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Can Chen

Publications and source records attributed to Can Chen.

At least 73 records · Page 4Linked to original sources

Parallel-mentoring for Offline Model-based Optimization

We study offline model-based optimization to maximize a black-box objective function with a static dataset of designs and scores. These designs encompass a variety of domains, including materials, robots and DNA sequences. A common approach trains a proxy on the static dataset to approximate the black-box objective function and performs gradient ascent to obtain new designs. However, this often results in poor designs due to the proxy inaccuracies for out-of-distribution designs. Recent studies indicate that: (a) gradient ascent with a mean ensemble of proxies generally outperforms simple gradient ascent, and (b) a trained proxy provides weak ranking supervision signals for design selection. Motivated by (a) and (b), we propose \textit{parallel-mentoring} as an effective and novel method that facilitates mentoring among parallel proxies, creating a more robust ensemble to mitigate the out-of-distribution issue. We focus on the three-proxy case and our method consists of two modules. The first module, \textit{voting-based pairwise supervision}, operates on three parallel proxies and captures their ranking supervision signals as pairwise comparison labels. These labels are combined through majority voting to generate consensus labels, which incorporate ranking supervision signals from all proxies and enable mutual mentoring. However, label noise arises due to possible incorrect consensus. To alleviate this, we introduce an \textit{adaptive soft-labeling} module with soft-labels initialized as consensus labels. Based on bi-level optimization, this module fine-tunes proxies in the inner level and learns more accurate labels in the outer level to adaptively mentor proxies, resulting in a more robust ensemble. Experiments validate the effectiveness of our method. Our code is available here.

cs.CE↗

Importance-aware Co-teaching for Offline Model-based Optimization

Offline model-based optimization aims to find a design that maximizes a property of interest using only an offline dataset, with applications in robot, protein, and molecule design, among others. A prevalent approach is gradient ascent, where a proxy model is trained on the offline dataset and then used to optimize the design. This method suffers from an out-of-distribution issue, where the proxy is not accurate for unseen designs. To mitigate this issue, we explore using a pseudo-labeler to generate valuable data for fine-tuning the proxy. Specifically, we propose \textit{\textbf{I}mportance-aware \textbf{C}o-\textbf{T}eaching for Offline Model-based Optimization}~(\textbf{ICT}). This method maintains three symmetric proxies with their mean ensemble as the final proxy, and comprises two steps. The first step is \textit{pseudo-label-driven co-teaching}. In this step, one proxy is iteratively selected as the pseudo-labeler for designs near the current optimization point, generating pseudo-labeled data. Subsequently, a co-teaching process identifies small-loss samples as valuable data and exchanges them between the other two proxies for fine-tuning, promoting knowledge transfer. This procedure is repeated three times, with a different proxy chosen as the pseudo-labeler each time, ultimately enhancing the ensemble performance. To further improve accuracy of pseudo-labels, we perform a secondary step of \textit{meta-learning-based sample reweighting}, which assigns importance weights to samples in the pseudo-labeled dataset and updates them via meta-learning. ICT achieves state-of-the-art results across multiple design-bench tasks, achieving the best mean rank of $3.1$ and median rank of $2$, among $15$ methods. Our source code can be found here.

cs.CE↗

Gradient-based Bi-level Optimization for Deep Learning: A Survey

Bi-level optimization, especially the gradient-based category, has been widely used in the deep learning community including hyperparameter optimization and meta-knowledge extraction. Bi-level optimization embeds one problem within another and the gradient-based category solves the outer-level task by computing the hypergradient, which is much more efficient than classical methods such as the evolutionary algorithm. In this survey, we first give a formal definition of the gradient-based bi-level optimization. Next, we delineate criteria to determine if a research problem is apt for bi-level optimization and provide a practical guide on structuring such problems into a bi-level optimization framework, a feature particularly beneficial for those new to this domain. More specifically, there are two formulations: the single-task formulation to optimize hyperparameters such as regularization parameters and the distilled data, and the multi-task formulation to extract meta-knowledge such as the model initialization. With a bi-level formulation, we then discuss four bi-level optimization solvers to update the outer variable including explicit gradient update, proxy update, implicit function update, and closed-form update. Finally, we wrap up the survey by highlighting two prospective future directions: (1) Effective Data Optimization for Science examined through the lens of task formulation. (2) Accurate Explicit Proxy Update analyzed from an optimization standpoint.

