arXiv subjects

Fabio Petroni

Publications and source records attributed to Fabio Petroni.

At least 19 recordsLinked to original sources

arXiv2026

EMBL AI Librarian: Life-Sciences Knowledge Layer for AI Agents

The web is increasingly accessed by AI agents rather than humans. Every agent needs knowledge, especially in the life-sciences, where agentic pipelines are growing fast. Access to the literature is a crucial part of that need, and resources such as Europe PMC, with over 40M indexed records, are widely used to meet it. Yet these resources were not built for AI agents: they take keywords and complex syntax and return whole papers, so every agent must learn the syntax, issue several searches, and read full papers to find the evidence it needs. We introduce EMBL AI Librarian, a knowledge layer that upgrades the Europe PMC interface for AI agents: an agent asks in natural language and receives evidence that answers it. A single LLM orchestrates the whole knowledge retrieval process: it plans complementary subqueries executed by the live Europe PMC search engine, then reads the selected papers and locates the relevant evidence. We evaluate Librarian across four benchmarks: literature synthesis, claim verification, open-domain question answering, and downstream biology tasks such as protocol questions and sequence manipulation. On ScholarQABench, Librarian improves Citation F1 by more than $16$ points over strong recently published baselines. Used as the retrieval layer of an existing claim-verification pipeline, it increases agreement with expert consensus; and on the open-form LitQA2 benchmark, a GPT-5.4 agent scores about $8$ points higher when grounded in Librarian than with web search. Overall, our results show that equipping life-science agents with the Librarian knowledge layer improves performance across a range of tasks. We release our code publicly at https://github.com/petroni-lab/librarian

cs.CL↗

arXiv2026

ReSIM: Re-ranking Binary Similarity Embeddings to Improve Function Search Performance

Binary Function Similarity (BFS), the problem of determining whether two binary functions originate from the same source code, has been extensively studied in recent research across security, software engineering, and machine learning communities. This interest arises from its central role in developing vulnerability detection systems, copyright infringement analysis, and malware phylogeny tools. Nearly all binary function similarity systems embed assembly functions into real-valued vectors, where similar functions map to points that lie close to each other in the metric space. These embeddings enable function search: a query function is embedded and compared against a database of candidate embeddings to retrieve the most similar matches. Despite their effectiveness, such systems rely on bi-encoder architectures that embed functions independently, limiting their ability to capture cross-function relationships and similarities. To address this limitation, we introduce ReSIM, a novel and enhanced function search system that complements embedding-based search with a neural re-ranker. Unlike traditional embedding models, our reranking module jointly processes query-candidate pairs to compute ranking scores based on their mutual representation, allowing for more accurate similarity assessment. By re-ranking the top results from embedding-based retrieval, ReSIM leverages fine-grained relation information that bi-encoders cannot capture. We evaluate ReSIM across seven embedding models on two benchmark datasets, demonstrating consistent improvements in search effectiveness, with average gains of 21.7% in terms of nDCG and 27.8% in terms of Recall.

cs.CR↗

arXiv2025

Beyond RAG: Task-Aware KV Cache Compression for Comprehensive Knowledge Reasoning

Incorporating external knowledge in large language models (LLMs) enhances their utility across diverse applications, but existing methods have trade-offs. Retrieval-Augmented Generation (RAG) fetches evidence via similarity search, but key information may fall outside top ranked results. Long-context models can process multiple documents but are computationally expensive and limited by context window size. Inspired by students condensing study material for open-book exams, we propose task-aware key-value (KV) cache compression, which compresses external knowledge in a zero- or few-shot setup. This enables LLMs to reason efficiently over a compacted representation of all relevant information. Experiments show our approach outperforms both RAG and task-agnostic compression methods. On LongBench v2, it improves accuracy by up to 7 absolute points over RAG with a 30x compression rate, while reducing inference latency from 0.43s to 0.16s. A synthetic dataset highlights that RAG performs well when sparse evidence suffices, whereas task-aware compression is superior for broad knowledge tasks.

