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Li Xing

Publications and source records attributed to Li Xing.

At least 19 recordsLinked to original sources

SVDq: 1.25-bit and 410x Key Cache Compression for LLM Attention

For the efficient inference of Large Language Models (LLMs), the effective compression of key-value (KV) cache is essential. Three main types of KV cache compression techniques, namely sparsity, channel compression, and quantization, have been identified. This study presents SVDq, a Singular Value Decomposition (SVD) - based mixed precision quantization method for K cache. Initially, K cache is transformed into latent channels using SVD basis representations. Since the values in latent channels decay rapidly and become negligible after only a few latent channels, our method then incorporates importance-aware quantization and compression for latent channels. This enables the effective allocation of higher precision to more significant channels. Theoretically, we prove that SVDq results in quantization errors (x0.1 or even lower) that are much lower than those of per-channel key quantization in the original space. Our findings based on RULER and LongBench benchmarks demonstrate that SVDq can achieve an equivalent key cache precision as low as 1.25-bit. When combined with key sparsity, it can reach a key compression ratio of up to 410x for attention computation, all while maintaining comparable model performance. Notably, our method is nearly lossless for LongBench datasets. This indicates that SVDq enables high-precision low-bit quantization, providing a more efficient solution for KV cache compression in LLMs.

cs.LG

Minor Issues Escalated to Critical Levels in Large Samples: A Permutation-Based Fix

In the big data era, the need to reevaluate traditional statistical methods is paramount due to the challenges posed by vast datasets. While larger samples theoretically enhance accuracy and hypothesis testing power without increasing false positives, practical concerns about inflated Type-I errors persist. The prevalent belief is that larger samples can uncover subtle effects, necessitating dual consideration of p-value and effect size. Yet, the reliability of p-values from large samples remains debated. This paper warns that larger samples can exacerbate minor issues into significant errors, leading to false conclusions. Through our simulation study, we demonstrate how growing sample sizes amplify issues arising from two commonly encountered violations of model assumptions in real-world data and lead to incorrect decisions. This underscores the need for vigilant analytical approaches in the era of big data. In response, we introduce a permutation-based test to counterbalance the effects of sample size and assumption discrepancies by neutralizing them between actual and permuted data. We demonstrate that this approach effectively stabilizes nominal Type I error rates across various sample sizes, thereby ensuring robust statistical inferences even amidst breached conventional assumptions in big data. For reproducibility, our R codes are publicly available at: \url{https://github.com/ubcxzhang/bigDataIssue}.

stat.ME

BOSS -- Biomarker Optimal Segmentation System

Motivation: Precision medicine is a major trend in the future of medicine. It aims to provide tailored medical treatment and prevention strategies based on an individual's unique characteristics and needs. Biomarker is the primary source of patients' unique features used in precision medicine. We often need to investigate many cutoff values of a continuous biomarker to find the optimal one and test if it can help segment patients into two groups with significantly different clinical outcomes. This requires multiple testing adjustments on tests conducted on overlapped data. The permutation-based approach is often a preferred solution, since it does not suffer the limitations of state-of-art theoretical methods. However, permutation is computationally expensive and limits its application scenarios, such as web applications requiring a fast response or the analysis of genomic study requiring to repeat analysis many times on tens of thousands of genes. Results: We proposed a novel method BOSS, Biomarker Optimal Segmentation System, to solve this problem. In simulation studies, we found BOSS's statistical power and type I error control are both non-inferior to the permutation approach, and it is hundreds of times faster than permutation. To illustrate our method, we applied BOSS to real data and revealed potentially converging biomarkers that have referential importance in exploring synergy and target-matched therapies in lung adenocarcinoma. Availability: An R package, boss, is being developed and will be available on CRAN

stat.ME

Proxy-based Super Twisting Control Algorithm for Aerial Manipulators

Aerial manipulators are composed of an aerial multi-rotor that is equipped with a 6-DOF servo robot arm. To achieve precise position and attitude control during the arm's motion, it is critical for the system to have high performance control capabilities. However, the coupling effect between the multi-rotor UAVs' movement poses a challenge to the entire system's control capability. We have proposed a new proxy-based super twisting control approach for quadrotor UAVs that mitigates the disturbance caused by moving manipulators. This approach helps improve the stability of the aerial manipulation system when carrying out hovering or trajectory tracking tasks. The controller's effectiveness has been validated through numerical simulation and further tested in the Gazebo simulation environment.

cs.RO

Temperature sensing using nitrogen-vacancy centers with multiple-poly crystal directions based on Zeeman splitting

