arXiv subjects

Zhenming Liu

Publications and source records attributed to Zhenming Liu.

At least 19 recordsLinked to original sources

arXiv2026

On the Regularization Landscape for the Linear Recommendation Models

Recently, a wide range of recommendation algorithms inspired by deep learning techniques have emerged as the performance leaders on several standard recommendation benchmarks. While these algorithms were built on different DL techniques (e.g., dropouts, autoencoder), they have similar performance and even similar cost functions. This paper studies whether the models' comparable performance are sheer coincidence, or they can be unified under a single framework. We find that all linear performance leaders effectively add only a nuclear-norm based regularizer, or a Frobenius-norm based regularizer. The former ones possess a (surprising) rigid structure that limits the models' predictive power but their solutions are low rank and have closed form. The latter ones are more expressive and more efficient for recommendation but their solutions are either full-rank or require executing hard-to-tune numeric procedures such as ADMM. Along this line of finding, we further propose two low-rank, closed-form solutions, derived from carefully generalizing Frobenius-norm based regularizers. The new solutions get the best of both nuclear-norm and Frobenius-norm world.

cs.AI↗

arXiv2025

Pretraining a Foundation Model for Small-Molecule Natural Products

Natural products, as metabolites from microorganisms, animals, or plants, exhibit diverse biological activities, making them crucial for drug discovery. Nowadays, existing deep learning methods for natural products research primarily rely on supervised learning approaches designed for specific downstream tasks. However, such one-model-for-a-task paradigm often lacks generalizability and leaves significant room for performance improvement. Additionally, existing molecular characterization methods are not well-suited for the unique tasks associated with natural products. To address these limitations, we have pre-trained a foundation model for natural products based on their unique properties. Our approach employs a novel pretraining strategy that is especially tailored to natural products. By incorporating contrastive learning and masked graph learning objectives, we emphasize evolutional information from molecular scaffolds while capturing side-chain information. Our framework achieves state-of-the-art (SOTA) results in various downstream tasks related to natural product mining and drug discovery. We first compare taxonomy classification with synthesized molecule-focused baselines to demonstrate that current models are inadequate for understanding natural synthesis. Furthermore, by diving into a fine-grained analysis at both the gene and microbial levels, NaFM demonstrates the ability to capture evolutionary information. Eventually, our method is experimented with virtual screening, illustrating informative natural product representations that can lead to more effective identification of potential drug candidates.

q-bio.QM↗

arXiv2024

MEMS Gyroscope Multi-Feature Calibration Using Machine Learning Technique

Gyroscopes are crucial for accurate angular velocity measurements in navigation, stabilization, and control systems. MEMS gyroscopes offer advantages like compact size and low cost but suffer from errors and inaccuracies that are complex and time varying. This study leverages machine learning (ML) and uses multiple signals of the MEMS resonator gyroscope to improve its calibration. XGBoost, known for its high predictive accuracy and ability to handle complex, non-linear relationships, and MLP, recognized for its capability to model intricate patterns through multiple layers and hidden dimensions, are employed to enhance the calibration process. Our findings show that both XGBoost and MLP models significantly reduce noise and enhance accuracy and stability, outperforming the traditional calibration techniques. Despite higher computational costs, DL models are ideal for high-stakes applications, while ML models are efficient for consumer electronics and environmental monitoring. Both ML and DL models demonstrate the potential of advanced calibration techniques in enhancing MEMS gyroscope performance and calibration efficiency.

cs.LG↗

arXiv2024

Development and Evaluation Study of Intelligent Cockpit in the Age of Large Models

