arXiv subjects

Min Lu

Publications and source records attributed to Min Lu.

29 records · Page 2Linked to original sources

arXiv2023

Predicting RNA Secondary Structure on Universal Quantum Computer

It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while learning-based algorithms face challenges in obtaining high-quality training data. Recently, quantum annealer has rapidly predicted the folding of the secondary structure, highlighting that quantum computing is a promising solution to this problem. However, gate model algorithms for universal quantum computing are not available. In this paper, gate-based quantum algorithms will be presented, which are highly flexible and can be applied to various physical devices. Mapped all possible secondary structure to the state of a quadratic Hamiltonian, the whole folding process is described as a quadratic unconstrained binary optimization model. Then the model can be solved through quantum approximation optimization algorithm. We demonstrate the performance with both numerical simulation and experimental realization. Throughout our benchmark dataset, simulation results suggest that our quantum approach is comparable in accuracy to classical methods. For non-nested sequences, our quantum approach outperforms classical energy-based methods. Experimental results also indicate our method is robust in current noisy devices. It is the first instance of universal quantum algorithms being employed to tackle RNA folding problems, and our work provides a valuable model for utilizing universal quantum computers in solving RNA folding problems.

quant-ph↗

arXiv2022

HiTailor: Interactive Transformation and Visualization for Hierarchical Tabular Data

Tabular visualization techniques integrate visual representations with tabular data to avoid additional cognitive load caused by splitting users' attention. However, most of the existing studies focus on simple flat tables instead of hierarchical tables, whose complex structure limits the expressiveness of visualization results and affects users' efficiency in visualization construction. We present HiTailor, a technique for presenting and exploring hierarchical tables. HiTailor constructs an abstract model, which defines row/column headings as biclustering and hierarchical structures. Based on our abstract model, we identify three pairs of operators, Swap/Transpose, ToStacked/ToLinear, Fold/Unfold, for transformations of hierarchical tables to support users' comprehensive explorations. After transformation, users can specify a cell or block of interest in hierarchical tables as a TableUnit for visualization, and HiTailor recommends other related TableUnits according to the abstract model using different mechanisms. We demonstrate the usability of the HiTailor system through a comparative study and a case study with domain experts, showing that HiTailor can present and explore hierarchical tables from different viewpoints. HiTailor is available at https://github.com/bitvis2021/HiTailor.

cs.HC↗

arXiv2021

Follow the Prophet: Accurate Online Conversion Rate Prediction in the Face of Delayed Feedback

The delayed feedback problem is one of the imperative challenges in online advertising, which is caused by the highly diversified feedback delay of a conversion varying from a few minutes to several days. It is hard to design an appropriate online learning system under these non-identical delay for different types of ads and users. In this paper, we propose to tackle the delayed feedback problem in online advertising by "Following the Prophet" (FTP for short). The key insight is that, if the feedback came instantly for all the logged samples, we could get a model without delayed feedback, namely the "prophet". Although the prophet cannot be obtained during online learning, we show that we could predict the prophet's predictions by an aggregation policy on top of a set of multi-task predictions, where each task captures the feedback patterns of different periods. We propose the objective and optimization approach for the policy, and use the logged data to imitate the prophet. Extensive experiments on three real-world advertising datasets show that our method outperforms the previous state-of-the-art baselines.

cs.LG↗

arXiv2021

Clusterplot: High-dimensional Cluster Visualization

We present Clusterplot, a multi-class high-dimensional data visualization tool designed to visualize cluster-level information offering an intuitive understanding of the cluster inter-relations. Our unique plots leverage 2D blobs devised to convey the geometrical and topological characteristics of clusters within the high-dimensional data, and their pairwise relations, such that general inter-cluster behavior is easily interpretable in the plot. Class identity supervision is utilized to drive the measuring of relations among clusters in high-dimension, particularly, proximity and overlap, which are then reflected spatially through the 2D blobs. We demonstrate the strength of our clusterplots and their ability to deliver a clear and intuitive informative exploration experience for high-dimensional clusters characterized by complex structure and significant overlap.

