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Jan 7

Reproducibility of the Methods in Medical Imaging with Deep Learning

Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates reproducibility guidelines, especially so in the medical imaging field. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in this direction by advocating open access, and recently also recommending authors to make their code public - both aspects being adopted by the majority of the conference submissions. This helps the reproducibility of the methods, however, there is currently little or no support for further evaluation of these supplementary material, making them vulnerable to poor quality, which affects the impact of the entire submission. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but slightly adjusted guidelines on reproducibility and the quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories has not improved over the years, leaving room for improvement in every aspect of designing repositories. Merely 22% of all submissions contain a repository that were deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL.

  • 5 authors
·
Oct 20, 2022

The Impact of Task Underspecification in Evaluating Deep Reinforcement Learning

Evaluations of Deep Reinforcement Learning (DRL) methods are an integral part of scientific progress of the field. Beyond designing DRL methods for general intelligence, designing task-specific methods is becoming increasingly prominent for real-world applications. In these settings, the standard evaluation practice involves using a few instances of Markov Decision Processes (MDPs) to represent the task. However, many tasks induce a large family of MDPs owing to variations in the underlying environment, particularly in real-world contexts. For example, in traffic signal control, variations may stem from intersection geometries and traffic flow levels. The select MDP instances may thus inadvertently cause overfitting, lacking the statistical power to draw conclusions about the method's true performance across the family. In this article, we augment DRL evaluations to consider parameterized families of MDPs. We show that in comparison to evaluating DRL methods on select MDP instances, evaluating the MDP family often yields a substantially different relative ranking of methods, casting doubt on what methods should be considered state-of-the-art. We validate this phenomenon in standard control benchmarks and the real-world application of traffic signal control. At the same time, we show that accurately evaluating on an MDP family is nontrivial. Overall, this work identifies new challenges for empirical rigor in reinforcement learning, especially as the outcomes of DRL trickle into downstream decision-making.

  • 5 authors
·
Oct 16, 2022

Empirical and Experimental Insights into Machine Learning-Based Defect Classification in Semiconductor Wafers

This survey paper offers a comprehensive review of methodologies utilizing machine learning (ML) classification techniques for identifying wafer defects in semiconductor manufacturing. Despite the growing body of research demonstrating the effectiveness of ML in wafer defect identification, there is a noticeable absence of comprehensive reviews on this subject. This survey attempts to fill this void by amalgamating available literature and providing an in-depth analysis of the advantages, limitations, and potential applications of various ML classification algorithms in the realm of wafer defect detection. An innovative taxonomy of methodologies that we present provides a detailed classification of algorithms into more refined categories and techniques. This taxonomy follows a three-tier structure, starting from broad methodology categories and ending with specific techniques. It aids researchers in comprehending the complex relationships between different algorithms and their techniques. We employ a rigorous empirical and experimental evaluation to rank these varying techniques. For the empirical evaluation, we assess techniques based on a set of five criteria. The experimental evaluation ranks the algorithms employing the same techniques, sub-categories, and categories. Also the paper illuminates the future prospects of ML classification techniques for wafer defect identification, underscoring potential advancements and opportunities for further research in this field

  • 1 authors
·
Oct 16, 2023

A Survey of Direct Preference Optimization

Large Language Models (LLMs) have demonstrated unprecedented generative capabilities, yet their alignment with human values remains critical for ensuring helpful and harmless deployments. While Reinforcement Learning from Human Feedback (RLHF) has emerged as a powerful paradigm for aligning LLMs with human preferences, its reliance on complex reward modeling introduces inherent trade-offs in computational efficiency and training stability. In this context, Direct Preference Optimization (DPO) has recently gained prominence as a streamlined alternative that directly optimizes LLMs using human preferences, thereby circumventing the need for explicit reward modeling. Owing to its theoretical elegance and computational efficiency, DPO has rapidly attracted substantial research efforts exploring its various implementations and applications. However, this field currently lacks systematic organization and comparative analysis. In this survey, we conduct a comprehensive overview of DPO and introduce a novel taxonomy, categorizing previous works into four key dimensions: data strategy, learning framework, constraint mechanism, and model property. We further present a rigorous empirical analysis of DPO variants across standardized benchmarks. Additionally, we discuss real-world applications, open challenges, and future directions for DPO. This work delivers both a conceptual framework for understanding DPO and practical guidance for practitioners, aiming to advance robust and generalizable alignment paradigms. All collected resources are available and will be continuously updated at https://github.com/liushunyu/awesome-direct-preference-optimization.