The development of Artificial Intelligence (AI) Large Models has a great impact on the application development of automotive Intelligent cockpit. The fusion development of Intelligent Cockpit and Large Models has become a new growth point of user experience in the industry, which also creates problems for related scholars, practitioners and users in terms of their understanding and evaluation of the user experience and the capability characteristics of the Intelligent Cockpit Large Models (ICLM). This paper aims to analyse the current situation of Intelligent cockpit, large model and AI Agent, to reveal the key of application research focuses on the integration of Intelligent Cockpit and Large Models, and to put forward a necessary limitation for the subsequent development of an evaluation system for the capability of automotive ICLM and user experience. The evaluation system, P-CAFE, proposed in this paper mainly proposes five dimensions of perception, cognition, action, feedback and evolution as the first-level indicators from the domains of cognitive architecture, user experience, and capability characteristics of large models, and many second-level indicators to satisfy the current status of the application and research focuses are selected. After expert evaluation, the weights of the indicators were determined, and the indicator system of P-CAFE was established. Finally, a complete evaluation method was constructed based on Fuzzy Hierarchical Analysis. It will lay a solid foundation for the application and evaluation of the automotive ICLM, and provide a reference for the development and improvement of the future ICLM.

cs.HC↗

arXiv2024

Latent Chemical Space Searching for Plug-in Multi-objective Molecule Generation

Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model adaptability, and practical application in drug discovery. In this study, we developed a versatile 'plug-in' molecular generation model that incorporates multiple objectives related to target affinity, drug-likeness, and synthesizability, facilitating its application in various drug development contexts. We improved the Particle Swarm Optimization (PSO) in the context of drug discoveries, and identified PSO-ENP as the optimal variant for multi-objective molecular generation and optimization through comparative experiments. The model also incorporates a novel target-ligand affinity predictor, enhancing the model's utility by supporting three-dimensional information and improving synthetic feasibility. Case studies focused on generating and optimizing drug-like big marine natural products were performed, underscoring PSO-ENP's effectiveness and demonstrating its considerable potential for practical drug discovery applications.

q-bio.BM↗

arXiv2024

Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Model

Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of chemical reactions. In this paper, we have proposed a unified framework that addresses both the reaction representation learning and molecule generation tasks, which allows for a more holistic approach. Inspired by the organic chemistry mechanism, we develop a novel pretraining framework that enables us to incorporate inductive biases into the model. Our framework achieves state-of-the-art results on challenging downstream tasks. By possessing chemical knowledge, our generative framework overcome the limitations of current molecule generation models that rely on a small number of reaction templates. In the extensive experiments, our model generates synthesizable drug-like structures of high quality. Overall, our work presents a significant step toward a large-scale deep-learning framework for a variety of reaction-based applications.

cs.LG↗

arXiv2023

Towards Reliable Item Sampling for Recommendation Evaluation

Since Rendle and Krichene argued that commonly used sampling-based evaluation metrics are "inconsistent" with respect to the global metrics (even in expectation), there have been a few studies on the sampling-based recommender system evaluation. Existing methods try either mapping the sampling-based metrics to their global counterparts or more generally, learning the empirical rank distribution to estimate the top-$K$ metrics. However, despite existing efforts, there is still a lack of rigorous theoretical understanding of the proposed metric estimators, and the basic item sampling also suffers from the "blind spot" issue, i.e., estimation accuracy to recover the top-$K$ metrics when $K$ is small can still be rather substantial. In this paper, we provide an in-depth investigation into these problems and make two innovative contributions. First, we propose a new item-sampling estimator that explicitly optimizes the error with respect to the ground truth, and theoretically highlight its subtle difference against prior work. Second, we propose a new adaptive sampling method which aims to deal with the "blind spot" problem and also demonstrate the expectation-maximization (EM) algorithm can be generalized for such a setting. Our experimental results confirm our statistical analysis and the superiority of the proposed works. This study helps lay the theoretical foundation for adopting item sampling metrics for recommendation evaluation, and provides strong evidence towards making item sampling a powerful and reliable tool for recommendation evaluation.

cs.IR↗

arXiv2022

Symphony in the Latent Space: Provably Integrating High-dimensional Techniques with Non-linear Machine Learning Models