cs.LG↗

Bidirectional Learning for Offline Model-based Biological Sequence Design

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module \textit{Adaptive}-$η$, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~\href{https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md}{here.}

cs.CE↗

Structure-aware Protein Self-supervised Learning

Protein representation learning methods have shown great potential to yield useful representation for many downstream tasks, especially on protein classification. Moreover, a few recent studies have shown great promise in addressing insufficient labels of proteins with self-supervised learning methods. However, existing protein language models are usually pretrained on protein sequences without considering the important protein structural information. To this end, we propose a novel structure-aware protein self-supervised learning method to effectively capture structural information of proteins. In particular, a well-designed graph neural network (GNN) model is pretrained to preserve the protein structural information with self-supervised tasks from a pairwise residue distance perspective and a dihedral angle perspective, respectively. Furthermore, we propose to leverage the available protein language model pretrained on protein sequences to enhance the self-supervised learning. Specifically, we identify the relation between the sequential information in the protein language model and the structural information in the specially designed GNN model via a novel pseudo bi-level optimization scheme. Experiments on several supervised downstream tasks verify the effectiveness of our proposed method.The code of the proposed method is available in \url{https://github.com/GGchen1997/STEPS_Bioinformatics}.

cs.LG↗

Bidirectional Learning for Offline Infinite-width Model-based Optimization

In offline model-based optimization, we strive to maximize a black-box objective function by only leveraging a static dataset of designs and their scores. This problem setting arises in numerous fields including the design of materials, robots, DNA sequences, and proteins. Recent approaches train a deep neural network (DNN) on the static dataset to act as a proxy function, and then perform gradient ascent on the existing designs to obtain potentially high-scoring designs. This methodology frequently suffers from the out-of-distribution problem where the proxy function often returns poor designs. To mitigate this problem, we propose BiDirectional learning for offline Infinite-width model-based optimization (BDI). BDI consists of two mappings: the forward mapping leverages the static dataset to predict the scores of the high-scoring designs, and the backward mapping leverages the high-scoring designs to predict the scores of the static dataset. The backward mapping, neglected in previous work, can distill more information from the static dataset into the high-scoring designs, which effectively mitigates the out-of-distribution problem. For a finite-width DNN model, the loss function of the backward mapping is intractable and only has an approximate form, which leads to a significant deterioration of the design quality. We thus adopt an infinite-width DNN model, and propose to employ the corresponding neural tangent kernel to yield a closed-form loss for more accurate design updates. Experiments on various tasks verify the effectiveness of BDI. The code is available at https://github.com/GGchen1997/BDI.

cs.CE↗

Hypergraph Analysis Toolbox for Chromosome Conformation

Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions. Hypergraphs are mathematically tractable objects that can be utilized to precisely represent and analyze multi-way interactions. Here we present the Hypergraph Analysis Toolbox (HAT), a software package for visualization and analysis of multi-way interactions in complex systems.

q-bio.QM↗

Graph Convolutional Network-based Feature Selection for High-dimensional and Low-sample Size Data

Feature selection is a powerful dimension reduction technique which selects a subset of relevant features for model construction. Numerous feature selection methods have been proposed, but most of them fail under the high-dimensional and low-sample size (HDLSS) setting due to the challenge of overfitting. In this paper, we present a deep learning-based method - GRAph Convolutional nEtwork feature Selector (GRACES) - to select important features for HDLSS data. We demonstrate empirical evidence that GRACES outperforms other feature selection methods on both synthetic and real-world datasets.

cs.LG↗

The 100-m X-ray Test Facility at IHEP

The 100-m X-ray Test Facility of the Institute of High Energy Physics (IHEP) was initially proposed in 2012 for the test and calibration of the X-ray detectors of the Hard X-ray Modulation Telescope (HXMT) with the capability to support future X-ray missions. The large instrument chamber connected with a long vacuum tube can accommodate the X-ray mirror, focal plane detector and other instruments. The X-ray sources are installed at the other end of the vacuum tube with a distance of 105 m, which can provide an almost parallel X-ray beam covering 0.2$\sim$60 keV energy band. The X-ray mirror modules of the Einstein Probe (EP) and the enhanced X-ray Timing and Polarimetry mission (eXTP) and payload of the Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor (GECAM) have been tested and calibrated with this facility. It has been also used to characterize the focal plane camera and aluminum filter used on the Einstein Probe. In this paper, we will introduce the overall configuration and capability of the facility, and give a brief introduction of some calibration results performed with this facility.

astro-ph.IM↗

Explicit Solutions and Stability Properties of Homogeneous Polynomial Dynamical Systems

