arXiv subjects

Jiayi Wang

Publications and source records attributed to Jiayi Wang.

At least 91 records · Page 5Linked to original sources

arXiv2024

An Efficient Representation of Whole-body Model Predictive Control for Online Compliant Dual-arm Mobile Manipulation

Dual-arm mobile manipulators can transport and manipulate large-size objects with simple end-effectors. To interact with dynamic environments with strict safety and compliance requirements, achieving whole-body motion planning online while meeting various hard constraints for such highly redundant mobile manipulators poses a significant challenge. We tackle this challenge by presenting an efficient representation of whole-body motion trajectories within our bilevel model-based predictive control (MPC) framework. We utilize Bézier-curve parameterization to represent the optimized collision-free trajectories of two collaborating end-effectors in the first MPC, facilitating fast long-horizon object-oriented motion planning in SE(3) while considering approximated feasibility constraints. This approach is further applied to parameterize whole-body trajectories in the second MPC for whole-body motion generation with predictive admittance control in a relatively short horizon while satisfying whole-body hard constraints. This representation enables two MPCs with continuous properties, thereby avoiding inaccurate model-state transition and dense decision-variable settings in existing MPCs using the discretization method. It strengthens the online execution of the bilevel MPC framework in high-dimensional space and facilitates the generation of consistent commands for our hybrid position/velocity-controlled robot. The simulation comparisons and real-world experiments demonstrate the efficiency and robustness of this approach in various scenarios for static and dynamic obstacle avoidance, and compliant interaction control with the manipulated object and external disturbances.

cs.RO↗

arXiv2024

DNABERT-S: Pioneering Species Differentiation with Species-Aware DNA Embeddings

We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA and RNA) is vital yet challenging, since many real-world species remain uncharacterized, lacking known genomes for reference. Embedding-based methods are therefore used to differentiate species in an unsupervised manner. DNABERT-S builds upon a pre-trained genome foundation model named DNABERT-2. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C$^2$LR) strategy. Empirical results on 23 diverse datasets show DNABERT-S's effectiveness, especially in realistic label-scarce scenarios. For example, it identifies twice more species from a mixture of unlabeled genomic sequences, doubles the Adjusted Rand Index (ARI) in species clustering, and outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training. Model, codes, and data are publicly available at \url{https://github.com/MAGICS-LAB/DNABERT_S}.

q-bio.GN↗

arXiv2024

Deep Learning-based Software Engineering: Progress, Challenges, and Opportunities

Researchers have recently achieved significant advances in deep learning techniques, which in turn has substantially advanced other research disciplines, such as natural language processing, image processing, speech recognition, and software engineering. Various deep learning techniques have been successfully employed to facilitate software engineering tasks, including code generation, software refactoring, and fault localization. Many papers have also been presented in top conferences and journals, demonstrating the applications of deep learning techniques in resolving various software engineering tasks. However, although several surveys have provided overall pictures of the application of deep learning techniques in software engineering, they focus more on learning techniques, that is, what kind of deep learning techniques are employed and how deep models are trained or fine-tuned for software engineering tasks. We still lack surveys explaining the advances of subareas in software engineering driven by deep learning techniques, as well as challenges and opportunities in each subarea. To this end, in this paper, we present the first task-oriented survey on deep learning-based software engineering. It covers twelve major software engineering subareas significantly impacted by deep learning techniques. Such subareas spread out the through the whole lifecycle of software development and maintenance, including requirements engineering, software development, testing, maintenance, and developer collaboration. As we believe that deep learning may provide an opportunity to revolutionize the whole discipline of software engineering, providing one survey covering as many subareas as possible in software engineering can help future research push forward the frontier of deep learning-based software engineering more systematically.

