arXiv subjects

Bhavya Kailkhura

Publications and source records attributed to Bhavya Kailkhura.

At least 37 records · Page 2Linked to original sources

arXiv2025

Teaching Pretrained Language Models to Think Deeper with Retrofitted Recurrence

Recent advances in depth-recurrent language models show that recurrence can decouple train-time compute and parameter count from test-time compute. In this work, we study how to convert existing pretrained non-recurrent language models into depth-recurrent models. We find that using a curriculum of recurrences to increase the effective depth of the model over the course of training preserves performance while reducing total computational cost. In our experiments, on mathematics, we observe that converting pretrained models to recurrent ones results in better performance at a given compute budget than simply post-training the original non-recurrent language model.

cs.CL↗

arXiv2025

UProp: Investigating the Uncertainty Propagation of LLMs in Multi-Step Agentic Decision-Making

As Large Language Models (LLMs) are integrated into safety-critical applications involving sequential decision-making in the real world, it is essential to know when to trust LLM decisions. Existing LLM Uncertainty Quantification (UQ) methods are primarily designed for single-turn question-answering formats, resulting in multi-step decision-making scenarios, e.g., LLM agentic system, being underexplored. In this paper, we introduce a principled, information-theoretic framework that decomposes LLM sequential decision uncertainty into two parts: (i) internal uncertainty intrinsic to the current decision, which is focused on existing UQ methods, and (ii) extrinsic uncertainty, a Mutual-Information (MI) quantity describing how much uncertainty should be inherited from preceding decisions. We then propose UProp, an efficient and effective extrinsic uncertainty estimator that converts the direct estimation of MI to the estimation of Pointwise Mutual Information (PMI) over multiple Trajectory-Dependent Decision Processes (TDPs). UProp is evaluated over extensive multi-step decision-making benchmarks, e.g., AgentBench and HotpotQA, with state-of-the-art LLMs, e.g., GPT-4.1 and DeepSeek-V3. Experimental results demonstrate that UProp significantly outperforms existing single-turn UQ baselines equipped with thoughtful aggregation strategies. Moreover, we provide a comprehensive analysis of UProp, including sampling efficiency, potential applications, and intermediate uncertainty propagation, to demonstrate its effectiveness. Codes will be available at https://github.com/jinhaoduan/UProp.

cs.CL↗

arXiv2025

AegisLLM: Scaling Agentic Systems for Self-Reflective Defense in LLM Security

We introduce AegisLLM, a cooperative multi-agent defense against adversarial attacks and information leakage. In AegisLLM, a structured workflow of autonomous agents - orchestrator, deflector, responder, and evaluator - collaborate to ensure safe and compliant LLM outputs, while self-improving over time through prompt optimization. We show that scaling agentic reasoning system at test-time - both by incorporating additional agent roles and by leveraging automated prompt optimization (such as DSPy)- substantially enhances robustness without compromising model utility. This test-time defense enables real-time adaptability to evolving attacks, without requiring model retraining. Comprehensive evaluations across key threat scenarios, including unlearning and jailbreaking, demonstrate the effectiveness of AegisLLM. On the WMDP unlearning benchmark, AegisLLM achieves near-perfect unlearning with only 20 training examples and fewer than 300 LM calls. For jailbreaking benchmarks, we achieve 51% improvement compared to the base model on StrongReject, with false refusal rates of only 7.9% on PHTest compared to 18-55% for comparable methods. Our results highlight the advantages of adaptive, agentic reasoning over static defenses, establishing AegisLLM as a strong runtime alternative to traditional approaches based on model modifications. Code is available at https://github.com/zikuicai/aegisllm

cs.LG↗

arXiv2025

A Comprehensive Survey in LLM(-Agent) Full Stack Safety: Data, Training and Deployment

