives. This paper proposes a novel analytically differentiable surrogate objective framework for real-world linear and semi-definite negative quadratic programming problems with soft linear and non-negative hard constraints. This framework gives the theoretical bounds on constraints' multipliers, and derives the closed-form solution with respect to predictive parameters and thus gradients for any variable in the problem. We evaluate our method in three applications extended with soft constraints: synthetic linear programming, portfolio optimization, and resource provisioning, demonstrating that our method outperforms traditional two-staged methods and other decision-focused approaches.

cs.LG↗

arXiv2021

Kinetic Energy Distribution of Fragments for Thermal Neutron-Induced $^{235}$U and $^{239}$Pu Fission Reactions

Focused on the generation and evolution of vast complementary pairs of the primary fission fragments at scission moment, Dinuclear and Statistical Model (DSM) is proposed. (1) It is assumed that the fissile nucleus elongates along a symmetric coaxis until it breaks into two primary fission fragments. (2) Every complementary pair of the primary fission fragments is approximatively described as two ellipsoids with large deformation at scission moment. (3) The kinetic energy in every complementary pair of the primary fragments is mainly provided by Coulomb repulsion, which is explicitly expressed through strict six-dimensional integrals. (4) Only three phenomenological coefficients are obtained to globally describe the quadrupole deformation parameters of arbitrary primary fragments both for $^{235}$U($n_{th}, f$) and $^{239}$Pu($n_{th}, f$) reactions, on the basis of the common characteristics of the measured data, such as mass and charge distributions, kinetic energy distributions. In the framework of DSM, the explicit average total kinetic energy distribution $\overline{TKE}(A)$ and the average kinetic energy distribution $\overline{KE}(A)$ are consistently represented. The theoretical results in this paper agree well with the experimental data. Furthermore, this model is expected as the reliable approach to generally evaluate the corresponding observebles for thermal neutron-induced fission of actinides.

nucl-th↗

arXiv2018

Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions

Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA-protein interactions are still not completely understood due to the lack of systematic theoretical methods able to efficiently interpret complex experimental observations. To fill this gap, we have developed a general theoretical framework based on the transfer-matrix calculations that can be used to accurately describe behaviour of DNA-protein interactions under force and torque constraints. Potential applications of the constructed theoretical approach are demonstrated by predicting how these constraints affect the DNA-binding properties of different types of architectural proteins. Obtained results provide important insights into potential physiological functions of mechanical forces in the chromosomal DNA organization by architectural proteins as well as into single-DNA manipulation studies of DNA-protein interactions.

q-bio.BM↗

arXiv2018

JSweep: A Patch-centric Data-driven Approach for Parallel Sweeps on Large-scale Meshes

In mesh-based numerical simulations, sweep is an important computation pattern. During sweeping a mesh, computations on cells are strictly ordered by data dependencies in given directions. Due to such a serial order, parallelizing sweep is challenging, especially for unstructured and deforming structured meshes. Meanwhile, recent high-fidelity multi-physics simulations of particle transport, including nuclear reactor and inertial confinement fusion, require {\em sweeps} on large scale meshes with billions of cells and hundreds of directions. In this paper, we present JSweep, a parallel data-driven computational framework integrated in the JAxMIN infrastructure. The essential of JSweep is a general patch-centric data-driven abstraction, coupled with a high performance runtime system leveraging hybrid parallelism of MPI+threads and achieving dynamic communication on contemporary multi-core clusters. Built on JSweep, we implement a representative data-driven algorithm, Sn transport, featuring optimizations of vertex clustering, multi-level priority strategy and patch-angle parallelism. Experimental evaluation with two real-world applications on structured and unstructured meshes respectively, demonstrates that JSweep can scale to tens of thousands of processor cores with reasonable parallel efficiency.