  • 12 authors
·
Mar 12, 2025

INGENIOUS: Using Informative Data Subsets for Efficient Pre-Training of Language Models

A salient characteristic of pre-trained language models (PTLMs) is a remarkable improvement in their generalization capability and emergence of new capabilities with increasing model capacity and pre-training dataset size. Consequently, we are witnessing the development of enormous models pushing the state-of-the-art. It is, however, imperative to realize that this inevitably leads to prohibitively long training times, extortionate computing costs, and a detrimental environmental impact. Significant efforts are underway to make PTLM training more efficient through innovations in model architectures, training pipelines, and loss function design, with scant attention being paid to optimizing the utility of training data. The key question that we ask is whether it is possible to train PTLMs by employing only highly informative subsets of the training data while maintaining downstream performance? Building upon the recent progress in informative data subset selection, we show how we can employ submodular optimization to select highly representative subsets of the training corpora and demonstrate that the proposed framework can be applied to efficiently train multiple PTLMs (BERT, BioBERT, GPT-2) using only a fraction of data. Further, we perform a rigorous empirical evaluation to show that the resulting models achieve up to sim99% of the performance of the fully-trained models. We made our framework publicly available at https://github.com/Efficient-AI/ingenious.

  • 7 authors
·
May 11, 2023

CWEval: Outcome-driven Evaluation on Functionality and Security of LLM Code Generation

Large Language Models (LLMs) have significantly aided developers by generating or assisting in code writing, enhancing productivity across various tasks. While identifying incorrect code is often straightforward, detecting vulnerabilities in functionally correct code is more challenging, especially for developers with limited security knowledge, which poses considerable security risks of using LLM-generated code and underscores the need for robust evaluation benchmarks that assess both functional correctness and security. Current benchmarks like CyberSecEval and SecurityEval attempt to solve it but are hindered by unclear and impractical specifications, failing to assess both functionality and security accurately. To tackle these deficiencies, we introduce CWEval, a novel outcome-driven evaluation framework designed to enhance the evaluation of secure code generation by LLMs. This framework not only assesses code functionality but also its security simultaneously with high-quality task specifications and outcome-driven test oracles which provides high accuracy. Coupled with CWEval-bench, a multilingual, security-critical coding benchmark, CWEval provides a rigorous empirical security evaluation on LLM-generated code, overcoming previous benchmarks' shortcomings. Through our evaluations, CWEval reveals a notable portion of functional but insecure code produced by LLMs, and shows a serious inaccuracy of previous evaluations, ultimately contributing significantly to the field of secure code generation. We open-source our artifact at: https://github.com/Co1lin/CWEval .

  • 5 authors
·
Jan 14, 2025

In-Context Linear Regression Demystified: Training Dynamics and Mechanistic Interpretability of Multi-Head Softmax Attention

We study how multi-head softmax attention models are trained to perform in-context learning on linear data. Through extensive empirical experiments and rigorous theoretical analysis, we demystify the emergence of elegant attention patterns: a diagonal and homogeneous pattern in the key-query (KQ) weights, and a last-entry-only and zero-sum pattern in the output-value (OV) weights. Remarkably, these patterns consistently appear from gradient-based training starting from random initialization. Our analysis reveals that such emergent structures enable multi-head attention to approximately implement a debiased gradient descent predictor -- one that outperforms single-head attention and nearly achieves Bayesian optimality up to proportional factor. Furthermore, compared to linear transformers, the softmax attention readily generalizes to sequences longer than those seen during training. We also extend our study to scenarios with non-isotropic covariates and multi-task linear regression. In the former, multi-head attention learns to implement a form of pre-conditioned gradient descent. In the latter, we uncover an intriguing regime where the interplay between head number and task number triggers a superposition phenomenon that efficiently resolves multi-task in-context learning. Our results reveal that in-context learning ability emerges from the trained transformer as an aggregated effect of its architecture and the underlying data distribution, paving the way for deeper understanding and broader applications of in-context learning.