cs.GR↗

arXiv2020

Dynamic Competing Risk Modeling COVID-19 in a Pandemic Scenario

The emergence of coronavirus disease 2019 (COVID-19) in the United States has forced federal and local governments to implement containment measures. Moreover, the severity of the situation has sparked engagement by both the research and clinical community with the goal of developing effective treatments for the disease. This article proposes a time dynamic prediction model with competing risks for the infected individual and develops a simple tool for policy makers to compare different strategies in terms of when to implement the strictest containment measures and how different treatments can increase or suppress infected cases. Two types of containment strategies are compared: (1) a constant containment strategy that could satisfy the needs of citizens for a long period; and (2) an adaptive containment strategy whose strict level changes across time. We consider how an effective treatment of the disease can affect the dynamics in a pandemic scenario. For illustration we consider a region with population 2.8 million and 200 initial infectious cases assuming a 4% mortality rate compared with a 2% mortality rate if a new drug is available. Our results show compared with a constant containment strategy, adaptive containment strategies shorten the outbreak length and reduce maximum daily number of cases. This, along with an effective treatment plan for the disease can minimize death rate.

q-bio.PE↗

arXiv2020

Field-aware Calibration: A Simple and Empirically Strong Method for Reliable Probabilistic Predictions

It is often observed that the probabilistic predictions given by a machine learning model can disagree with averaged actual outcomes on specific subsets of data, which is also known as the issue of miscalibration. It is responsible for the unreliability of practical machine learning systems. For example, in online advertising, an ad can receive a click-through rate prediction of 0.1 over some population of users where its actual click rate is 0.15. In such cases, the probabilistic predictions have to be fixed before the system can be deployed. In this paper, we first introduce a new evaluation metric named field-level calibration error that measures the bias in predictions over the sensitive input field that the decision-maker concerns. We show that existing post-hoc calibration methods have limited improvements in the new field-level metric and other non-calibration metrics such as the AUC score. To this end, we propose Neural Calibration, a simple yet powerful post-hoc calibration method that learns to calibrate by making full use of the field-aware information over the validation set. We present extensive experiments on five large-scale datasets. The results showed that Neural Calibration significantly improves against uncalibrated predictions in common metrics such as the negative log-likelihood, Brier score and AUC, as well as the proposed field-level calibration error.

cs.LG↗

arXiv2017

A Machine Learning Alternative to P-values

This paper presents an alternative approach to p-values in regression settings. This approach, whose origins can be traced to machine learning, is based on the leave-one-out bootstrap for prediction error. In machine learning this is called the out-of-bag (OOB) error. To obtain the OOB error for a model, one draws a bootstrap sample and fits the model to the in-sample data. The out-of-sample prediction error for the model is obtained by calculating the prediction error for the model using the out-of-sample data. Repeating and averaging yields the OOB error, which represents a robust cross-validated estimate of the accuracy of the underlying model. By a simple modification to the bootstrap data involving "noising up" a variable, the OOB method yields a variable importance (VIMP) index, which directly measures how much a specific variable contributes to the prediction precision of a model. VIMP provides a scientifically interpretable measure of the effect size of a variable, we call the "predictive effect size", that holds whether the researcher's model is correct or not, unlike the p-value whose calculation is based on the assumed correctness of the model. We also discuss a marginal VIMP index, also easily calculated, which measures the marginal effect of a variable, or what we call "the discovery effect". The OOB procedure can be applied to both parametric and nonparametric regression models and requires only that the researcher can repeatedly fit their model to bootstrap and modified bootstrap data. We illustrate this approach on a survival data set involving patients with systolic heart failure and to a simulated survival data set where the model is incorrectly specified to illustrate its robustness to model misspecification.