This paper revisits building machine learning algorithms that involve interactions between entities, such as those between financial assets in an actively managed portfolio, or interactions between users in a social network. Our goal is to forecast the future evolution of ensembles of multivariate time series in such applications (e.g., the future return of a financial asset or the future popularity of a Twitter account). Designing ML algorithms for such systems requires addressing the challenges of high-dimensional interactions and non-linearity. Existing approaches usually adopt an ad-hoc approach to integrating high-dimensional techniques into non-linear models and recent studies have shown these approaches have questionable efficacy in time-evolving interacting systems. To this end, we propose a novel framework, which we dub as the additive influence model. Under our modeling assumption, we show that it is possible to decouple the learning of high-dimensional interactions from the learning of non-linear feature interactions. To learn the high-dimensional interactions, we leverage kernel-based techniques, with provable guarantees, to embed the entities in a low-dimensional latent space. To learn the non-linear feature-response interactions, we generalize prominent machine learning techniques, including designing a new statistically sound non-parametric method and an ensemble learning algorithm optimized for vector regressions. Extensive experiments on two common applications demonstrate that our new algorithms deliver significantly stronger forecasting power compared to standard and recently proposed methods.

cs.LG↗

arXiv2021

Equity2Vec: End-to-end Deep Learning Framework for Cross-sectional Asset Pricing

Pricing assets has attracted significant attention from the financial technology community. We observe that the existing solutions overlook the cross-sectional effects and not fully leveraged the heterogeneous data sets, leading to sub-optimal performance. To this end, we propose an end-to-end deep learning framework to price the assets. Our framework possesses two main properties: 1) We propose Equity2Vec, a graph-based component that effectively captures both long-term and evolving cross-sectional interactions. 2) The framework simultaneously leverages all the available heterogeneous alpha sources including technical indicators, financial news signals, and cross-sectional signals. Experimental results on datasets from the real-world stock market show that our approach outperforms the existing state-of-the-art approaches. Furthermore, market trading simulations demonstrate that our framework monetizes the signals effectively.

cs.LG↗

arXiv2021

Rosella: A Self-Driving Distributed Scheduler for Heterogeneous Clusters

Large-scale interactive web services and advanced AI applications make sophisticated decisions in real-time, based on executing a massive amount of computation tasks on thousands of servers. Task schedulers, which often operate in heterogeneous and volatile environments, require high throughput, i.e., scheduling millions of tasks per second, and low latency, i.e., incurring minimal scheduling delays for millisecond-level tasks. Scheduling is further complicated by other users' workloads in a shared system, other background activities, and the diverse hardware configurations inside datacenters. We present Rosella, a new self-driving, distributed approach for task scheduling in heterogeneous clusters. Rosella automatically learns the compute environment and adjusts its scheduling policy in real-time. The solution provides high throughput and low latency simultaneously because it runs in parallel on multiple machines with minimum coordination and only performs simple operations for each scheduling decision. Our learning module monitors total system load and uses the information to dynamically determine optimal estimation strategy for the backends' compute-power. Rosella generalizes power-of-two-choice algorithms to handle heterogeneous workers, reducing the max queue length of O(log n) obtained by prior algorithms to O(log log n). We evaluate Rosella with a variety of workloads on a 32-node AWS cluster. Experimental results show that Rosella significantly reduces task response time, and adapts to environment changes quickly.

cs.DC↗

arXiv2021

Toward Efficient Interactions between Python and Native Libraries

Python has become a popular programming language because of its excellent programmability. Many modern software packages utilize Python for high-level algorithm design and depend on native libraries written in C/C++/Fortran for efficient computation kernels. Interaction between Python code and native libraries introduces performance losses because of the abstraction lying on the boundary of Python and native libraries. On the one side, Python code, typically run with interpretation, is disjoint from its execution behavior. On the other side, native libraries do not include program semantics to understand algorithm defects. To understand the interaction inefficiencies, we extensively study a large collection of Python software packages and categorize them according to the root causes of inefficiencies. We extract two inefficiency patterns that are common in interaction inefficiencies. Based on these patterns, we develop PieProf, a lightweight profiler, to pinpoint interaction inefficiencies in Python applications. The principle of PieProf is to measure the inefficiencies in the native execution and associate inefficiencies with high-level Python code to provide a holistic view. Guided by PieProf, we optimize 17 real-world applications, yielding speedups up to 6.3$\times$ on application level.