The remarkable success of Large Language Models (LLMs) has illuminated a promising pathway toward achieving Artificial General Intelligence for both academic and industrial communities, owing to their unprecedented performance across various applications. As LLMs continue to gain prominence in both research and commercial domains, their security and safety implications have become a growing concern, not only for researchers and corporations but also for every nation. Currently, existing surveys on LLM safety primarily focus on specific stages of the LLM lifecycle, e.g., deployment phase or fine-tuning phase, lacking a comprehensive understanding of the entire "lifechain" of LLMs. To address this gap, this paper introduces, for the first time, the concept of "full-stack" safety to systematically consider safety issues throughout the entire process of LLM training, deployment, and eventual commercialization. Compared to the off-the-shelf LLM safety surveys, our work demonstrates several distinctive advantages: (I) Comprehensive Perspective. We define the complete LLM lifecycle as encompassing data preparation, pre-training, post-training, deployment and final commercialization. To our knowledge, this represents the first safety survey to encompass the entire lifecycle of LLMs. (II) Extensive Literature Support. Our research is grounded in an exhaustive review of over 800+ papers, ensuring comprehensive coverage and systematic organization of security issues within a more holistic understanding. (III) Unique Insights. Through systematic literature analysis, we have developed reliable roadmaps and perspectives for each chapter. Our work identifies promising research directions, including safety in data generation, alignment techniques, model editing, and LLM-based agent systems. These insights provide valuable guidance for researchers pursuing future work in this field.

cs.CR↗

arXiv2025

The Common Pile v0.1: An 8TB Dataset of Public Domain and Openly Licensed Text

Large language models (LLMs) are typically trained on enormous quantities of unlicensed text, a practice that has led to scrutiny due to possible intellectual property infringement and ethical concerns. Training LLMs on openly licensed text presents a first step towards addressing these issues, but prior data collection efforts have yielded datasets too small or low-quality to produce performant LLMs. To address this gap, we collect, curate, and release the Common Pile v0.1, an eight terabyte collection of openly licensed text designed for LLM pretraining. The Common Pile comprises content from 30 sources that span diverse domains including research papers, code, books, encyclopedias, educational materials, audio transcripts, and more. Crucially, we validate our efforts by training two 7 billion parameter LLMs on text from the Common Pile: Comma v0.1-1T and Comma v0.1-2T, trained on 1 and 2 trillion tokens respectively. Both models attain competitive performance to LLMs trained on unlicensed text with similar computational budgets, such as Llama 1 and 2 7B. In addition to releasing the Common Pile v0.1 itself, we also release the code used in its creation as well as the training mixture and checkpoints for the Comma v0.1 models.

cs.CL↗

arXiv2025

Act Only When It Pays: Efficient Reinforcement Learning for LLM Reasoning via Selective Rollouts

Reinforcement learning, such as PPO and GRPO, has powered recent breakthroughs in LLM reasoning. Scaling rollout to sample more prompts enables models to selectively use higher-quality data for training, which can stabilize RL training and improve model performance. However, this comes at the cost of significant computational overhead. In this paper, we show that a substantial portion of this overhead can be avoided by skipping uninformative prompts before rollout. Our analysis of reward dynamics reveals a strong temporal consistency in prompt value: prompts that are uninformative in one epoch of training are likely to remain uninformative in future epochs. Based on these insights, we propose GRESO (GRPO with Efficient Selective Rollout), an online, lightweight pre-rollout filtering algorithm that predicts and skips uninformative prompts using reward training dynamics. By evaluating GRESO on a broad range of math reasoning benchmarks and models, such as Qwen2.5-Math-1.5B, DeepSeek-R1-Distill-Qwen-1.5B, and Qwen2.5-Math-7B, we show that GRESO achieves up to 2.4x wall-clock time speedup in rollout and up to 2.0x speedup in total training time without accuracy degradation.

cs.AI↗

arXiv2025

LLM Unlearning Reveals a Stronger-Than-Expected Coreset Effect in Current Benchmarks