cs.CL↗

arXiv2023

Lost in the Middle: How Language Models Use Long Contexts

While recent language models have the ability to take long contexts as input, relatively little is known about how well they use longer context. We analyze the performance of language models on two tasks that require identifying relevant information in their input contexts: multi-document question answering and key-value retrieval. We find that performance can degrade significantly when changing the position of relevant information, indicating that current language models do not robustly make use of information in long input contexts. In particular, we observe that performance is often highest when relevant information occurs at the beginning or end of the input context, and significantly degrades when models must access relevant information in the middle of long contexts, even for explicitly long-context models. Our analysis provides a better understanding of how language models use their input context and provides new evaluation protocols for future long-context language models.

cs.CL↗

arXiv2023

Can discrete information extraction prompts generalize across language models?

We study whether automatically-induced prompts that effectively extract information from a language model can also be used, out-of-the-box, to probe other language models for the same information. After confirming that discrete prompts induced with the AutoPrompt algorithm outperform manual and semi-manual prompts on the slot-filling task, we demonstrate a drop in performance for AutoPrompt prompts learned on a model and tested on another. We introduce a way to induce prompts by mixing language models at training time that results in prompts that generalize well across models. We conduct an extensive analysis of the induced prompts, finding that the more general prompts include a larger proportion of existing English words and have a less order-dependent and more uniform distribution of information across their component tokens. Our work provides preliminary evidence that it's possible to generate discrete prompts that can be induced once and used with a number of different models, and gives insights on the properties characterizing such prompts.

cs.CL↗

arXiv2022

Atlas: Few-shot Learning with Retrieval Augmented Language Models

Large language models have shown impressive few-shot results on a wide range of tasks. However, when knowledge is key for such results, as is the case for tasks such as question answering and fact checking, massive parameter counts to store knowledge seem to be needed. Retrieval augmented models are known to excel at knowledge intensive tasks without the need for as many parameters, but it is unclear whether they work in few-shot settings. In this work we present Atlas, a carefully designed and pre-trained retrieval augmented language model able to learn knowledge intensive tasks with very few training examples. We perform evaluations on a wide range of tasks, including MMLU, KILT and NaturalQuestions, and study the impact of the content of the document index, showing that it can easily be updated. Notably, Atlas reaches over 42% accuracy on Natural Questions using only 64 examples, outperforming a 540B parameters model by 3% despite having 50x fewer parameters.

cs.CL↗

arXiv2022

EditEval: An Instruction-Based Benchmark for Text Improvements

Evaluation of text generation to date has primarily focused on content created sequentially, rather than improvements on a piece of text. Writing, however, is naturally an iterative and incremental process that requires expertise in different modular skills such as fixing outdated information or making the style more consistent. Even so, comprehensive evaluation of a model's capacity to perform these skills and the ability to edit remains sparse. This work presents EditEval: An instruction-based, benchmark and evaluation suite that leverages high-quality existing and new datasets for automatic evaluation of editing capabilities such as making text more cohesive and paraphrasing. We evaluate several pre-trained models, which shows that InstructGPT and PEER perform the best, but that most baselines fall below the supervised SOTA, particularly when neutralizing and updating information. Our analysis also shows that commonly used metrics for editing tasks do not always correlate well, and that optimization for prompts with the highest performance does not necessarily entail the strongest robustness to different models. Through the release of this benchmark and a publicly available leaderboard challenge, we hope to unlock future research in developing models capable of iterative and more controllable editing.