cs.PL↗

arXiv2021

BATS: A Spectral Biclustering Approach to Single Document Topic Modeling and Segmentation

Existing topic modeling and text segmentation methodologies generally require large datasets for training, limiting their capabilities when only small collections of text are available. In this work, we reexamine the inter-related problems of "topic identification" and "text segmentation" for sparse document learning, when there is a single new text of interest. In developing a methodology to handle single documents, we face two major challenges. First is sparse information: with access to only one document, we cannot train traditional topic models or deep learning algorithms. Second is significant noise: a considerable portion of words in any single document will produce only noise and not help discern topics or segments. To tackle these issues, we design an unsupervised, computationally efficient methodology called BATS: Biclustering Approach to Topic modeling and Segmentation. BATS leverages three key ideas to simultaneously identify topics and segment text: (i) a new mechanism that uses word order information to reduce sample complexity, (ii) a statistically sound graph-based biclustering technique that identifies latent structures of words and sentences, and (iii) a collection of effective heuristics that remove noise words and award important words to further improve performance. Experiments on four datasets show that our approach outperforms several state-of-the-art baselines when considering topic coherence, topic diversity, segmentation, and runtime comparison metrics.

cs.IR↗

arXiv2020

On Extending NLP Techniques from the Categorical to the Latent Space: KL Divergence, Zipf's Law, and Similarity Search

Despite the recent successes of deep learning in natural language processing (NLP), there remains widespread usage of and demand for techniques that do not rely on machine learning. The advantage of these techniques is their interpretability and low cost when compared to frequently opaque and expensive machine learning models. Although they may not be be as performant in all cases, they are often sufficient for common and relatively simple problems. In this paper, we aim to modernize these older methods while retaining their advantages by extending approaches from categorical or bag-of-words representations to word embeddings representations in the latent space. First, we show that entropy and Kullback-Leibler divergence can be efficiently estimated using word embeddings and use this estimation to compare text across several categories. Next, we recast the heavy-tailed distribution known as Zipf's law that is frequently observed in the categorical space to the latent space. Finally, we look to improve the Jaccard similarity measure for sentence suggestion by introducing a new method of identifying similar sentences based on the set cover problem. We compare the performance of this algorithm against several baselines including Word Mover's Distance and the Levenshtein distance.

cs.CL↗

arXiv2020

Adaptive Reduced Rank Regression

We study the low rank regression problem $\my = M\mx + ε$, where $\mx$ and $\my$ are $d_1$ and $d_2$ dimensional vectors respectively. We consider the extreme high-dimensional setting where the number of observations $n$ is less than $d_1 + d_2$. Existing algorithms are designed for settings where $n$ is typically as large as $\Rank(M)(d_1+d_2)$. This work provides an efficient algorithm which only involves two SVD, and establishes statistical guarantees on its performance. The algorithm decouples the problem by first estimating the precision matrix of the features, and then solving the matrix denoising problem. To complement the upper bound, we introduce new techniques for establishing lower bounds on the performance of any algorithm for this problem. Our preliminary experiments confirm that our algorithm often out-performs existing baselines, and is always at least competitive.

cs.DS↗

arXiv2020

RackSched: A Microsecond-Scale Scheduler for Rack-Scale Computers (Technical Report)

