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Ke Ding

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4 papers

2 author rows

AAAI Conference 2026 Conference Paper

NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable Representations

Ke Ding
Brian Parker
Jiayu Wen

Pre-training large language models on genomic sequences has become a powerful approach for learning biologically meaningful representations. While masked language modeling (MLM)-based approaches, such as DNABERT and Nucleotide Transformer (NT), achieve strong performance, they are hindered by inefficiencies due to partial token supervision, pre-training/fine-tuning mismatches, and high computational costs. We introduce NucEL, the first ELECTRA-style pre-training framework for genomic foundation models, which overcomes these challenges. Through a discriminator network identifying tokens modified by a generator, NucEL achieves comprehensive token-level supervision across all sequence positions, thereby markedly improving training efficiency relative to the partial supervision of masked positions inherent in MLM frameworks. By integrating ModernBERT’s architectural advancements, including hybrid local-global attention and flash attention mechanisms, NucEL establishes an optimized BERT architecture for genomic sequence modeling. Unlike traditional methods that tokenize genomic sequences into 6-mers, NucEL implements single-nucleotide tokenization, enabling fine-grained resolution and improving both efficiency and interpretability. Pre-trained on the human genome only, NucEL achieves state-of-the-art performance on benchmark datasets across diverse downstream tasks in both human and non-human species, including regulatory element identification (e.g., promoters, enhancers), transcription factor binding prediction in human and mouse, open chromatin region classification, and histone modification profiles, surpassing MLM-based models of similar size and rivaling models 25 times larger, such as NT. Ablation studies provide critical insights into tokenization and masking strategies, optimizing ELECTRA-style pretraining for DNA sequences. Attention analyses reveal NucEL’s superior ability to capture biologically relevant sequence motifs compared to NT, offering valuable insights into its hierarchical learning process and regulatory element modeling capabilities. This work highlights the potential of ELECTRA-style pretraining as an efficient and effective strategy for advancing genomic representation learning with broad implications for future genomic research.

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ICLR Conference 2025 Conference Paper

HELMET: How to Evaluate Long-context Models Effectively and Thoroughly

Howard Yen
Tianyu Gao 0001
Minmin Hou
Ke Ding
Daniel Fleischer
Peter Izsak
Moshe Wasserblat
Danqi Chen 0001

Many benchmarks exist for evaluating long-context language models (LCLMs), yet developers often rely on synthetic tasks such as needle-in-a-haystack (NIAH) or an arbitrary subset of tasks. However, it remains unclear whether these benchmarks reflect the diverse downstream applications of LCLMs, and such inconsistencies further complicate model comparison. We investigate the underlying reasons behind these practices and find that existing benchmarks often provide noisy signals due to limited coverage of applications, insufficient context lengths, unreliable metrics, and incompatibility with base models. In this work, we introduce HELMET (How to Evaluate Long-context Models Effectively and Thoroughly), a comprehensive benchmark encompassing seven diverse, application-centric categories. We also address several issues in previous benchmarks by adding controllable lengths up to 128K tokens, model-based evaluation for reliable metrics, and few-shot prompting for robustly evaluating base models. Consequently, we demonstrate that HELMET offers more reliable and consistent rankings of frontier LCLMs. Through a comprehensive study of 59 LCLMs, we find that (1) synthetic tasks like NIAH do not reliably predict downstream performance; (2) the diverse categories in HELMET exhibit distinct trends and low correlations with each other; and (3) while most LCLMs achieve perfect NIAH scores, open-source models significantly lag behind closed ones when tasks require full-context reasoning or following complex instructions---the gap widens as length increases. Finally, we recommend using our RAG tasks for fast model development, as they are easy to run and better predict other downstream performance; ultimately, we advocate for a holistic evaluation across diverse tasks.

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ICML Conference 2025 Conference Paper

OrcaLoca: An LLM Agent Framework for Software Issue Localization

Zhongming Yu
Hejia Zhang 0001
Yujie Zhao
Hanxian Huang
Matrix Yao
Ke Ding
Jishen Zhao

Recent developments in Large Language Model (LLM) agents are revolutionizing Autonomous Software Engineering (ASE), enabling automated coding, problem fixes, and feature improvements. However, localization – precisely identifying software problems by navigating to relevant code sections – remains a significant challenge. Current approaches often yield suboptimal results due to a lack of effective integration between LLM agents and precise code search mechanisms. This paper introduces OrcaLoca, an LLM agent framework that improves accuracy for software issue localization by integrating priority-based scheduling for LLM-guided action, action decomposition with relevance scoring, and distance-aware context pruning. Experimental results demonstrate that OrcaLoca becomes the new open-source state-of-the-art (SOTA) in function match rate (65. 33%) on SWE-bench Lite. It also improves the final resolved rate of an open-source framework by 6. 33 percentage points through its patch generation integration.

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NeurIPS Conference 2024 Conference Paper

Defensive Unlearning with Adversarial Training for Robust Concept Erasure in Diffusion Models

Yimeng Zhang
Xin Chen
Jinghan Jia
Yihua Zhang
Chongyu Fan
Jiancheng Liu
Mingyi Hong
Ke Ding

Diffusion models (DMs) have achieved remarkable success in text-to-image generation, but they also pose safety risks, such as the potential generation of harmful content and copyright violations. The techniques of machine unlearning, also known as concept erasing, have been developed to address these risks. However, these techniques remain vulnerable to adversarial prompt attacks, which can prompt DMs post-unlearning to regenerate undesired images containing concepts (such as nudity) meant to be erased. This work aims to enhance the robustness of concept erasing by integrating the principle of adversarial training (AT) into machine unlearning, resulting in the robust unlearning framework referred to as AdvUnlearn. However, achieving this effectively and efficiently is highly nontrivial. First, we find that a straightforward implementation of AT compromises DMs’ image generation quality post-unlearning. To address this, we develop a utility-retaining regularization on an additional retain set, optimizing the trade-off between concept erasure robustness and model utility in AdvUnlearn. Moreover, we identify the text encoder as a more suitable module for robustification compared to UNet, ensuring unlearning effectiveness. And the acquired text encoder can serve as a plug-and-play robust unlearner for various DM types. Empirically, we perform extensive experiments to demonstrate the robustness advantage of AdvUnlearn across various DM unlearning scenarios, including the erasure of nudity, objects, and style concepts. In addition to robustness, AdvUnlearn also achieves a balanced tradeoff with model utility. To our knowledge, this is the first work to systematically explore robust DM unlearning through AT, setting it apart from existing methods that overlook robustness in concept erasing. Codes are available at https: //github. com/OPTML-Group/AdvUnlearn. Warning: This paper contains model outputs that may be offensive in nature.

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