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Researcher profile

John T. Halloran

John T. Halloran contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceCryptography and SecurityMolecular Networks

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Published work

3 published item(s)

preprint2026arXiv

Be Kind, Rewrite: Benign Projections via Rewriting Defend Against LLM Data Poisoning Attacks

Large language models (LLMs) are highly susceptible to backdoor attacks (BAs), wherein training samples are poisoned using trigger-based harmful content. Furthermore, existing defenses have proven ineffective when extensively tested across BA patterns. To better combat BAs, we explore the use of LLM rewriting as a proactive defense against data poisoning. First, we theoretically show that when LLM rewriting utilizes open-book benign samples--termed open-book benign rewriting (OBBR)--the probability of a rewritten output being benign is strictly greater than that of closed-book rewriting. Thus, OBBR neutralizes harmful content by projecting training samples to the space of benign prompts. We then show that, in contrast to previous defenses, OBBR effectively mitigates a large number of existing BAs: across five known BAs and four widely used LLMs, OBBR increases safety performance by an average 51% compared to state-of-the-art BA defenses and 25.7% compared to closed-book rewriting methods. Finally, we show that OBBR is computationally efficient relative to other BA defenses, does not degrade model performance on natural language tasks after fine-tuning, and is capable of defending against non-trigger based data poisoning attacks.

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preprint2026arXiv

Leveraging RAG for Training-Free Alignment of LLMs

Large language model (LLM) alignment algorithms typically consist of post-training over preference pairs. While such algorithms are widely used to enable safety guardrails and align LLMs with general human preferences, we show that state-of-the-art alignment algorithms require significant computational resources while being far less capable of enabling refusal guardrails for recent agentic attacks. Thus, to improve refusal guardrails against such attacks without drastically increasing computational overhead, we introduce Retrieval Augmented Generation for Pref erence alignment (RAG-Pref), a simple RAG-based alignment algorithm which conditions on preferred and dispreferred samples to leverage contrastive information during inference. RAG-Pref is online (training-free), compatible with off-the-shelf packages, and, when combined with offline (training-based) alignment algorithms, enables more than an average 3.7 factor improvement in agentic attack refusals across five widely used LLMs, compared to 2.9 for other online alignment algorithms and 1.5 for offline alignment alone. We conclude by showing that, in stark contrast to other online alignment methods, RAG-Pref similarly increases performance on general human-preference alignment tasks and does not drastically increase overall computational requirements.

0 citations0 reviewsNo code linkedOpen access
preprint2014arXiv

Faster graphical model identification of tandem mass spectra using peptide word lattices

Liquid chromatography coupled with tandem mass spectrometry, also known as shotgun proteomics, is a widely-used high-throughput technology for identifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by a typical shotgun proteomics experiment begins by assigning to each observed spectrum the peptide hypothesized to be responsible for generating the spectrum, typically done by searching each spectrum against a database of peptides. We have recently described a machine learning method---Dynamic Bayesian Network for Rapid Identification of Peptides (DRIP)---that not only achieves state-of-the-art spectrum identification performance on a variety of datasets but also provides a trainable model capable of returning valuable auxiliary information regarding specific peptide-spectrum matches. In this work, we present two significant improvements to DRIP. First, we describe how to use word lattices, which are widely used in natural language processing, to significantly speed up DRIP's computations. To our knowledge, all existing shotgun proteomics search engines compute independent scores between a given observed spectrum and each possible candidate peptide from the database. The key idea of the word lattice is to represent the set of candidate peptides in a single data structure, thereby allowing sharing of redundant computations among the different candidates. We demonstrate that using lattices in conjunction with DRIP leads to speedups on the order of tens across yeast and worm data sets. Second, we introduce a variant of DRIP that uses a discriminative training framework, performing maximum mutual entropy estimation rather than maximum likelihood estimation. This modification improves DRIP's statistical power, enabling us to increase the number of identified spectrum at a 1% false discovery rate on yeast and worm data sets.

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