Daily Papers

Safe and trustworthy use of Large Language Models (LLM) in the processing of healthcare documents and scientific papers could substantially help clinicians, scientists and policymakers in overcoming information overload and focusing on the most relevant information at a given moment. Retrieval Augmented Generation (RAG) is a promising method to leverage the potential of LLMs while enhancing the accuracy of their outcomes. This report assesses the potentials and shortcomings of such approaches in the automatic knowledge synthesis of different types of documents in the health domain. To this end, it describes: (1) an internally developed proof of concept pipeline that employs state-of-the-art practices to deliver safe and trustable analysis for healthcare documents and scientific papers called RAGEv (Retrieval Augmented Generation Evaluation); (2) a set of evaluation tools for LLM-based document retrieval and generation; (3) a benchmark dataset to verify the accuracy and veracity of the results called RAGEv-Bench. It concludes that careful implementations of RAG techniques could minimize most of the common problems in the use of LLMs for document processing in the health domain, obtaining very high scores both on short yes/no answers and long answers. There is a high potential for incorporating it into the day-to-day work of policy support tasks, but additional efforts are required to obtain a consistent and trustworthy tool.

Delegating complete application development to coding agents requires preserving the intended design rather than simply producing plausible outputs through naive prompting. Game development provides a demanding testbed, as long-form Game Design Documents (GDDs) describe requirements that must work together across game logic, visual rendering, and player interactions. However, existing game-development benchmarks typically use compact specifications and provide limited support for evaluating interdependent requirements across these aspects in long-form GDDs. We introduce A2Z GameSpec-Bench, a benchmark of 100 long-form GDDs for evaluating end-to-end game development by agents. We measure faithfulness by checking whether the game satisfies the GDD requirements and preserves the relationships among them. Each GDD is turned into a dependency-aware contract that contains rules, constraints, and prerequisite relations. Following game-development practices, we combine source-code inspection with agent-generated test policies for scenario-based replay and adaptive playtesting. The contract remains fixed across agents and revision rounds, while judgments and evidence linked to the same requirements support consistent comparison and failure detection. Our evaluations show that current agents struggle to jointly satisfy interdependent requirements across code implementation and actual play. Requirement-specific feedback improves GDD Fidelity by 10.9% relative to self-revision after two rounds. A2Z GameSpec-Bench assesses end-to-end specification-following ability beyond implementation judgments and provides targeted feedback to support more faithful game development. Code and datasets are available at https://a2z-gamespec-bench.github.io.

This paper presents a novel approach to epidemic surveillance, leveraging the power of Artificial Intelligence and Large Language Models (LLMs) for effective interpretation of unstructured big data sources, like the popular ProMED and WHO Disease Outbreak News. We explore several LLMs, evaluating their capabilities in extracting valuable epidemic information. We further enhance the capabilities of the LLMs using in-context learning, and test the performance of an ensemble model incorporating multiple open-source LLMs. The findings indicate that LLMs can significantly enhance the accuracy and timeliness of epidemic modelling and forecasting, offering a promising tool for managing future pandemic events.

Quantitative tools are increasingly appealing for decision support in healthcare, driven by the growing capabilities of advanced AI systems. However, understanding the predictive uncertainties surrounding a tool's output is crucial for decision-makers to ensure reliable and transparent decisions. In this paper, we present a case study on pulmonary nodule detection for lung cancer screening, enhancing an advanced detection model with an uncertainty quantification technique called conformal risk control (CRC). We demonstrate that prediction sets with conformal guarantees are attractive measures of predictive uncertainty in the safety-critical healthcare domain, allowing end-users to achieve arbitrary validity by trading off false positives and providing formal statistical guarantees on model performance. Among ground-truth nodules annotated by at least three radiologists, our model achieves a sensitivity that is competitive with that generally achieved by individual radiologists, with a slight increase in false positives. Furthermore, we illustrate the risks of using off-the-shelve prediction models when faced with ontological uncertainty, such as when radiologists disagree on what constitutes the ground truth on pulmonary nodules.