  • 4 authors
·
Mar 16, 2025

An Empirical Study of Qwen3 Quantization

The Qwen series has emerged as a leading family of open-source Large Language Models (LLMs), demonstrating remarkable capabilities in natural language understanding tasks. With the recent release of Qwen3, which exhibits superior performance across diverse benchmarks, there is growing interest in deploying these models efficiently in resource-constrained environments. Low-bit quantization presents a promising solution, yet its impact on Qwen3's performance remains underexplored. This study conducts a systematic evaluation of Qwen3's robustness under various quantization settings, aiming to uncover both opportunities and challenges in compressing this state-of-the-art model. We rigorously assess 5 existing classic post-training quantization techniques applied to Qwen3, spanning bit-widths from 1 to 8 bits, and evaluate their effectiveness across multiple datasets. Our findings reveal that while Qwen3 maintains competitive performance at moderate bit-widths, it experiences notable degradation in linguistic tasks under ultra-low precision, underscoring the persistent hurdles in LLM compression. These results emphasize the need for further research to mitigate performance loss in extreme quantization scenarios. We anticipate that this empirical analysis will provide actionable insights for advancing quantization methods tailored to Qwen3 and future LLMs, ultimately enhancing their practicality without compromising accuracy. Our project is released on https://github.com/Efficient-ML/Qwen3-Quantization and https://huggingface.co/collections/Efficient-ML/qwen3-quantization-68164450decb1c868788cb2b.

  • 10 authors
·
May 4, 2025 1

An Empirical Study of NetOps Capability of Pre-Trained Large Language Models

Large language models (LLMs) can respond to human language queries and have shown powerful potential applications in network operations (NetOps). Thanks to the large amount of commonsense knowledge inherent, LLMs achieve much better inference accuracy than traditional models and emerge with strong abilities in generalization, reasoning, and code generation. These abilities may have a crucial boost to automated and intelligent NetOps. However, it remains under-explored how well LLMs perform in various NetOps tasks. In this work, we make a systematic assessment of the capabilities, strengths, and limitations of selected LLMs in the field of NetOps. The evaluation is conducted on a collection of 5,732 questions about NetOps, encompassing 26 publicly available general-domain LLMs, including ChatGPT, LLaMA, Falcon, etc. We also finetune some of these LLMs with our collected NetOps corpus and evaluate the resulting models. The evaluation method follows the widely adopted benchmarks for general-domain LLMs, combined with Chain-of-Thought Prompts and Retrieval-Augmented Generation. The results show that only GPT-4 achieves high accuracy equivalent to passing the NetOps certification exam for humans, while all the other LLMs have much lower accuracy. However, some open models like LLaMA 2 still demonstrate significant potential. Furthermore, we evaluate the impact of factors such as model parameters, prompt engineering, instruction fine-tuning etc. This work shall be treated as the initial effort to systematic evaluation of LLMs in NetOps, and a more rigorous study is required for production use. The evaluation code and dataset will be released to benefit future research.

  • 9 authors
·
Sep 11, 2023 1

Can large language models provide useful feedback on research papers? A large-scale empirical analysis

Expert feedback lays the foundation of rigorous research. However, the rapid growth of scholarly production and intricate knowledge specialization challenge the conventional scientific feedback mechanisms. High-quality peer reviews are increasingly difficult to obtain. Researchers who are more junior or from under-resourced settings have especially hard times getting timely feedback. With the breakthrough of large language models (LLM) such as GPT-4, there is growing interest in using LLMs to generate scientific feedback on research manuscripts. However, the utility of LLM-generated feedback has not been systematically studied. To address this gap, we created an automated pipeline using GPT-4 to provide comments on the full PDFs of scientific papers. We evaluated the quality of GPT-4's feedback through two large-scale studies. We first quantitatively compared GPT-4's generated feedback with human peer reviewer feedback in 15 Nature family journals (3,096 papers in total) and the ICLR machine learning conference (1,709 papers). The overlap in the points raised by GPT-4 and by human reviewers (average overlap 30.85% for Nature journals, 39.23% for ICLR) is comparable to the overlap between two human reviewers (average overlap 28.58% for Nature journals, 35.25% for ICLR). The overlap between GPT-4 and human reviewers is larger for the weaker papers. We then conducted a prospective user study with 308 researchers from 110 US institutions in the field of AI and computational biology to understand how researchers perceive feedback generated by our GPT-4 system on their own papers. Overall, more than half (57.4%) of the users found GPT-4 generated feedback helpful/very helpful and 82.4% found it more beneficial than feedback from at least some human reviewers. While our findings show that LLM-generated feedback can help researchers, we also identify several limitations.