We demonstrate a novel method based on the Zeeman splitting of electronic spins to improve the performance for temperature sensing of negatively-charged nitrogen-vacancy (NV) centers in multiple-poly diamond. The theoretical model for selection principle of resonance peaks corresponding to a single NV axis for determining the temperature dependence is clarified. The spectral linewidth is effectively narrowed and the thermometer is insensitive to magnetic field fluctuations. Repeatability and accuracy of the relationship calibration between the zero-field splitting (ZFS) parameter D and temperature T in the range of 298 K to 323 K is significantly improved, and the results of coefficient dD/dT is 75.33 kHz/K. Finally, this method promotes the average temperature measurement sensitivity (below 10 Hz) of our setup from 0.49 K/Hz1/2 to 0.22 K/Hz1/2.

quant-ph

Novel Modelling Strategies for High-frequency Stock Trading Data

Full electronic automation in stock exchanges has recently become popular, generating high-frequency intraday data and motivating the development of near real-time price forecasting methods. Machine learning algorithms are widely applied to mid-price stock predictions. Processing raw data as inputs for prediction models (e.g., data thinning and feature engineering) can primarily affect the performance of the prediction methods. However, researchers rarely discuss this topic. This motivated us to propose three novel modelling strategies for processing raw data. We illustrate how our novel modelling strategies improve forecasting performance by analyzing high-frequency data of the Dow Jones 30 component stocks. In these experiments, our strategies often lead to statistically significant improvement in predictions. The three strategies improve the F1 scores of the SVM models by 0.056, 0.087, and 0.016, respectively.

stat.AP

Dynamics of Fecal Coliform Bacteria along Canada's Coast

The vast coastline provides Canada with a flourishing seafood industry including bivalve shellfish production. To sustain a healthy bivalve molluscan shellfish production, the Canadian Shellfish Sanitation Program was established to monitor the health of shellfish harvesting habitats, and fecal coliform bacteria data have been collected at nearly 15,000 marine sample sites across six coastal provinces in Canada since 1979. We applied Functional Principal Component Analysis and subsequent correlation analyses to find annual variation patterns of bacteria levels at sites in each province. The overall magnitude and the seasonality of fecal contamination were modelled by functional principal component one and two, respectively. The amplitude was related to human and warm-blooded animal activities; the seasonality was strongly correlated with river discharge driven by precipitation and snow melt in British Columbia, but such correlation in provinces along the Atlantic coast could not be properly evaluated due to lack of data during winter.

stat.AP

Microwave heating effect on diamond sample of NV centers

Diamond samples of defects with negative charged nitrogen-vacancy (NV) centers are promising solid state spin sensors suitable for quantum information processing, high sensitive measurements of magnetic, electric and thermal fields in nanoscale. The diamond defect with a NV center is unique for its robust temperature-dependent zero field splitting Dgs of the triplet ground state. This property enables optical readout of electron spin states through manipulation of the ground triplet state using microwave resonance with Dgs from 100 K to about 600 K. Thus, prohibiting Dgs from unwanted external thermal disturbances is crucial for an accurate measurement using diamond NV sensors. Our observation demonstrates the existence of a prominent microwave heating effect on the diamond samples of NV centers. The effect is inevitable to shift Dgs and cause measurement errors. The temperature increment caused by the effect monotonically depends on the power and the duration of microwave irradiation. The effect is obvious with the microwave irradiation in the continuous mode and some pulse sequence modes, but is neglectable for the quantum lock-in XY8-N method.

cond-mat.mes-hall

A measurement method of transverse light-shift in atomic spin co-magnetometer

We disclose a method to obtain the transverse light-shift along the probe light of a single-axis alkali metal-noble gas co-magnetometer. The relationship between transverse compensating field and light-shift is deduced through the steady-state solution of Bloch equations. The variety of probe light intensity is used to obtain the residual magnetic field, and step modulation tests are applied to acquire the total spin-relaxation rate of electron spins and self-compensation point. Finally, the transverse light-shift is reduced from -0.115 nT to -0.039 nT by optimizing the probe light wavelength, and the value of the calibration coefficient can be increased simultaneously.

physics.app-ph

Temperature dependence of nitrogen-vacancy center ensembles in diamond based on an optical fiber

The nitrogen-vacancy (NV) centers in diamond sensing has been considered to be a promising micro-nano scale thermometer due to its high stability, good temperature resolution and integration. In this work, we fabricated the sensing core by attaching a diamond plate containing NV centers to the section of a cut-off multi-mode fiber. Then we measured the zero-field splitting parameter (D) of NV center ensembles using continuous-wave optical detected magnetic resonance (CW-ODMR) technique. A home-made thermostatic system and two calibrated platinum resistance thermometers were applied for reference temperature measurement. The effects from preparation time and count time in the pulse sequence, laser power, microwave power, and microwave frequency step were investigated. Moreover, the experimental D and T from 298.15 K to 383.15 K was obtained with the standard uncertainty of u(D) = (3.62268~8.54464)x10^-5 GHz and u(T) = (0.013~ 0.311) K. The experimental results are well consistent with the work of Toyli, et al. (Toyli, et al., 2012) using the similar diamond sample. The extrapolation for D-T at 0 K and 700 K also agree with other references, and meanwhile dD/dT varies with temperature. Finally, comparing the D-T relationship measured by different research groups, we can know that the NV concentration resulting in different electron density and manufacturing procedure resulting in different thermal expansion would lead to different D-T relationship. It is worthy to continue further comprehensive research especially from the metrological point of view to develop NV center as a practical and accurate micro-nano scale thermometry.