Large language model unlearning has become a critical challenge in ensuring safety and controlled model behavior by removing undesired data-model influences from the pretrained model while preserving general utility. Significant recent efforts have been dedicated to developing LLM unlearning benchmarks such as WMDP (Weapons of Mass Destruction Proxy) and MUSE (Machine Unlearning Six-way Evaluation), facilitating standardized unlearning performance assessment and method comparison. Despite their usefulness, we uncover for the first time a novel coreset effect within these benchmarks. Specifically, we find that LLM unlearning achieved with the original (full) forget set can be effectively maintained using a significantly smaller subset (functioning as a "coreset"), e.g., as little as 5% of the forget set, even when selected at random. This suggests that LLM unlearning in these benchmarks can be performed surprisingly easily, even in an extremely low-data regime. We demonstrate that this coreset effect remains strong, regardless of the LLM unlearning method used, such as NPO (Negative Preference Optimization) and RMU (Representation Misdirection Unlearning), the popular ones in these benchmarks. The surprisingly strong coreset effect is also robust across various data selection methods, ranging from random selection to more sophisticated heuristic approaches. We explain the coreset effect in LLM unlearning through a keyword-based perspective, showing that keywords extracted from the forget set alone contribute significantly to unlearning effectiveness and indicating that current unlearning is driven by a compact set of high-impact tokens rather than the entire dataset. We further justify the faithfulness of coreset-unlearned models along additional dimensions, such as mode connectivity and robustness to jailbreaking attacks. Codes are available at https://github.com/OPTML-Group/MU-Coreset.

cs.CL↗

arXiv2025

Double Visual Defense: Adversarial Pre-training and Instruction Tuning for Improving Vision-Language Model Robustness

This paper investigates the robustness of vision-language models against adversarial visual perturbations and introduces a novel ``double visual defense" to enhance this robustness. Unlike previous approaches that resort to lightweight adversarial fine-tuning of a pre-trained CLIP model, we perform large-scale adversarial vision-language pre-training from scratch using web-scale data. We then strengthen the defense by incorporating adversarial visual instruction tuning. The resulting models from each stage, $Δ$CLIP and $Δ^2$LLaVA, show substantially enhanced zero-shot robustness and set a new state-of-the-art in adversarial defense for vision-language models. For example, the adversarial robustness of $Δ$CLIP surpasses that of the previous best models on ImageNet-1k by ~20%. %For example, $Δ$CLIP surpasses the previous best models on ImageNet-1k by ~20% in terms of adversarial robustness. Similarly, compared to prior art, $Δ^2$LLaVA brings a ~30% robustness improvement to image captioning task and a ~20% robustness improvement to visual question answering task. Furthermore, our models exhibit stronger zero-shot recognition capability, fewer hallucinations, and superior reasoning performance compared to baselines. Our project page is https://doublevisualdefense.github.io/.

cs.CV↗

arXiv2025

Mixture of Robust Experts (MoRE):A Robust Denoising Method towards multiple perturbations

To tackle the susceptibility of deep neural networks to adversarial examples, the adversarial training has been proposed which provides a notion of security through an inner maximization problem presenting the first-order adversaries embedded within the outer minimization of the training loss. To generalize the adversarial robustness over different perturbation types, the adversarial training method has been augmented with the improved inner maximization presenting a union of multiple perturbations e.g., various $\ell_p$ norm-bounded perturbations. However, the improved inner maximization only enjoys limited flexibility in terms of the allowable perturbation types. In this work, through a gating mechanism, we assemble a set of expert networks, each one either adversarially trained to deal with a particular perturbation type or normally trained for boosting accuracy on clean data. The gating module assigns weights dynamically to each expert to achieve superior accuracy under various data types e.g., adversarial examples, adverse weather perturbations, and clean input. In order to deal with the obfuscated gradients issue, the training of the gating module is conducted together with fine-tuning of the last fully connected layers of expert networks through adversarial training approach. Using extensive experiments, we show that our Mixture of Robust Experts (MoRE) approach enables a flexible integration of a broad range of robust experts with superior performance.

cs.LG↗

arXiv2025

GRNFormer: A Biologically-Guided Framework for Integrating Gene Regulatory Networks into RNA Foundation Models