In this paper, we provide a system-theoretic treatment of certain continuous-time homogeneous polynomial dynamical systems (HPDS) via tensor algebra. In particular, if a system of homogeneous polynomial differential equations can be represented by an orthogonally decomposable (odeco) tensor, we can construct its explicit solution by exploiting tensor Z-eigenvalues and Z-eigenvectors. We refer to such HPDS as odeco HPDS. By utilizing the form of the explicit solution, we are able to discuss the stability properties of an odeco HPDS. We illustrate that the Z-eigenvalues of the corresponding dynamic tensor can be used to establish necessary and sufficient stability conditions, similar to these from linear systems theory. In addition, we are able to obtain the complete solution to an odeco HPDS with constant control. Finally, we establish results which enable one to determine if a general HPDS can be transformed to or approximated by an odeco HPDS, where the previous results can be applied. We demonstrate our framework with simulated and real-world examples.

math.DS↗

A Survey on Hyperlink Prediction

As a natural extension of link prediction on graphs, hyperlink prediction aims for the inference of missing hyperlinks in hypergraphs, where a hyperlink can connect more than two nodes. Hyperlink prediction has applications in a wide range of systems, from chemical reaction networks, social communication networks, to protein-protein interaction networks. In this paper, we provide a systematic and comprehensive survey on hyperlink prediction. We propose a new taxonomy to classify existing hyperlink prediction methods into four categories: similarity-based, probability-based, matrix optimization-based, and deep learning-based methods. To compare the performance of methods from different categories, we perform a benchmark study on various hypergraph applications using representative methods from each category. Notably, deep learning-based methods prevail over other methods in hyperlink prediction.

cs.LG↗

SPENDER: A Platform for Secure and Privacy-Preserving Decentralized P2P E-Commerce

The blockchain technology empowers secure, trustless, and privacy-preserving trading with cryptocurrencies. However, existing blockchain-based trading platforms only support trading cryptocurrencies with digital assets (e.g., NFTs). Although several payment service providers have started to accept cryptocurrency as a payment method for tangible goods (e.g., Visa, PayPal), customers still need to trust and hand over their private information to centralized E-commerce platforms (e.g., Amazon, eBay). To enable trustless and privacy-preserving trading between cryptocurrencies and real goods, we propose SPENDER, a smart-contract-based platform for Secure and Privacy-PresErviNg Decentralized P2P E-commeRce. The design of our platform enables various advantageous features and brings unlimited future potential. Moreover, our platform provides a complete paradigm for designing real-world Web3 infrastructures on the blockchain, which broadens the application scope and exploits the intrinsic values of cryptocurrencies. The platform has been built and tested on the Terra ecosystem, and we plan to open-source the code later.

cs.CR↗

Unbiased Implicit Feedback via Bi-level Optimization

Implicit feedback is widely leveraged in recommender systems since it is easy to collect and provides weak supervision signals. Recent works reveal a huge gap between the implicit feedback and user-item relevance due to the fact that implicit feedback is also closely related to the item exposure. To bridge this gap, existing approaches explicitly model the exposure and propose unbiased estimators to improve the relevance. Unfortunately, these unbiased estimators suffer from the high gradient variance, especially for long-tail items, leading to inaccurate gradient updates and degraded model performance. To tackle this challenge, we propose a low-variance unbiased estimator from a probabilistic perspective, which effectively bounds the variance of the gradient. Unlike previous works which either estimate the exposure via heuristic-based strategies or use a large biased training set, we propose to estimate the exposure via an unbiased small-scale validation set. Specifically, we first parameterize the user-item exposure by incorporating both user and item information, and then construct an unbiased validation set from the biased training set. By leveraging the unbiased validation set, we adopt bi-level optimization to automatically update exposure-related parameters along with recommendation model parameters during the learning. Experiments on two real-world datasets and two semi-synthetic datasets verify the effectiveness of our method.

cs.IR↗

On the Stability of Multilinear Dynamical Systems

This paper investigates the stability properties of discrete-time multilinear dynamical systems via tensor spectral theory. In particular, if the dynamic tensor of a multilinear dynamical system is orthogonally decomposable (odeco), we can construct its explicit solution by exploiting tensor Z-eigenvalues and Z-eigenvectors. Based on the form of the explicit solution, we illustrate that the Z-eigenvalues of the dynamic tensor play a significant role in the stability analysis, offering necessary and sufficient conditions. In addition, by utilizing the upper bounds of Z-spectral radii, we are able to determine the asymptotic stability of the multilinear dynamical system efficiently. Furthermore, we extend the stability results to the multilinear dynamical systems with non-odeco dynamic tensors by exploiting tensor singular values. We demonstrate our results via numerical examples.