stat.ML↗

arXiv2017

Estimating Individual Treatment Effect in Observational Data Using Random Forest Methods

Estimation of individual treatment effect in observational data is complicated due to the challenges of confounding and selection bias. A useful inferential framework to address this is the counterfactual (potential outcomes) model which takes the hypothetical stance of asking what if an individual had received both treatments. Making use of random forests (RF) within the counterfactual framework we estimate individual treatment effects by directly modeling the response. We find accurate estimation of individual treatment effects is possible even in complex heterogeneous settings but that the type of RF approach plays an important role in accuracy. Methods designed to be adaptive to confounding, when used in parallel with out-of-sample estimation, do best. One method found to be especially promising is counterfactual synthetic forests. We illustrate this new methodology by applying it to a large comparative effectiveness trial, Project Aware, in order to explore the role drug use plays in sexual risk. The analysis reveals important connections between risky behavior, drug usage, and sexual risk.

stat.ML↗

arXiv2016

Emergent infinite-randomness fixed points from the extensive random bipartitions of the spin-1 Affleck-Kennedy-Lieb-Tasaki topological state

Quantum entanglement under an extensive bipartition can reveal the critical boundary theory of a topological phase in the parameter space. In this study we demonstrate that the infinite-randomness fixed point for spin-1/2 degrees of freedom can emerge from an extensive random bipartition of the spin-1 Affleck-Kennedy-Lieb-Tasaki chain. The nested entanglement entropy of the ground state of the reduced density matrix exhibits a logarithmic scaling with an effective central charge $\tilde{c} = 0.72 \pm 0.02 \approx \ln 2$. We further discuss, in the language of bulk quantum entanglement, how to understand all phase boundaries and the surrounding Griffiths phases for the antiferromagnetic Heisenberg spin-1 chain with quenched disorder and dimerization.

cond-mat.str-el↗

arXiv2013

Rotational Projection Statistics for 3D Local Surface Description and Object Recognition

Recognizing 3D objects in the presence of noise, varying mesh resolution, occlusion and clutter is a very challenging task. This paper presents a novel method named Rotational Projection Statistics (RoPS). It has three major modules: Local Reference Frame (LRF) definition, RoPS feature description and 3D object recognition. We propose a novel technique to define the LRF by calculating the scatter matrix of all points lying on the local surface. RoPS feature descriptors are obtained by rotationally projecting the neighboring points of a feature point onto 2D planes and calculating a set of statistics (including low-order central moments and entropy) of the distribution of these projected points. Using the proposed LRF and RoPS descriptor, we present a hierarchical 3D object recognition algorithm. The performance of the proposed LRF, RoPS descriptor and object recognition algorithm was rigorously tested on a number of popular and publicly available datasets. Our proposed techniques exhibited superior performance compared to existing techniques. We also showed that our method is robust with respect to noise and varying mesh resolution. Our RoPS based algorithm achieved recognition rates of 100%, 98.9%, 95.4% and 96.0% respectively when tested on the Bologna, UWA, Queen's and Ca' Foscari Venezia Datasets.

cs.CV↗

arXiv2011

Effects of gradient coupling on amplitude death in nonidentical oscillators

In this work, we investigate gradient coupling effect on amplitude death in an array of N cou- pled nonidentical oscillators with no-flux boundary conditions and periodic boundary conditions respectively. We find that the effects of gradient coupling on amplitude death in diffusive coupled nonidentical oscillators is quite different between those two boundaries conditions. With no-flux boundary conditions, there is a system size related critical gradient coupling $r_c$ within which the gradient coupling tends to monotonically enlarge the amplitude death domain in the parameter space. With the periodical boundary conditions, there is an optimal gradient coupling constant $r_o$ to realize largest AD domain. The gradient coupling first enlarges then decreases the amplitude death domain of diffusive coupled oscillators. The amplitude death domain of parameter space are analytically predicted for small number of gradient coupled oscillators.

nlin.CD↗