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: $3.6\%$ increase in drug response prediction correlation, $9.6\%$ improvement in single-cell drug classification AUC, and $1.1\%$ average gain in gene perturbation prediction accuracy.

cs.LG↗

arXiv2025

EAIRA: Establishing a Methodology for Evaluating AI Models as Scientific Research Assistants

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

cs.AI↗

arXiv2025

ELFS: Label-Free Coreset Selection with Proxy Training Dynamics

High-quality human-annotated data is crucial for modern deep learning pipelines, yet the human annotation process is both costly and time-consuming. Given a constrained human labeling budget, selecting an informative and representative data subset for labeling can significantly reduce human annotation effort. Well-performing state-of-the-art (SOTA) coreset selection methods require ground truth labels over the whole dataset, failing to reduce the human labeling burden. Meanwhile, SOTA label-free coreset selection methods deliver inferior performance due to poor geometry-based difficulty scores. In this paper, we introduce ELFS (Effective Label-Free Coreset Selection), a novel label-free coreset selection method. ELFS significantly improves label-free coreset selection by addressing two challenges: 1) ELFS utilizes deep clustering to estimate training dynamics-based data difficulty scores without ground truth labels; 2) Pseudo-labels introduce a distribution shift in the data difficulty scores, and we propose a simple but effective double-end pruning method to mitigate bias on calculated scores. We evaluate ELFS on four vision benchmarks and show that, given the same vision encoder, ELFS consistently outperforms SOTA label-free baselines. For instance, when using SwAV as the encoder, ELFS outperforms D2 by up to 10.2% in accuracy on ImageNet-1K. We make our code publicly available on GitHub.

cs.CV↗

arXiv2025

Scaling up Test-Time Compute with Latent Reasoning: A Recurrent Depth Approach

We study a novel language model architecture that is capable of scaling test-time computation by implicitly reasoning in latent space. Our model works by iterating a recurrent block, thereby unrolling to arbitrary depth at test-time. This stands in contrast to mainstream reasoning models that scale up compute by producing more tokens. Unlike approaches based on chain-of-thought, our approach does not require any specialized training data, can work with small context windows, and can capture types of reasoning that are not easily represented in words. We scale a proof-of-concept model to 3.5 billion parameters and 800 billion tokens. We show that the resulting model can improve its performance on reasoning benchmarks, sometimes dramatically, up to a computation load equivalent to 50 billion parameters.

cs.LG↗

arXiv2025

Layer-Level Self-Exposure and Patch: Affirmative Token Mitigation for Jailbreak Attack Defense

As large language models (LLMs) are increasingly deployed in diverse applications, including chatbot assistants and code generation, aligning their behavior with safety and ethical standards has become paramount. However, jailbreak attacks, which exploit vulnerabilities to elicit unintended or harmful outputs, threaten LLMs' safety significantly. In this paper, we introduce Layer-AdvPatcher, a novel methodology designed to defend against jailbreak attacks by utilizing an unlearning strategy to patch specific layers within LLMs through self-augmented datasets. Our insight is that certain layer(s), tend to produce affirmative tokens when faced with harmful prompts. By identifying these layers and adversarially exposing them to generate more harmful data, one can understand their inherent and diverse vulnerabilities to attacks. With these exposures, we then "unlearn" these issues, reducing the impact of affirmative tokens and hence minimizing jailbreak risks while keeping the model's responses to safe queries intact. We conduct extensive experiments on two models, four benchmark datasets, and multiple state-of-the-art jailbreak attacks to demonstrate the efficacy of our approach. Results indicate that our framework reduces the harmfulness and attack success rate of jailbreak attacks without compromising utility for benign queries compared to recent defense methods. Our code is publicly available at: https://github.com/oyy2000/LayerAdvPatcher

cs.CR↗

arXiv2025

Speculative Diffusion Decoding: Accelerating Language Generation through Diffusion