  • 12 authors
·
Oct 3, 2023

Sigma: Differential Rescaling of Query, Key and Value for Efficient Language Models

We introduce Sigma, an efficient large language model specialized for the system domain, empowered by a novel architecture including DiffQKV attention, and pre-trained on our meticulously collected system domain data. DiffQKV attention significantly enhances the inference efficiency of Sigma by optimizing the Query (Q), Key (K), and Value (V) components in the attention mechanism differentially, based on their varying impacts on the model performance and efficiency indicators. Specifically, we (1) conduct extensive experiments that demonstrate the model's varying sensitivity to the compression of K and V components, leading to the development of differentially compressed KV, and (2) propose augmented Q to expand the Q head dimension, which enhances the model's representation capacity with minimal impacts on the inference speed. Rigorous theoretical and empirical analyses reveal that DiffQKV attention significantly enhances efficiency, achieving up to a 33.36% improvement in inference speed over the conventional grouped-query attention (GQA) in long-context scenarios. We pre-train Sigma on 6T tokens from various sources, including 19.5B system domain data that we carefully collect and 1T tokens of synthesized and rewritten data. In general domains, Sigma achieves comparable performance to other state-of-arts models. In the system domain, we introduce the first comprehensive benchmark AIMicius, where Sigma demonstrates remarkable performance across all tasks, significantly outperforming GPT-4 with an absolute improvement up to 52.5%.

  • 34 authors
·
Jan 23, 2025 2

Accelerating Sinkhorn Algorithm with Sparse Newton Iterations

Computing the optimal transport distance between statistical distributions is a fundamental task in machine learning. One remarkable recent advancement is entropic regularization and the Sinkhorn algorithm, which utilizes only matrix scaling and guarantees an approximated solution with near-linear runtime. Despite the success of the Sinkhorn algorithm, its runtime may still be slow due to the potentially large number of iterations needed for convergence. To achieve possibly super-exponential convergence, we present Sinkhorn-Newton-Sparse (SNS), an extension to the Sinkhorn algorithm, by introducing early stopping for the matrix scaling steps and a second stage featuring a Newton-type subroutine. Adopting the variational viewpoint that the Sinkhorn algorithm maximizes a concave Lyapunov potential, we offer the insight that the Hessian matrix of the potential function is approximately sparse. Sparsification of the Hessian results in a fast O(n^2) per-iteration complexity, the same as the Sinkhorn algorithm. In terms of total iteration count, we observe that the SNS algorithm converges orders of magnitude faster across a wide range of practical cases, including optimal transportation between empirical distributions and calculating the Wasserstein W_1, W_2 distance of discretized densities. The empirical performance is corroborated by a rigorous bound on the approximate sparsity of the Hessian matrix.

  • 7 authors
·
Jan 20, 2024

Two Experts Are All You Need for Steering Thinking: Reinforcing Cognitive Effort in MoE Reasoning Models Without Additional Training

Mixture-of-Experts (MoE) architectures within Large Reasoning Models (LRMs) have achieved impressive reasoning capabilities by selectively activating experts to facilitate structured cognitive processes. Despite notable advances, existing reasoning models often suffer from cognitive inefficiencies like overthinking and underthinking. To address these limitations, we introduce a novel inference-time steering methodology called Reinforcing Cognitive Experts (RICE), designed to improve reasoning performance without additional training or complex heuristics. Leveraging normalized Pointwise Mutual Information (nPMI), we systematically identify specialized experts, termed ''cognitive experts'' that orchestrate meta-level reasoning operations characterized by tokens like ''<think>''. Empirical evaluations with leading MoE-based LRMs (DeepSeek-R1 and Qwen3-235B) on rigorous quantitative and scientific reasoning benchmarks demonstrate noticeable and consistent improvements in reasoning accuracy, cognitive efficiency, and cross-domain generalization. Crucially, our lightweight approach substantially outperforms prevalent reasoning-steering techniques, such as prompt design and decoding constraints, while preserving the model's general instruction-following skills. These results highlight reinforcing cognitive experts as a promising, practical, and interpretable direction to enhance cognitive efficiency within advanced reasoning models.

  • 15 authors
·
May 20, 2025 2

Scalable Neural Network Kernels

We introduce the concept of scalable neural network kernels (SNNKs), the replacements of regular feedforward layers (FFLs), capable of approximating the latter, but with favorable computational properties. SNNKs effectively disentangle the inputs from the parameters of the neural network in the FFL, only to connect them in the final computation via the dot-product kernel. They are also strictly more expressive, as allowing to model complicated relationships beyond the functions of the dot-products of parameter-input vectors. We also introduce the neural network bundling process that applies SNNKs to compactify deep neural network architectures, resulting in additional compression gains. In its extreme version, it leads to the fully bundled network whose optimal parameters can be expressed via explicit formulae for several loss functions (e.g. mean squared error), opening a possibility to bypass backpropagation. As a by-product of our analysis, we introduce the mechanism of the universal random features (or URFs), applied to instantiate several SNNK variants, and interesting on its own in the context of scalable kernel methods. We provide rigorous theoretical analysis of all these concepts as well as an extensive empirical evaluation, ranging from point-wise kernel estimation to Transformers' fine-tuning with novel adapter layers inspired by SNNKs. Our mechanism provides up to 5x reduction in the number of trainable parameters, while maintaining competitive accuracy.