cs.CL↗

arXiv2022

Entity Tagging: Extracting Entities in Text Without Mention Supervision

Detection and disambiguation of all entities in text is a crucial task for a wide range of applications. The typical formulation of the problem involves two stages: detect mention boundaries and link all mentions to a knowledge base. For a long time, mention detection has been considered as a necessary step for extracting all entities in a piece of text, even if the information about mention spans is ignored by some downstream applications that merely focus on the set of extracted entities. In this paper we show that, in such cases, detection of mention boundaries does not bring any considerable performance gain in extracting entities, and therefore can be skipped. To conduct our analysis, we propose an "Entity Tagging" formulation of the problem, where models are evaluated purely on the set of extracted entities without considering mentions. We compare a state-of-the-art mention-aware entity linking solution against GET, a mention-agnostic sequence-to-sequence model that simply outputs a list of disambiguated entities given an input context. We find that these models achieve comparable performance when trained both on a fully and partially annotated dataset across multiple benchmarks, demonstrating that GET can extract disambiguated entities with strong performance without explicit mention boundaries supervision.

cs.IR↗

arXiv2022

PEER: A Collaborative Language Model

Textual content is often the output of a collaborative writing process: We start with an initial draft, ask for suggestions, and repeatedly make changes. Agnostic of this process, today's language models are trained to generate only the final result. As a consequence, they lack several abilities crucial for collaborative writing: They are unable to update existing texts, difficult to control and incapable of verbally planning or explaining their actions. To address these shortcomings, we introduce PEER, a collaborative language model that is trained to imitate the entire writing process itself: PEER can write drafts, add suggestions, propose edits and provide explanations for its actions. Crucially, we train multiple instances of PEER able to infill various parts of the writing process, enabling the use of self-training techniques for increasing the quality, amount and diversity of training data. This unlocks PEER's full potential by making it applicable in domains for which no edit histories are available and improving its ability to follow instructions, to write useful comments, and to explain its actions. We show that PEER achieves strong performance across various domains and editing tasks.

cs.CL↗

arXiv2022

Improving Wikipedia Verifiability with AI

Verifiability is a core content policy of Wikipedia: claims that are likely to be challenged need to be backed by citations. There are millions of articles available online and thousands of new articles are released each month. For this reason, finding relevant sources is a difficult task: many claims do not have any references that support them. Furthermore, even existing citations might not support a given claim or become obsolete once the original source is updated or deleted. Hence, maintaining and improving the quality of Wikipedia references is an important challenge and there is a pressing need for better tools to assist humans in this effort. Here, we show that the process of improving references can be tackled with the help of artificial intelligence (AI). We develop a neural network based system, called Side, to identify Wikipedia citations that are unlikely to support their claims, and subsequently recommend better ones from the web. We train this model on existing Wikipedia references, therefore learning from the contributions and combined wisdom of thousands of Wikipedia editors. Using crowd-sourcing, we observe that for the top 10% most likely citations to be tagged as unverifiable by our system, humans prefer our system's suggested alternatives compared to the originally cited reference 70% of the time. To validate the applicability of our system, we built a demo to engage with the English-speaking Wikipedia community and find that Side's first citation recommendation collects over 60% more preferences than existing Wikipedia citations for the same top 10% most likely unverifiable claims according to Side. Our results indicate that an AI-based system could be used, in tandem with humans, to improve the verifiability of Wikipedia. More generally, we hope that our work can be used to assist fact checking efforts and increase the general trustworthiness of information online.

cs.IR↗

arXiv2022

Learning To Recognize Procedural Activities with Distant Supervision

In this paper we consider the problem of classifying fine-grained, multi-step activities (e.g., cooking different recipes, making disparate home improvements, creating various forms of arts and crafts) from long videos spanning up to several minutes. Accurately categorizing these activities requires not only recognizing the individual steps that compose the task but also capturing their temporal dependencies. This problem is dramatically different from traditional action classification, where models are typically optimized on videos that span only a few seconds and that are manually trimmed to contain simple atomic actions. While step annotations could enable the training of models to recognize the individual steps of procedural activities, existing large-scale datasets in this area do not include such segment labels due to the prohibitive cost of manually annotating temporal boundaries in long videos. To address this issue, we propose to automatically identify steps in instructional videos by leveraging the distant supervision of a textual knowledge base (wikiHow) that includes detailed descriptions of the steps needed for the execution of a wide variety of complex activities. Our method uses a language model to match noisy, automatically-transcribed speech from the video to step descriptions in the knowledge base. We demonstrate that video models trained to recognize these automatically-labeled steps (without manual supervision) yield a representation that achieves superior generalization performance on four downstream tasks: recognition of procedural activities, step classification, step forecasting and egocentric video classification.