The rapid evolution of artificial intelligence (AI), together with the increased availability of social media and news for epidemiological surveillance, are marking a pivotal moment in epidemiology and public health research. Leveraging the power of generative AI, we use an ensemble approach which incorporates multiple Large Language Models (LLMs) to extract valuable actionable epidemiological information from the World Health Organization (WHO) Disease Outbreak News (DONs). DONs is a collection of regular reports on global outbreaks curated by the WHO and the adopted decision-making processes to respond to them. The extracted information is made available in a daily-updated dataset and a knowledge graph, referred to as eKG, derived to provide a nuanced representation of the public health domain knowledge. We provide an overview of this new dataset and describe the structure of eKG, along with the services and tools used to access and utilize the data that we are building on top. These innovative data resources open altogether new opportunities for epidemiological research, and the analysis and surveillance of disease outbreaks.

LLMs have emerged as powerful tools for interpreting multimodal data. In medicine, they hold particular promise for synthesizing large volumes of clinical information into actionable insights and digital health applications. Yet, a major limitation remains their inability to handle time series. To overcome this gap, we present OpenTSLM, a family of Time Series Language Models (TSLMs) created by integrating time series as a native modality to pretrained LLMs, enabling reasoning over multiple time series of any length. We investigate two architectures for OpenTSLM. The first, OpenTSLM-SoftPrompt, models time series implicitly by concatenating learnable time series tokens with text tokens via soft prompting. Although parameter-efficient, we hypothesize that explicit time series modeling scales better and outperforms implicit approaches. We thus introduce OpenTSLM-Flamingo, which integrates time series with text via cross-attention. We benchmark both variants against baselines that treat time series as text tokens or plots, across a suite of text-time-series Chain-of-Thought (CoT) reasoning tasks. We introduce three datasets: HAR-CoT, Sleep-CoT, and ECG-QA-CoT. Across all, OpenTSLM models outperform baselines, reaching 69.9 F1 in sleep staging and 65.4 in HAR, compared to 9.05 and 52.2 for finetuned text-only models. Notably, even 1B-parameter OpenTSLM models surpass GPT-4o (15.47 and 2.95). OpenTSLM-Flamingo matches OpenTSLM-SoftPrompt in performance and outperforms on longer sequences, while maintaining stable memory requirements. By contrast, SoftPrompt grows exponentially in memory with sequence length, requiring around 110 GB compared to 40 GB VRAM when training on ECG-QA with LLaMA-3B. Expert reviews by clinicians find strong reasoning capabilities exhibited by OpenTSLMs on ECG-QA. To facilitate further research, we provide all code, datasets, and models open-source.

We present the measurements and cosmological implications of the galaxy two-point clustering using over 4.7 million unique galaxy and quasar redshifts in the range 0.1<z<2.1 divided into six redshift bins over a sim 7,500 square degree footprint, from the first year of observations with the Dark Energy Spectroscopic Instrument (DESI Data Release 1). By fitting the full power spectrum, we extend previous DESI DR1 baryon acoustic oscillation (BAO) measurements to include redshift-space distortions and signals from the matter-radiation equality scale. For the first time, this Full-Shape analysis is blinded at the catalogue-level to avoid confirmation bias and the systematic errors are accounted for at the two-point clustering level, which automatically propagates them into any cosmological parameter. When analysing the data in terms of compressed model-agnostic variables, we obtain a combined precision of 4.7\% on the amplitude of the redshift space distortion signal reaching similar precision with just one year of DESI data than with 20 years of observation from previous generation surveys. We analyse the data to directly constrain the cosmological parameters within the LambdaCDM model using perturbation theory and combine this information with the reconstructed DESI DR1 galaxy BAO. Using a Big Bang Nucleosynthesis Gaussian prior on the baryon density parameter, and a Gaussian prior on the spectral index, we constrain the matter density is Omega_m=0.296pm 0.010 and the Hubble constant H_0=(68.63 pm 0.79)[{rm km, s^{-1}Mpc^{-1}}]. Additionally, we measure the amplitude of clustering sigma_8=0.841 pm 0.034. The DESI DR1 results are in agreement with the LambdaCDM model based on general relativity with parameters consistent with those from Planck. The cosmological interpretation of these results in combination with external datasets are presented in a companion paper.