  • 5 authors
·
Oct 19, 2023

Why Do Transformers Fail to Forecast Time Series In-Context?

Time series forecasting (TSF) remains a challenging and largely unsolved problem in machine learning, despite significant recent efforts leveraging Large Language Models (LLMs), which predominantly rely on Transformer architectures. Empirical evidence consistently shows that even powerful Transformers often fail to outperform much simpler models, e.g., linear models, on TSF tasks; however, a rigorous theoretical understanding of this phenomenon remains limited. In this paper, we provide a theoretical analysis of Transformers' limitations for TSF through the lens of In-Context Learning (ICL) theory. Specifically, under AR(p) data, we establish that: (1) Linear Self-Attention (LSA) models cannot achieve lower expected MSE than classical linear models for in-context forecasting; (2) as the context length approaches to infinity, LSA asymptotically recovers the optimal linear predictor; and (3) under Chain-of-Thought (CoT) style inference, predictions collapse to the mean exponentially. We empirically validate these findings through carefully designed experiments. Our theory not only sheds light on several previously underexplored phenomena but also offers practical insights for designing more effective forecasting architectures. We hope our work encourages the broader research community to revisit the fundamental theoretical limitations of TSF and to critically evaluate the direct application of increasingly sophisticated architectures without deeper scrutiny.

  • 4 authors
·
Oct 10, 2025 2

On the Provable Advantage of Unsupervised Pretraining

Unsupervised pretraining, which learns a useful representation using a large amount of unlabeled data to facilitate the learning of downstream tasks, is a critical component of modern large-scale machine learning systems. Despite its tremendous empirical success, the rigorous theoretical understanding of why unsupervised pretraining generally helps remains rather limited -- most existing results are restricted to particular methods or approaches for unsupervised pretraining with specialized structural assumptions. This paper studies a generic framework, where the unsupervised representation learning task is specified by an abstract class of latent variable models Phi and the downstream task is specified by a class of prediction functions Psi. We consider a natural approach of using Maximum Likelihood Estimation (MLE) for unsupervised pretraining and Empirical Risk Minimization (ERM) for learning downstream tasks. We prove that, under a mild ''informative'' condition, our algorithm achieves an excess risk of mathcal{O}(mathcal{C_Phi/m} + mathcal{C_Psi/n}) for downstream tasks, where C_Phi, C_Psi are complexity measures of function classes Phi, Psi, and m, n are the number of unlabeled and labeled data respectively. Comparing to the baseline of mathcal{O}(mathcal{C_{Phi circ Psi}/n}) achieved by performing supervised learning using only the labeled data, our result rigorously shows the benefit of unsupervised pretraining when m gg n and C_{Phicirc Psi} > C_Psi. This paper further shows that our generic framework covers a wide range of approaches for unsupervised pretraining, including factor models, Gaussian mixture models, and contrastive learning.

  • 4 authors
·
Mar 2, 2023

Adaptive Safety Evaluation for Connected and Automated Vehicles with Sparse Control Variates

Safety performance evaluation is critical for developing and deploying connected and automated vehicles (CAVs). One prevailing way is to design testing scenarios using prior knowledge of CAVs, test CAVs in these scenarios, and then evaluate their safety performances. However, significant differences between CAVs and prior knowledge could severely reduce the evaluation efficiency. Towards addressing this issue, most existing studies focus on the adaptive design of testing scenarios during the CAV testing process, but so far they cannot be applied to high-dimensional scenarios. In this paper, we focus on the adaptive safety performance evaluation by leveraging the testing results, after the CAV testing process. It can significantly improve the evaluation efficiency and be applied to high-dimensional scenarios. Specifically, instead of directly evaluating the unknown quantity (e.g., crash rates) of CAV safety performances, we evaluate the differences between the unknown quantity and known quantity (i.e., control variates). By leveraging the testing results, the control variates could be well designed and optimized such that the differences are close to zero, so the evaluation variance could be dramatically reduced for different CAVs. To handle the high-dimensional scenarios, we propose the sparse control variates method, where the control variates are designed only for the sparse and critical variables of scenarios. According to the number of critical variables in each scenario, the control variates are stratified into strata and optimized within each stratum using multiple linear regression techniques. We justify the proposed method's effectiveness by rigorous theoretical analysis and empirical study of high-dimensional overtaking scenarios.

  • 6 authors
·
Dec 1, 2022