cs.SE↗

arXiv2024

NAS: N-step computation of All Solutions to the footstep planning problem

How many ways are there to climb a staircase in a given number of steps? Infinitely many, if we focus on the continuous aspect of the problem. A finite, possibly large number if we consider the discrete aspect, \emph{i.e.} on which surface which effectors are going to step and in what order. We introduce NAS, an algorithm that considers both aspects simultaneously and computes \emph{all} the possible solutions to such a contact planning problem, under standard assumptions. To our knowledge NAS is the first algorithm to produce a globally optimal policy, efficiently queried in real time for planning the next footsteps of a humanoid robot. Our empirical results (in simulation and on the Talos platform) demonstrate that, despite the theoretical exponential complexity, optimisations reduce the practical complexity of NAS to a manageable bilinear form, maintaining completeness guarantees and enabling efficient GPU parallelisation. NAS is demonstrated in a variety of scenarios for the Talos robot, both in simulation and on the hardware platform. Future work will focus on further reducing computation times and extending the algorithm's applicability beyond gaited locomotion. Our video is available at \url{https://youtu.be/I5yFe0ez0sI}

cs.RO↗

arXiv2024

ClinicalLab: Aligning Agents for Multi-Departmental Clinical Diagnostics in the Real World

LLMs have achieved significant performance progress in various NLP applications. However, LLMs still struggle to meet the strict requirements for accuracy and reliability in the medical field and face many challenges in clinical applications. Existing clinical diagnostic evaluation benchmarks for evaluating medical agents powered by LLMs have severe limitations. Firstly, most existing medical evaluation benchmarks face the risk of data leakage or contamination. Secondly, existing benchmarks often neglect the characteristics of multiple departments and specializations in modern medical practice. Thirdly, existing evaluation methods are limited to multiple-choice questions, which do not align with the real-world diagnostic scenarios. Lastly, existing evaluation methods lack comprehensive evaluations of end-to-end real clinical scenarios. These limitations in benchmarks in turn obstruct advancements of LLMs and agents for medicine. To address these limitations, we introduce ClinicalLab, a comprehensive clinical diagnosis agent alignment suite. ClinicalLab includes ClinicalBench, an end-to-end multi-departmental clinical diagnostic evaluation benchmark for evaluating medical agents and LLMs. ClinicalBench is based on real cases that cover 24 departments and 150 diseases. ClinicalLab also includes four novel metrics (ClinicalMetrics) for evaluating the effectiveness of LLMs in clinical diagnostic tasks. We evaluate 17 LLMs and find that their performance varies significantly across different departments. Based on these findings, in ClinicalLab, we propose ClinicalAgent, an end-to-end clinical agent that aligns with real-world clinical diagnostic practices. We systematically investigate the performance and applicable scenarios of variants of ClinicalAgent on ClinicalBench. Our findings demonstrate the importance of aligning with modern medical practices in designing medical agents.

cs.CL↗

arXiv2024

Risk-Aware Security-Constrained Unit Commitment: Taming the Curse of Real-Time Volatility and Consumer Exposure

We propose an enhancement to wholesale electricity markets whereby the exposure of consumers to increasingly large and volatile consumer payments arising as a byproduct of volatile real-time net loads -- i.e., loads minus renewable outputs -- and prices, both compared to day-ahead cleared values. We incorporate a robust estimate of such excess payments into the day-ahead computation and specifically seek to account for volatility in real-time net loads and renewable generation. Our model features a data-driven uncertainty set based on principal component analysis, which accommodates both load and wind production volatility and captures locational correlation of uncertain data. To solve the model more efficiently, we develop a decomposition algorithm that can handle nonconvex subproblems. Our extensive experiments on a realistic NYISO data set show that the risk-aware model protects the consumers from potential high costs caused by adverse circumstances.

math.OC↗

arXiv2024

A New Theoretical Perspective on Data Heterogeneity in Federated Optimization

In federated learning (FL), data heterogeneity is the main reason that existing theoretical analyses are pessimistic about the convergence rate. In particular, for many FL algorithms, the convergence rate grows dramatically when the number of local updates becomes large, especially when the product of the gradient divergence and local Lipschitz constant is large. However, empirical studies can show that more local updates can improve the convergence rate even when these two parameters are large, which is inconsistent with the theoretical findings. This paper aims to bridge this gap between theoretical understanding and practical performance by providing a theoretical analysis from a new perspective on data heterogeneity. In particular, we propose a new and weaker assumption compared to the local Lipschitz gradient assumption, named the heterogeneity-driven pseudo-Lipschitz assumption. We show that this and the gradient divergence assumptions can jointly characterize the effect of data heterogeneity. By deriving a convergence upper bound for FedAvg and its extensions, we show that, compared to the existing works, local Lipschitz constant is replaced by the much smaller heterogeneity-driven pseudo-Lipschitz constant and the corresponding convergence upper bound can be significantly reduced for the same number of local updates, although its order stays the same. In addition, when the local objective function is quadratic, more insights on the impact of data heterogeneity can be obtained using the heterogeneity-driven pseudo-Lipschitz constant. For example, we can identify a region where FedAvg can outperform mini-batch SGD even when the gradient divergence can be arbitrarily large. Our findings are validated using experiments.