Speculative decoding has emerged as a widely adopted method to accelerate large language model inference without sacrificing the quality of the model outputs. While this technique has facilitated notable speed improvements by enabling parallel sequence verification, its efficiency remains inherently limited by the reliance on incremental token generation in existing draft models. To overcome this limitation, this paper proposes an adaptation of speculative decoding which uses discrete diffusion models to generate draft sequences. This allows parallelization of both the drafting and verification steps, providing significant speedups to the inference process. Our proposed approach, $\textit{Speculative Diffusion Decoding (SpecDiff)}$, is validated on standard language generation benchmarks and empirically demonstrated to provide up to 7.2x speedups over standard generation processes and up to 1.75x speedups over existing speculative decoding approaches.

cs.CL↗

arXiv2025

Extracting and Understanding the Superficial Knowledge in Alignment

Alignment of large language models (LLMs) with human values and preferences, often achieved through fine-tuning based on human feedback, is essential for ensuring safe and responsible AI behaviors. However, the process typically requires substantial data and computation resources. Recent studies have revealed that alignment might be attainable at lower costs through simpler methods, such as in-context learning. This leads to the question: Is alignment predominantly superficial? In this paper, we delve into this question and provide a quantitative analysis. We formalize the concept of superficial knowledge, defining it as knowledge that can be acquired through easily token restyling, without affecting the model's ability to capture underlying causal relationships between tokens. We propose a method to extract and isolate superficial knowledge from aligned models, focusing on the shallow modifications to the final token selection process. By comparing models augmented only with superficial knowledge to fully aligned models, we quantify the superficial portion of alignment. Our findings reveal that while superficial knowledge constitutes a significant portion of alignment, particularly in safety and detoxification tasks, it is not the whole story. Tasks requiring reasoning and contextual understanding still rely on deeper knowledge. Additionally, we demonstrate two practical advantages of isolated superficial knowledge: (1) it can be transferred between models, enabling efficient offsite alignment of larger models using extracted superficial knowledge from smaller models, and (2) it is recoverable, allowing for the restoration of alignment in compromised models without sacrificing performance.

cs.CL↗

arXiv2024

Transformers Can Do Arithmetic with the Right Embeddings

The poor performance of transformers on arithmetic tasks seems to stem in large part from their inability to keep track of the exact position of each digit inside of a large span of digits. We mend this problem by adding an embedding to each digit that encodes its position relative to the start of the number. In addition to the boost these embeddings provide on their own, we show that this fix enables architectural modifications such as input injection and recurrent layers to improve performance even further. With positions resolved, we can study the logical extrapolation ability of transformers. Can they solve arithmetic problems that are larger and more complex than those in their training data? We find that training on only 20 digit numbers with a single GPU for one day, we can reach state-of-the-art performance, achieving up to 99% accuracy on 100 digit addition problems. Finally, we show that these gains in numeracy also unlock improvements on other multi-step reasoning tasks including sorting and multiplication.

cs.LG↗

arXiv2024

Training Dynamics of Transformers to Recognize Word Co-occurrence via Gradient Flow Analysis

Understanding the training dynamics of transformers is important to explain the impressive capabilities behind large language models. In this work, we study the dynamics of training a shallow transformer on a task of recognizing co-occurrence of two designated words. In the literature of studying training dynamics of transformers, several simplifications are commonly adopted such as weight reparameterization, attention linearization, special initialization, and lazy regime. In contrast, we analyze the gradient flow dynamics of simultaneously training three attention matrices and a linear MLP layer from random initialization, and provide a framework of analyzing such dynamics via a coupled dynamical system. We establish near minimum loss and characterize the attention model after training. We discover that gradient flow serves as an inherent mechanism that naturally divide the training process into two phases. In Phase 1, the linear MLP quickly aligns with the two target signals for correct classification, whereas the softmax attention remains almost unchanged. In Phase 2, the attention matrices and the MLP evolve jointly to enlarge the classification margin and reduce the loss to a near minimum value. Technically, we prove a novel property of the gradient flow, termed \textit{automatic balancing of gradients}, which enables the loss values of different samples to decrease almost at the same rate and further facilitates the proof of near minimum training loss. We also conduct experiments to verify our theoretical results.

cs.LG↗