cs.DC↗

arXiv2018

Structural-elastic determination of the mechanical lifetime of biomolecules

The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical expression of the force-dependent molecular lifetime to understand transitions overcoming a single barrier. Unlike previous models derived in the framework of Kramers theory that requires a presumed one-dimensional free energy landscape, our model is derived based on the structural-elastic properties of molecules which is not restricted by the shape and dimensionality of the underlying free energy landscape. Importantly, the parameters of this model provide direct information of the structural-elastic features of the molecules between the transition and the native states. We demonstrate the applications of this model by applying it to explain complex force-dependent lifetime data for several molecules reported in recent experiments, and predict the structural-elastic properties of the transition states of these molecules.

physics.bio-ph↗

arXiv2015

Revisiting the anomalous bending elasticity of sharply bent DNA

Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question.

physics.bio-ph↗

arXiv2015

Automatic Prosody Prediction for Chinese Speech Synthesis using BLSTM-RNN and Embedding Features

Prosody affects the naturalness and intelligibility of speech. However, automatic prosody prediction from text for Chinese speech synthesis is still a great challenge and the traditional conditional random fields (CRF) based method always heavily relies on feature engineering. In this paper, we propose to use neural networks to predict prosodic boundary labels directly from Chinese characters without any feature engineering. Experimental results show that stacking feed-forward and bidirectional long short-term memory (BLSTM) recurrent network layers achieves superior performance over the CRF-based method. The embedding features learned from raw text further enhance the performance.

cs.CL↗

arXiv2013

GRE: A Graph Runtime Engine for Large-Scale Distributed Graph-Parallel Applications

Large-scale distributed graph-parallel computing is challenging. On one hand, due to the irregular computation pattern and lack of locality, it is hard to express parallelism efficiently. On the other hand, due to the scale-free nature, real-world graphs are hard to partition in balance with low cut. To address these challenges, several graph-parallel frameworks including Pregel and GraphLab (PowerGraph) have been developed recently. In this paper, we present an alternative framework, Graph Runtime Engine (GRE). While retaining the vertex-centric programming model, GRE proposes two new abstractions: 1) a Scatter-Combine computation model based on active message to exploit massive fined-grained edge-level parallelism, and 2) a Agent-Graph data model based on vertex factorization to partition and represent directed graphs. GRE is implemented on commercial off-the-shelf multi-core cluster. We experimentally evaluate GRE with three benchmark programs (PageRank, Single Source Shortest Path and Connected Components) on real-world and synthetic graphs of millions billion of vertices. Compared to PowerGraph, GRE shows 2.5~17 times better performance on 8~16 machines (192 cores). Specifically, the PageRank in GRE is the fastest when comparing to counterparts of other frameworks (PowerGraph, Spark,Twister) reported in public literatures. Besides, GRE significantly optimizes memory usage so that it can process a large graph of 1 billion vertices and 17 billion edges on our cluster with totally 768GB memory, while PowerGraph can only process less than half of this graph scale.

cs.DC↗

arXiv2009

Temperature dependence of circular DNA topological states

Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo simulation, we predict the temperature dependence of the linking number distribution of small circular DNAs. Our predictions are based on flexible defect excitations resulted from local melting or unstacking of DNA base pairs. We found that the reduced bending rigidity alone can lead to measurable changes of the variance of linking number distribution of short circular DNAs. If the defect is accompanied by local unwinding, the effect becomes much more prominent. The predictions can be easily investigated in experiments, providing a new method to study the micromechanics of sharply bent DNAs and the thermal stability of specific DNA sequences. Furthermore, the predictions are directly applicable to the studies of binding of DNA distorting proteins that can locally reduce DNA rigidity, form DNA kinks, or introduce local unwinding.

q-bio.BM↗

arXiv2008

Effects of kink and flexible hinge defects on mechanical responses of short double stranded DNA molecules

We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible polymer model. The defects discussed are kinks and flexible hinges either permanently fixed on DNA or thermally excited. Their effects on extension shift, the effective persistence length, the end-to-end distance distribution, and the cyclization probability are computed using a transfer-matrix method. Our predictions will be useful in future experimental designs to study DNA nicks or mismatch base pairs, mechanics of specific DNA sequences, and specific DNA-protein interaction using magnetic tweezer, fluorescence resonance energy transfer or plasmon resonance technique, and the traditional biochemistry cyclization probability measurements.

q-bio.BM↗