cs.CV↗

arXiv2022

EDIN: An End-to-end Benchmark and Pipeline for Unknown Entity Discovery and Indexing

Existing work on Entity Linking mostly assumes that the reference knowledge base is complete, and therefore all mentions can be linked. In practice this is hardly ever the case, as knowledge bases are incomplete and because novel concepts arise constantly. This paper created the Unknown Entity Discovery and Indexing (EDIN) benchmark where unknown entities, that is entities without a description in the knowledge base and labeled mentions, have to be integrated into an existing entity linking system. By contrasting EDIN with zero-shot entity linking, we provide insight on the additional challenges it poses. Building on dense-retrieval based entity linking, we introduce the end-to-end EDIN pipeline that detects, clusters, and indexes mentions of unknown entities in context. Experiments show that indexing a single embedding per entity unifying the information of multiple mentions works better than indexing mentions independently.

cs.CL↗

arXiv2022

The Web Is Your Oyster - Knowledge-Intensive NLP against a Very Large Web Corpus

In order to address increasing demands of real-world applications, the research for knowledge-intensive NLP (KI-NLP) should advance by capturing the challenges of a truly open-domain environment: web-scale knowledge, lack of structure, inconsistent quality and noise. To this end, we propose a new setup for evaluating existing knowledge intensive tasks in which we generalize the background corpus to a universal web snapshot. We investigate a slate of NLP tasks which rely on knowledge - either factual or common sense, and ask systems to use a subset of CCNet - the Sphere corpus - as a knowledge source. In contrast to Wikipedia, otherwise a common background corpus in KI-NLP, Sphere is orders of magnitude larger and better reflects the full diversity of knowledge on the web. Despite potential gaps in coverage, challenges of scale, lack of structure and lower quality, we find that retrieval from Sphere enables a state of the art system to match and even outperform Wikipedia-based models on several tasks. We also observe that while a dense index can outperform a sparse BM25 baseline on Wikipedia, on Sphere this is not yet possible. To facilitate further research and minimise the community's reliance on proprietary, black-box search engines, we share our indices, evaluation metrics and infrastructure.

cs.CL↗

arXiv2022

Open Vocabulary Extreme Classification Using Generative Models

The extreme multi-label classification (XMC) task aims at tagging content with a subset of labels from an extremely large label set. The label vocabulary is typically defined in advance by domain experts and assumed to capture all necessary tags. However in real world scenarios this label set, although large, is often incomplete and experts frequently need to refine it. To develop systems that simplify this process, we introduce the task of open vocabulary XMC (OXMC): given a piece of content, predict a set of labels, some of which may be outside of the known tag set. Hence, in addition to not having training data for some labels - as is the case in zero-shot classification - models need to invent some labels on-the-fly. We propose GROOV, a fine-tuned seq2seq model for OXMC that generates the set of labels as a flat sequence and is trained using a novel loss independent of predicted label order. We show the efficacy of the approach, experimenting with popular XMC datasets for which GROOV is able to predict meaningful labels outside the given vocabulary while performing on par with state-of-the-art solutions for known labels.