Low-latency online services have strict Service Level Objectives (SLOs) that require datacenter systems to support high throughput at microsecond-scale tail latency. Dataplane operating systems have been designed to scale up multi-core servers with minimal overhead for such SLOs. However, as application demands continue to increase, scaling up is not enough, and serving larger demands requires these systems to scale out to multiple servers in a rack. We present RackSched, the first rack-level microsecond-scale scheduler that provides the abstraction of a rack-scale computer (i.e., a huge server with hundreds to thousands of cores) to an external service with network-system co-design. The core of RackSched is a two-layer scheduling framework that integrates inter-server scheduling in the top-of-rack (ToR) switch with intra-server scheduling in each server. We use a combination of analytical results and simulations to show that it provides near-optimal performance as centralized scheduling policies, and is robust for both low-dispersion and high-dispersion workloads. We design a custom switch data plane for the inter-server scheduler, which realizes power-of-k-choices, ensures request affinity, and tracks server loads accurately and efficiently. We implement a RackSched prototype on a cluster of commodity servers connected by a Barefoot Tofino switch. End-to-end experiments on a twelve-server testbed show that RackSched improves the throughput by up to 1.44x, and scales out the throughput near linearly, while maintaining the same tail latency as one server until the system is saturated.

cs.DC↗

arXiv2020

On Efficient Constructions of Checkpoints

Efficient construction of checkpoints/snapshots is a critical tool for training and diagnosing deep learning models. In this paper, we propose a lossy compression scheme for checkpoint constructions (called LC-Checkpoint). LC-Checkpoint simultaneously maximizes the compression rate and optimizes the recovery speed, under the assumption that SGD is used to train the model. LC-Checkpointuses quantization and priority promotion to store the most crucial information for SGD to recover, and then uses a Huffman coding to leverage the non-uniform distribution of the gradient scales. Our extensive experiments show that LC-Checkpoint achieves a compression rate up to $28\times$ and recovery speedup up to $5.77\times$ over a state-of-the-art algorithm (SCAR).

cs.LG↗

arXiv2020

TF3P: Three-dimensional Force Fields Fingerprint Learned by Deep Capsular Network

Molecular fingerprints are the workhorse in ligand-based drug discovery. In recent years, an increasing number of research papers reported fascinating results on using deep neural networks to learn 2D molecular representations as fingerprints. It is anticipated that the integration of deep learning would also contribute to the prosperity of 3D fingerprints. Here, we unprecedentedly introduce deep learning into 3D small molecule fingerprints, presenting a new one we termed as the three-dimensional force fields fingerprint (TF3P). TF3P is learned by a deep capsular network whose training is in no need of labeled datasets for specific predictive tasks. TF3P can encode the 3D force fields information of molecules and demonstrates the stronger ability to capture 3D structural changes, to recognize molecules alike in 3D but not in 2D, and to identify similar targets inaccessible by other 2D or 3D fingerprints based on only ligands similarity. Furthermore, TF3P is compatible with both statistical models (e.g. similarity ensemble approach) and machine learning models. Altogether, we report TF3P as a new 3D small molecule fingerprint with a promising future in ligand-based drug discovery. All codes are written in Python and available at https://github.com/canisw/tf3p.

q-bio.QM↗

arXiv2019

DeepScaffold: a comprehensive tool for scaffold-based de novo drug discovery using deep learning

The ultimate goal of drug design is to find novel compounds with desirable pharmacological properties. Designing molecules retaining particular scaffolds as the core structures of the molecules is one of the efficient ways to obtain potential drug candidates with desirable properties. We proposed a scaffold-based molecular generative model for scaffold-based drug discovery, which performs molecule generation based on a wide spectrum of scaffold definitions, including BM-scaffolds, cyclic skeletons, as well as scaffolds with specifications on side-chain properties. The model can generalize the learned chemical rules of adding atoms and bonds to a given scaffold. Furthermore, the generated compounds were evaluated by molecular docking in DRD2 targets and the results demonstrated that this approach can be effectively applied to solve several drug design problems, including the generation of compounds containing a given scaffold and de novo drug design of potential drug candidates with specific docking scores. Finally, a command line interface is created.

q-bio.QM↗