cs.LG↗

arXiv2024

Label-free Neural Semantic Image Synthesis

Recent work has shown great progress in integrating spatial conditioning to control large, pre-trained text-to-image diffusion models. Despite these advances, existing methods describe the spatial image content using hand-crafted conditioning inputs, which are either semantically ambiguous (e.g., edges) or require expensive manual annotations (e.g., semantic segmentation). To address these limitations, we propose a new label-free way of conditioning diffusion models to enable fine-grained spatial control. We introduce the concept of neural semantic image synthesis, which uses neural layouts extracted from pre-trained foundation models as conditioning. Neural layouts are advantageous as they provide rich descriptions of the desired image, containing both semantics and detailed geometry of the scene. We experimentally show that images synthesized via neural semantic image synthesis achieve similar or superior pixel-level alignment of semantic classes compared to those created using expensive semantic label maps. At the same time, they capture better semantics, instance separation, and object orientation than other label-free conditioning options, such as edges or depth. Moreover, we show that images generated by neural layout conditioning can effectively augment real data for training various perception tasks.

cs.CV↗

arXiv2024

A Fine-grained Analysis of Fitted Q-evaluation: Beyond Parametric Models

In this paper, we delve into the statistical analysis of the fitted Q-evaluation (FQE) method, which focuses on estimating the value of a target policy using offline data generated by some behavior policy. We provide a comprehensive theoretical understanding of FQE estimators under both parameteric and nonparametric models on the $Q$-function. Specifically, we address three key questions related to FQE that remain largely unexplored in the current literature: (1) Is the optimal convergence rate for estimating the policy value regarding the sample size $n$ ($n^{-1/2}$) achievable for FQE under a non-parametric model with a fixed horizon ($T$)? (2) How does the error bound depend on the horizon $T$? (3) What is the role of the probability ratio function in improving the convergence of FQE estimators? Specifically, we show that under the completeness assumption of $Q$-functions, which is mild in the non-parametric setting, the estimation errors for policy value using both parametric and non-parametric FQE estimators can achieve an optimal rate in terms of $n$. The corresponding error bounds in terms of both $n$ and $T$ are also established. With an additional realizability assumption on ratio functions, the rate of estimation errors can be improved from $T^{1.5}/\sqrt{n}$ to $T/\sqrt{n}$, which matches the sharpest known bound in the current literature under the tabular setting.

math.ST↗

arXiv2024

ODFormer: Semantic Fundus Image Segmentation Using Transformer for Optic Nerve Head Detection

Optic nerve head (ONH) detection has been a crucial area of study in ophthalmology for years. However, the significant discrepancy between fundus image datasets, each generated using a single type of fundus camera, poses challenges to the generalizability of ONH detection approaches developed based on semantic segmentation networks. Despite the numerous recent advancements in general-purpose semantic segmentation methods using convolutional neural networks (CNNs) and Transformers, there is currently a lack of benchmarks for these state-of-the-art (SoTA) networks specifically trained for ONH detection. Therefore, in this article, we make contributions from three key aspects: network design, the publication of a dataset, and the establishment of a comprehensive benchmark. Our newly developed ONH detection network, referred to as ODFormer, is based upon the Swin Transformer architecture and incorporates two novel components: a multi-scale context aggregator and a lightweight bidirectional feature recalibrator. Our published large-scale dataset, known as TongjiU-DROD, provides multi-resolution fundus images for each participant, captured using two distinct types of cameras. Our established benchmark involves three datasets: DRIONS-DB, DRISHTI-GS1, and TongjiU-DROD, created by researchers from different countries and containing fundus images captured from participants of diverse races and ages. Extensive experimental results demonstrate that our proposed ODFormer outperforms other state-of-the-art (SoTA) networks in terms of performance and generalizability. Our dataset and source code are publicly available at mias.group/ODFormer.