physics.app-ph

A systematic evaluation of methods for cell phenotype classification using single-cell RNA sequencing data

Background: Single-cell RNA sequencing (scRNA-seq) yields valuable insights about gene expression and gives critical information about complex tissue cellular composition. In the analysis of single-cell RNA sequencing, the annotations of cell subtypes are often done manually, which is time-consuming and irreproducible. Garnett is a cell-type annotation software based the on elastic net method. Besides cell-type annotation, supervised machine learning methods can also be applied to predict other cell phenotypes from genomic data. Despite the popularity of such applications, there is no existing study to systematically investigate the performance of those supervised algorithms in various sizes of scRNA-seq data sets. Methods and Results: This study evaluates 13 popular supervised machine learning algorithms to classify cell phenotypes, using published real and simulated data sets with diverse cell sizes. The benchmark contained two parts. In the first part, we used real data sets to assess the popular supervised algorithms' computing speed and cell phenotype classification performance. The classification performances were evaluated using AUC statistics, F1-score, precision, recall, and false-positive rate. In the second part, we evaluated gene selection performance using published simulated data sets with a known list of real genes. Conclusion: The study outcomes showed that ElasticNet with interactions performed best in small and medium data sets. NB was another appropriate method for medium data sets. In large data sets, XGB works excellent. Ensemble algorithms were not significantly superior to individual machine learning methods. Adding interactions to ElasticNet can help, and the improvement was significant in small data sets.

q-bio.GN

Multi-Stage Graph Peeling Algorithm for Probabilistic Core Decomposition

Mining dense subgraphs where vertices connect closely with each other is a common task when analyzing graphs. A very popular notion in subgraph analysis is core decomposition. Recently, Esfahani et al. presented a probabilistic core decomposition algorithm based on graph peeling and Central Limit Theorem (CLT) that is capable of handling very large graphs. Their proposed peeling algorithm (PA) starts from the lowest degree vertices and recursively deletes these vertices, assigning core numbers, and updating the degree of neighbour vertices until it reached the maximum core. However, in many applications, particularly in biology, more valuable information can be obtained from dense sub-communities and we are not interested in small cores where vertices do not interact much with others. To make the previous PA focus more on dense subgraphs, we propose a multi-stage graph peeling algorithm (M-PA) that has a two-stage data screening procedure added before the previous PA. After removing vertices from the graph based on the user-defined thresholds, we can reduce the graph complexity largely and without affecting the vertices in subgraphs that we are interested in. We show that M-PA is more efficient than the previous PA and with the properly set filtering threshold, can produce very similar if not identical dense subgraphs to the previous PA (in terms of graph density and clustering coefficient).

stat.ML

Handling highly correlated genes in prediction analysis of genomic studies

Background: Selecting feature genes to predict phenotypes is one of the typical tasks in analyzing genomics data. Though many general-purpose algorithms were developed for prediction, dealing with highly correlated genes in the prediction model is still not well addressed. High correlation among genes introduces technical problems, such as multi-collinearity issues, leading to unreliable prediction models. Furthermore, when a causal gene (whose variants have an actual biological effect on a phenotype) is highly correlated with other genes, most algorithms select the feature gene from the correlated group in a purely data-driven manner. Since the correlation structure among genes could change substantially when condition changes, the prediction model based on not correctly selected feature genes is unreliable. Therefore, we aim to keep the causal biological signal in the prediction process and build a more robust prediction model. Method: We propose a grouping algorithm, which treats highly correlated genes as a group and uses their common pattern to represent the group's biological signal in feature selection. Our novel grouping algorithm can be integrated into existing prediction algorithms to enhance their prediction performance. Our proposed grouping method has two advantages. First, using the gene group's common patterns makes the prediction more robust and reliable under condition change. Second, it reports whole correlated gene groups as discovered biomarkers for prediction tasks, allowing researchers to conduct follow-up studies to identify causal genes within the identified groups. Result: Using real benchmark scRNA-seq datasets with simulated cell phenotypes, we demonstrate our novel method significantly outperforms standard models in both (1) prediction of cell phenotypes and (2) feature gene selection.

stat.AP

The Optimal Design of Clinical Trials with Potential Biomarker Effects, A Novel Computational Approach