In 2021 May the Dark Energy Spectroscopic Instrument (DESI) collaboration began a 5-year spectroscopic redshift survey to produce a detailed map of the evolving three-dimensional structure of the universe between z=0 and zapprox4. DESI's principle scientific objectives are to place precise constraints on the equation of state of dark energy, the gravitationally driven growth of large-scale structure, and the sum of the neutrino masses, and to explore the observational signatures of primordial inflation. We present DESI Data Release 1 (DR1), which consists of all data acquired during the first 13 months of the DESI main survey, as well as a uniform reprocessing of the DESI Survey Validation data which was previously made public in the DESI Early Data Release. The DR1 main survey includes high-confidence redshifts for 18.7M objects, of which 13.1M are spectroscopically classified as galaxies, 1.6M as quasars, and 4M as stars, making DR1 the largest sample of extragalactic redshifts ever assembled. We summarize the DR1 observations, the spectroscopic data-reduction pipeline and data products, large-scale structure catalogs, value-added catalogs, and describe how to access and interact with the data. In addition to fulfilling its core cosmological objectives with unprecedented precision, we expect DR1 to enable a wide range of transformational astrophysical studies and discoveries.

We present cosmological results from the measurement of baryon acoustic oscillations (BAO) in galaxy, quasar and Lyman-α forest tracers from the first year of observations from the Dark Energy Spectroscopic Instrument (DESI), to be released in the DESI Data Release 1. DESI BAO provide robust measurements of the transverse comoving distance and Hubble rate, or their combination, relative to the sound horizon, in seven redshift bins from over 6 million extragalactic objects in the redshift range 0.1<z<4.2. DESI BAO data alone are consistent with the standard flat ΛCDM cosmological model with a matter density Ω_m=0.295pm 0.015. Paired with a BBN prior and the robustly measured acoustic angular scale from the CMB, DESI requires H_0=(68.52pm0.62) km/s/Mpc. In conjunction with CMB anisotropies from Planck and CMB lensing data from Planck and ACT, we find Ω_m=0.307pm 0.005 and H_0=(67.97pm0.38) km/s/Mpc. Extending the baseline model with a constant dark energy equation of state parameter w, DESI BAO alone require w=-0.99^{+0.15}_{-0.13}. In models with a time-varying dark energy equation of state parametrized by w_0 and w_a, combinations of DESI with CMB or with SN~Ia individually prefer w_0>-1 and w_a<0. This preference is 2.6σ for the DESI+CMB combination, and persists or grows when SN~Ia are added in, giving results discrepant with the ΛCDM model at the 2.5σ, 3.5σ or 3.9σ levels for the addition of Pantheon+, Union3, or DES-SN5YR datasets respectively. For the flat ΛCDM model with the sum of neutrino mass sum m_ν free, combining the DESI and CMB data yields an upper limit sum m_ν< 0.072 (0.113) eV at 95% confidence for a sum m_ν>0 (sum m_ν>0.059) eV prior. These neutrino-mass constraints are substantially relaxed in models beyond ΛCDM. [Abridged.]

We present baryon acoustic oscillation (BAO) measurements from more than 14 million galaxies and quasars drawn from the Dark Energy Spectroscopic Instrument (DESI) Data Release 2 (DR2), based on three years of operation. For cosmology inference, these galaxy measurements are combined with DESI Lyman-α forest BAO results presented in a companion paper. The DR2 BAO results are consistent with DESI DR1 and SDSS, and their distance-redshift relationship matches those from recent compilations of supernovae (SNe) over the same redshift range. The results are well described by a flat ΛCDM model, but the parameters preferred by BAO are in mild, 2.3σ tension with those determined from the cosmic microwave background (CMB), although the DESI results are consistent with the acoustic angular scale θ_* that is well-measured by Planck. This tension is alleviated by dark energy with a time-evolving equation of state parametrized by w_0 and w_a, which provides a better fit to the data, with a favored solution in the quadrant with w_0>-1 and w_a<0. This solution is preferred over ΛCDM at 3.1σ for the combination of DESI BAO and CMB data. When also including SNe, the preference for a dynamical dark energy model over ΛCDM ranges from 2.8-4.2σ depending on which SNe sample is used. We present evidence from other data combinations which also favor the same behavior at high significance. From the combination of DESI and CMB we derive 95% upper limits on the sum of neutrino masses, finding sum m_ν<0.064 eV assuming ΛCDM and sum m_ν<0.16 eV in the w_0w_a model. Unless there is an unknown systematic error associated with one or more datasets, it is clear that ΛCDM is being challenged by the combination of DESI BAO with other measurements and that dynamical dark energy offers a possible solution.