eess.IV↗

arXiv2024

Truncated Variance Reduced Value Iteration

We provide faster randomized algorithms for computing an $ε$-optimal policy in a discounted Markov decision process with $A_{\text{tot}}$-state-action pairs, bounded rewards, and discount factor $γ$. We provide an $\tilde{O}(A_{\text{tot}}[(1 - γ)^{-3}ε^{-2} + (1 - γ)^{-2}])$-time algorithm in the sampling setting, where the probability transition matrix is unknown but accessible through a generative model which can be queried in $\tilde{O}(1)$-time, and an $\tilde{O}(s + (1-γ)^{-2})$-time algorithm in the offline setting where the probability transition matrix is known and $s$-sparse. These results improve upon the prior state-of-the-art which either ran in $\tilde{O}(A_{\text{tot}}[(1 - γ)^{-3}ε^{-2} + (1 - γ)^{-3}])$ time [Sidford, Wang, Wu, Ye 2018] in the sampling setting, $\tilde{O}(s + A_{\text{tot}} (1-γ)^{-3})$ time [Sidford, Wang, Wu, Yang, Ye 2018] in the offline setting, or time at least quadratic in the number of states using interior point methods for linear programming. We achieve our results by building upon prior stochastic variance-reduced value iteration methods [Sidford, Wang, Wu, Yang, Ye 2018]. We provide a variant that carefully truncates the progress of its iterates to improve the variance of new variance-reduced sampling procedures that we introduce to implement the steps. Our method is essentially model-free and can be implemented in $\tilde{O}(A_{\text{tot}})$-space when given generative model access. Consequently, our results take a step in closing the sample-complexity gap between model-free and model-based methods.

cs.LG↗

arXiv2024

ADELT: Transpilation Between Deep Learning Frameworks

We propose the Adversarial DEep Learning Transpiler (ADELT), a novel approach to source-to-source transpilation between deep learning frameworks. ADELT uniquely decouples code skeleton transpilation and API keyword mapping. For code skeleton transpilation, it uses few-shot prompting on large language models (LLMs), while for API keyword mapping, it uses contextual embeddings from a code-specific BERT. These embeddings are trained in a domain-adversarial setup to generate a keyword translation dictionary. ADELT is trained on an unlabeled web-crawled deep learning corpus, without relying on any hand-crafted rules or parallel data. It outperforms state-of-the-art transpilers, improving pass@1 rate by 17.4 pts and 15.0 pts for PyTorch-Keras and PyTorch-MXNet transpilation pairs respectively. We provide open access to our code at https://github.com/gonglinyuan/adelt.

cs.CL↗

arXiv2024

AfriMTE and AfriCOMET: Enhancing COMET to Embrace Under-resourced African Languages

Despite the recent progress on scaling multilingual machine translation (MT) to several under-resourced African languages, accurately measuring this progress remains challenging, since evaluation is often performed on n-gram matching metrics such as BLEU, which typically show a weaker correlation with human judgments. Learned metrics such as COMET have higher correlation; however, the lack of evaluation data with human ratings for under-resourced languages, complexity of annotation guidelines like Multidimensional Quality Metrics (MQM), and limited language coverage of multilingual encoders have hampered their applicability to African languages. In this paper, we address these challenges by creating high-quality human evaluation data with simplified MQM guidelines for error detection and direct assessment (DA) scoring for 13 typologically diverse African languages. Furthermore, we develop AfriCOMET: COMET evaluation metrics for African languages by leveraging DA data from well-resourced languages and an African-centric multilingual encoder (AfroXLM-R) to create the state-of-the-art MT evaluation metrics for African languages with respect to Spearman-rank correlation with human judgments (0.441).

cs.CL↗

arXiv2024

Online Multi-Contact Receding Horizon Planning via Value Function Approximation

Planning multi-contact motions in a receding horizon fashion requires a value function to guide the planning with respect to the future, e.g., building momentum to traverse large obstacles. Traditionally, the value function is approximated by computing trajectories in a prediction horizon (never executed) that foresees the future beyond the execution horizon. However, given the non-convex dynamics of multi-contact motions, this approach is computationally expensive. To enable online Receding Horizon Planning (RHP) of multi-contact motions, we find efficient approximations of the value function. Specifically, we propose a trajectory-based and a learning-based approach. In the former, namely RHP with Multiple Levels of Model Fidelity, we approximate the value function by computing the prediction horizon with a convex relaxed model. In the latter, namely Locally-Guided RHP, we learn an oracle to predict local objectives for locomotion tasks, and we use these local objectives to construct local value functions for guiding a short-horizon RHP. We evaluate both approaches in simulation by planning centroidal trajectories of a humanoid robot walking on moderate slopes, and on large slopes where the robot cannot maintain static balance. Our results show that locally-guided RHP achieves the best computation efficiency (95\%-98.6\% cycles converge online). This computation advantage enables us to demonstrate online receding horizon planning of our real-world humanoid robot Talos walking in dynamic environments that change on-the-fly.