As a future trend of healthcare, personalized medicine tailors medical treatments to individual patients. It requires to identify a subset of patients with the best response to treatment. The subset can be defined by a biomarker (e.g. expression of a gene) and its cutoff value. Topics on subset identification have received massive attention. There are over 2 million hits by keyword searches on Google Scholar. However, how to properly incorporate the identified subsets/biomarkers to design clinical trials is not trivial and rarely discussed in the literature, which leads to a gap between research results and real-world drug development. To fill in this gap, we formulate the problem of clinical trial design into an optimization problem involving high-dimensional integration, and propose a novel computational solution based on Monte-Carlo and smoothing methods. Our method utilizes the modern techniques of General-Purpose computing on Graphics Processing Units for large-scale parallel computing. Compared to the standard method in three-dimensional problems, our approach is more accurate and 133 times faster. This advantage increases when dimensionality increases. Our method is scalable to higher-dimensional problems since the precision bound is a finite number not affected by dimensionality. Our software will be available on GitHub and CRAN, which can be applied to guide the design of clinical trials to incorporate the biomarker better. Although our research is motivated by the design of clinical trials, the method can be used widely to solve other optimization problems involving high-dimensional integration.

stat.ME

Optimal Study Design for Reducing Variances of Coefficient Estimators in Change-Point Models

In longitudinal studies, we observe measurements of the same variables at different time points to track the changes in their pattern over time. In such studies, scheduling of the data collection waves (i.e. time of participants' visits) is often pre-determined to accommodate ease of project management and compliance. Hence, it is common to schedule those visits at equally spaced time intervals. However, recent publications based on simulated experiments indicate that the power of studies and the precision of model parameter estimators is related to the participants' visiting schemes. In this paper, we consider the longitudinal studies that investigate the changing pattern of a disease outcome, (e.g. the accelerated cognitive decline of senior adults). Such studies are often analyzed by the broken-stick model, consisting of two segments of linear models connected at an unknown change-point. We formulate this design problem into a high-dimensional optimization problem and derive its analytical solution. Based on this solution, we propose an optimal design of the visiting scheme that maximizes the power (i.e. reduce the variance of estimators) to identify the onset of accelerated decline. Using both simulation studies and evidence from real data, we demonstrate our optimal design outperforms the standard equally-spaced design. Applying our novel design to plan the longitudinal studies, researchers can improve the power of detecting pattern change without collecting extra data.

stat.ME

Logistic Box-Cox Regression to Assess the Shape and Median Effect under Uncertainty about Model Specification

The shape of the relationship between a continuous exposure variable and a binary disease variable is often central to epidemiologic investigations. This paper investigates a number of issues surrounding inference and the shape of the relationship. Presuming that the relationship can be expressed in terms of regression coefficients and a shape parameter, we investigate how well the shape can be inferred in settings which might typify epidemiologic investigations and risk assessment. We also consider a suitable definition of the median effect of exposure, and investigate how precisely this can be inferred. This is done both in the case of using a model acknowledging uncertainty about the shape parameter and in the case of ignoring this uncertainty and using a two-step method, where in step one we transform the predictor and in step two we fit a simple linear model with transformed predictor. All these investigations require a family of exposure-disease relationships indexed by a shape parameter. For this purpose, we employ a family based on the Box-Cox transformation.

stat.ME

Simultaneous prediction of multiple outcomes using revised stacking algorithms

Motivation: HIV is difficult to treat because its virus mutates at a high rate and mutated viruses easily develop resistance to existing drugs. If the relationships between mutations and drug resistances can be determined from historical data, patients can be provided personalized treatment according to their own mutation information. The HIV Drug Resistance Database was built to investigate the relationships. Our goal is to build a model using data in this database, which simultaneously predicts the resistance of multiple drugs using mutation information from sequences of viruses for any new patient. Results: We propose two variations of a stacking algorithm which borrow information among multiple prediction tasks to improve multivariate prediction performance. The most attractive feature of our proposed methods is the flexibility with which complex multivariate prediction models can be constructed using any univariate prediction models. Using cross-validation studies, we show that our proposed methods outperform other popular multivariate prediction methods. Availability: An R package will be made available.

q-bio.QM

Closed-loop Control of Compensation Point in the K-Rb-$^{21}$Ne Comagnetometer

We investigate the real-time closed-loop control of compensation point in the K-Rb-$^{21}$Ne comagnetometer operated in the spin-exchange relaxation-free regime. By locking the electron resonance, the alkali metal electrons are free from the fluctuations of the longitudinal ambient magnetic field and nuclear magnetization, which could improve the systematic stability, enlarge the linear measuring range, and suppress the cross-talk error of the comagnetometer. This is the first demonstration of closed-loop control of magnetic field in the single nuclear species comagnetometer, which will be of great significance for rotation sensing as gyroscopes and other high precision metrology applications of the comagnetometer.

physics.atom-ph