math.OC↗

The In-Flight Realtime Trigger and Localization Software of GECAM

Realtime trigger and localization of bursts are the key functions of GECAM, which is an all-sky gamma-ray monitor launched in Dec 10, 2020. We developed a multifunctional trigger and localization software operating on the CPU of the GECAM electronic box (EBOX). This onboard software has the following features: high trigger efficiency for real celestial bursts with a suppression of false triggers caused by charged particle bursts and background fluctuation, dedicated localization algorithm optimized for short and long bursts respetively, short time latency of the trigger information which is downlinked throught the BeiDou satellite navigation System (BDS). This paper presents the detailed design and deveopment of this trigger and localization software system of GECAM, including the main functions, general design, workflow and algorithms, as well as the verification and demonstration of this software, including the on-ground trigger tests with simulated gamma-ray bursts made by a dedicated X-ray tube and the in-flight performance to real gamma-ray bursts and magnetar bursts.

astro-ph.IM↗

Performance of a focal plane detector for soft X-ray imaging spectroscopy based on back-illuminated sCMOS

Spectroscopy focusing array (SFA) and Polarimetry focusing array (PFA) are the two major payloads of enhanced X-ray Timing and Polarimetry mission (eXTP). Nested Wolter-\RNum{1} X-ray mirror module is implemented in SFA and PFA to achive high effective area. When evaluating the properties of the mirror module, the alignment of the optical axis of the X-ray mirror module and a quasi-parallel X-ray beam is a prerequisite to ensure the accuracy of the results. Hence, to assist the alignment of the X-ray mirror module, an X-ray focal plane detector is designed based on the back-illuminated scientific Complementary Metal-Oxide-Semiconductor Transistor (sCMOS) sensor GSENSE6060BSI, one of the largest detection areas, is produced by \textit{Gpixel Inc}. Then the characteristics of readout noise, dark current, and split-pixel event properties of the detector are studied with the self-developed multi-target fluorescence X-ray source in a 100 m long X-ray test facility. The energy calibration is carried out with the single-pixel event and the energy non-linearity of the detector is also obtained. Eventually, the simulation of the eXTP mirror module based on the optical model is conducted and the alignment test of the Wolter-\RNum{1} X-ray mirror module designed for \textit{EP/FXT} (Einstein Probe/Follow-up X-ray Telescope) with "Burkert test" method is shown.

physics.ins-det↗

Generalized Data Weighting via Class-level Gradient Manipulation

Label noise and class imbalance are two major issues coexisting in real-world datasets. To alleviate the two issues, state-of-the-art methods reweight each instance by leveraging a small amount of clean and unbiased data. Yet, these methods overlook class-level information within each instance, which can be further utilized to improve performance. To this end, in this paper, we propose Generalized Data Weighting (GDW) to simultaneously mitigate label noise and class imbalance by manipulating gradients at the class level. To be specific, GDW unrolls the loss gradient to class-level gradients by the chain rule and reweights the flow of each gradient separately. In this way, GDW achieves remarkable performance improvement on both issues. Aside from the performance gain, GDW efficiently obtains class-level weights without introducing any extra computational cost compared with instance weighting methods. Specifically, GDW performs a gradient descent step on class-level weights, which only relies on intermediate gradients. Extensive experiments in various settings verify the effectiveness of GDW. For example, GDW outperforms state-of-the-art methods by $2.56\%$ under the $60\%$ uniform noise setting in CIFAR10. Our code is available at https://github.com/GGchen1997/GDW-NIPS2021.

cs.CV↗

Design and test of a portable Gamma-Ray Burst simulator for GECAM

The main scientific goal of the Gravitational wave high-energy Electromagnetic Counterpart All-sky Monitor (GECAM) is to monitor various types of Gamma-Ray Bursts (GRB) originated from merger of binary compact stars, which could also produce gravitational wave, and collapse of massive stars. In order to study the response of GECAM Gamma-Ray Detectors (GRDs) to high-energy bursts and test the in-flight trigger and localization software of GECAM before the launch, a portable GRB simulator device is designed and implemented based on grid controlled X-ray tube (GCXT) and direct digital synthesis (DDS) technologies. The design of this GRB simulator which modulates X-ray flux powered by high voltage up to 20 kV is demonstrated, and the time jitter (FWHM) of the device is about 0.9 $μ$s. Before the launch in December, 2020, both two GECAM satellites were irradiated by different types of GRBs (including short and long bursts in duration) generated by this GRB simulator. The light curves detected with GECAM/GRDs are consistent with the programmed input functions within statistical uncertainties, indicating the good performance of both the GRDs and the GRB simulator.

physics.ins-det↗