cs.RO↗

arXiv2024

Strings from the Library of Babel: Random Sampling as a Strong Baseline for Prompt Optimisation

Recent prompt optimisation approaches use the generative nature of language models to produce prompts -- even rivaling the performance of human-curated prompts. In this paper, we demonstrate that randomly sampling tokens from the model vocabulary as ``separators'' can be as effective as language models for prompt-style text classification. Our experiments show that random separators are competitive baselines, having less than a 1% difference compared to previous self-optimisation methods and showing a 12% average relative improvement over strong human baselines across nine text classification tasks and eight language models. We further analyse this phenomenon in detail using three different random generation strategies, establishing that the language space is rich with potentially good separators, with a greater than 40% average chance that a randomly drawn separator performs better than human-curated separators. These observations challenge the common assumption that an effective prompt should be human readable or task relevant and establish a strong baseline for prompt optimisation research.

cs.CL↗

arXiv2024

Demystifying Why Local Aggregation Helps: Convergence Analysis of Hierarchical SGD

Hierarchical SGD (H-SGD) has emerged as a new distributed SGD algorithm for multi-level communication networks. In H-SGD, before each global aggregation, workers send their updated local models to local servers for aggregations. Despite recent research efforts, the effect of local aggregation on global convergence still lacks theoretical understanding. In this work, we first introduce a new notion of "upward" and "downward" divergences. We then use it to conduct a novel analysis to obtain a worst-case convergence upper bound for two-level H-SGD with non-IID data, non-convex objective function, and stochastic gradient. By extending this result to the case with random grouping, we observe that this convergence upper bound of H-SGD is between the upper bounds of two single-level local SGD settings, with the number of local iterations equal to the local and global update periods in H-SGD, respectively. We refer to this as the "sandwich behavior". Furthermore, we extend our analytical approach based on "upward" and "downward" divergences to study the convergence for the general case of H-SGD with more than two levels, where the "sandwich behavior" still holds. Our theoretical results provide key insights of why local aggregation can be beneficial in improving the convergence of H-SGD.

cs.LG↗

arXiv2024

Ten simple rules for collaborating with wet lab researchers for computational researchers

Computational biologists are frequently engaged in collaborative data analysis with wet lab researchers. These interdisciplinary projects, as necessary as they are to the scientific endeavour, can be surprisingly challenging due to cultural differences in operations and values. In these Ten Simple Rules guide we aim to help dry lab researchers identify sources of friction; and provide actionable tools to facilitate respectful, open, transparent and rewarding collaborations.

q-bio.OT↗

arXiv2024

Prediction of Tropical Pacific Rain Rates with Over-parameterized Neural Networks

The prediction of tropical rain rates from atmospheric profiles poses significant challenges, mainly due to the heavy-tailed distribution exhibited by tropical rainfall. This study introduces over-parameterized neural networks not only to forecast tropical rain rates, but also to explain their heavy-tailed distribution. The prediction is separately conducted for three rain types (stratiform, deep convective, and shallow convective) observed by the Global Precipitation Measurement satellite radar over the West and East Pacific regions. Atmospheric profiles of humidity, temperature, and zonal and meridional winds from the MERRA-2 reanalysis are considered as features. Although over-parameterized neural networks are well-known for their ``double descent phenomenon," little has been explored about their applicability to climate data and capability of capturing the tail behavior of data. In our results, over-parameterized neural networks accurately predict the rain rate distributions and outperform other machine learning methods. Spatial maps show that over-parameterized neural networks also successfully describe spatial patterns of each rain type across the tropical Pacific. In addition, we assess the feature importance for each over-parameterized neural network to provide insight into the key factors driving the predictions, with low-level humidity and temperature variables being the overall most important. These findings highlight the capability of over-parameterized neural networks in predicting the distribution of the rain rate and explaining extreme values.

physics.ao-ph↗