cs.CL↗

arXiv2022

Autoregressive Search Engines: Generating Substrings as Document Identifiers

Knowledge-intensive language tasks require NLP systems to both provide the correct answer and retrieve supporting evidence for it in a given corpus. Autoregressive language models are emerging as the de-facto standard for generating answers, with newer and more powerful systems emerging at an astonishing pace. In this paper we argue that all this (and future) progress can be directly applied to the retrieval problem with minimal intervention to the models' architecture. Previous work has explored ways to partition the search space into hierarchical structures and retrieve documents by autoregressively generating their unique identifier. In this work we propose an alternative that doesn't force any structure in the search space: using all ngrams in a passage as its possible identifiers. This setup allows us to use an autoregressive model to generate and score distinctive ngrams, that are then mapped to full passages through an efficient data structure. Empirically, we show this not only outperforms prior autoregressive approaches but also leads to an average improvement of at least 10 points over more established retrieval solutions for passage-level retrieval on the KILT benchmark, establishing new state-of-the-art downstream performance on some datasets, while using a considerably lighter memory footprint than competing systems. Code and pre-trained models at https://github.com/facebookresearch/SEAL.

cs.CL↗

arXiv2022

GenIE: Generative Information Extraction

Structured and grounded representation of text is typically formalized by closed information extraction, the problem of extracting an exhaustive set of (subject, relation, object) triplets that are consistent with a predefined set of entities and relations from a knowledge base schema. Most existing works are pipelines prone to error accumulation, and all approaches are only applicable to unrealistically small numbers of entities and relations. We introduce GenIE (generative information extraction), the first end-to-end autoregressive formulation of closed information extraction. GenIE naturally exploits the language knowledge from the pre-trained transformer by autoregressively generating relations and entities in textual form. Thanks to a new bi-level constrained generation strategy, only triplets consistent with the predefined knowledge base schema are produced. Our experiments show that GenIE is state-of-the-art on closed information extraction, generalizes from fewer training data points than baselines, and scales to a previously unmanageable number of entities and relations. With this work, closed information extraction becomes practical in realistic scenarios, providing new opportunities for downstream tasks. Finally, this work paves the way towards a unified end-to-end approach to the core tasks of information extraction. Code, data and models available at https://github.com/epfl-dlab/GenIE.

cs.CL↗

arXiv2021

Boosted Dense Retriever

We propose DrBoost, a dense retrieval ensemble inspired by boosting. DrBoost is trained in stages: each component model is learned sequentially and specialized by focusing only on retrieval mistakes made by the current ensemble. The final representation is the concatenation of the output vectors of all the component models, making it a drop-in replacement for standard dense retrievers at test time. DrBoost enjoys several advantages compared to standard dense retrieval models. It produces representations which are 4x more compact, while delivering comparable retrieval results. It also performs surprisingly well under approximate search with coarse quantization, reducing latency and bandwidth needs by another 4x. In practice, this can make the difference between serving indices from disk versus from memory, paving the way for much cheaper deployments.

cs.CL↗

arXiv2021

MiniHack the Planet: A Sandbox for Open-Ended Reinforcement Learning Research

Progress in deep reinforcement learning (RL) is heavily driven by the availability of challenging benchmarks used for training agents. However, benchmarks that are widely adopted by the community are not explicitly designed for evaluating specific capabilities of RL methods. While there exist environments for assessing particular open problems in RL (such as exploration, transfer learning, unsupervised environment design, or even language-assisted RL), it is generally difficult to extend these to richer, more complex environments once research goes beyond proof-of-concept results. We present MiniHack, a powerful sandbox framework for easily designing novel RL environments. MiniHack is a one-stop shop for RL experiments with environments ranging from small rooms to complex, procedurally generated worlds. By leveraging the full set of entities and environment dynamics from NetHack, one of the richest grid-based video games, MiniHack allows designing custom RL testbeds that are fast and convenient to use. With this sandbox framework, novel environments can be designed easily, either using a human-readable description language or a simple Python interface. In addition to a variety of RL tasks and baselines, MiniHack can wrap existing RL benchmarks and provide ways to seamlessly add additional complexity.

cs.LG↗