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Dec 8

MAIRA-2: Grounded Radiology Report Generation

Radiology reporting is a complex task that requires detailed image understanding, integration of multiple inputs, including comparison with prior imaging, and precise language generation. This makes it ideal for the development and use of generative multimodal models. Here, we extend report generation to include the localisation of individual findings on the image - a task we call grounded report generation. Prior work indicates that grounding is important for clarifying image understanding and interpreting AI-generated text. Therefore, grounded reporting stands to improve the utility and transparency of automated report drafting. To enable evaluation of grounded reporting, we propose a novel evaluation framework - RadFact - leveraging the reasoning capabilities of large language models (LLMs). RadFact assesses the factuality of individual generated sentences, as well as correctness of generated spatial localisations when present. We introduce MAIRA-2, a large multimodal model combining a radiology-specific image encoder with a LLM, and trained for the new task of grounded report generation on chest X-rays. MAIRA-2 uses more comprehensive inputs than explored previously: the current frontal image, the current lateral image, the prior frontal image and prior report, as well as the Indication, Technique and Comparison sections of the current report. We demonstrate that these additions significantly improve report quality and reduce hallucinations, establishing a new state of the art on findings generation (without grounding) on MIMIC-CXR while demonstrating the feasibility of grounded reporting as a novel and richer task.

  • 20 authors
·
Jun 6, 2024

Insights into a radiology-specialised multimodal large language model with sparse autoencoders

Interpretability can improve the safety, transparency and trust of AI models, which is especially important in healthcare applications where decisions often carry significant consequences. Mechanistic interpretability, particularly through the use of sparse autoencoders (SAEs), offers a promising approach for uncovering human-interpretable features within large transformer-based models. In this study, we apply Matryoshka-SAE to the radiology-specialised multimodal large language model, MAIRA-2, to interpret its internal representations. Using large-scale automated interpretability of the SAE features, we identify a range of clinically relevant concepts - including medical devices (e.g., line and tube placements, pacemaker presence), pathologies such as pleural effusion and cardiomegaly, longitudinal changes and textual features. We further examine the influence of these features on model behaviour through steering, demonstrating directional control over generations with mixed success. Our results reveal practical and methodological challenges, yet they offer initial insights into the internal concepts learned by MAIRA-2 - marking a step toward deeper mechanistic understanding and interpretability of a radiology-adapted multimodal large language model, and paving the way for improved model transparency. We release the trained SAEs and interpretations: https://huggingface.co/microsoft/maira-2-sae.

  • 6 authors
·
Jul 17

The Mira-Titan Universe IV. High Precision Power Spectrum Emulation

Modern cosmological surveys are delivering datasets characterized by unprecedented quality and statistical completeness; this trend is expected to continue into the future as new ground- and space-based surveys come online. In order to maximally extract cosmological information from these observations, matching theoretical predictions are needed. At low redshifts, the surveys probe the nonlinear regime of structure formation where cosmological simulations are the primary means of obtaining the required information. The computational cost of sufficiently resolved large-volume simulations makes it prohibitive to run very large ensembles. Nevertheless, precision emulators built on a tractable number of high-quality simulations can be used to build very fast prediction schemes to enable a variety of cosmological inference studies. We have recently introduced the Mira-Titan Universe simulation suite designed to construct emulators for a range of cosmological probes. The suite covers the standard six cosmological parameters {omega_m,omega_b, sigma_8, h, n_s, w_0} and, in addition, includes massive neutrinos and a dynamical dark energy equation of state, {omega_{nu}, w_a}. In this paper we present the final emulator for the matter power spectrum based on 111 cosmological simulations, each covering a (2.1Gpc)^3 volume and evolving 3200^3 particles. An additional set of 1776 lower-resolution simulations and TimeRG perturbation theory results for the power spectrum are used to cover scales straddling the linear to mildly nonlinear regimes. The emulator provides predictions at the two to three percent level of accuracy over a wide range of cosmological parameters and is publicly released as part of this paper.

  • 9 authors
·
Jul 25, 2022

Vid2Robot: End-to-end Video-conditioned Policy Learning with Cross-Attention Transformers

While large-scale robotic systems typically rely on textual instructions for tasks, this work explores a different approach: can robots infer the task directly from observing humans? This shift necessitates the robot's ability to decode human intent and translate it into executable actions within its physical constraints and environment. We introduce Vid2Robot, a novel end-to-end video-based learning framework for robots. Given a video demonstration of a manipulation task and current visual observations, Vid2Robot directly produces robot actions. This is achieved through a unified representation model trained on a large dataset of human video and robot trajectory. The model leverages cross-attention mechanisms to fuse prompt video features to the robot's current state and generate appropriate actions that mimic the observed task. To further improve policy performance, we propose auxiliary contrastive losses that enhance the alignment between human and robot video representations. We evaluate Vid2Robot on real-world robots, demonstrating a 20% improvement in performance compared to other video-conditioned policies when using human demonstration videos. Additionally, our model exhibits emergent capabilities, such as successfully transferring observed motions from one object to another, and long-horizon composition, thus showcasing its potential for real-world applications. Project website: vid2robot.github.io

  • 13 authors
·
Mar 19, 2024 1

A Sentinel-2 multi-year, multi-country benchmark dataset for crop classification and segmentation with deep learning

In this work we introduce Sen4AgriNet, a Sentinel-2 based time series multi country benchmark dataset, tailored for agricultural monitoring applications with Machine and Deep Learning. Sen4AgriNet dataset is annotated from farmer declarations collected via the Land Parcel Identification System (LPIS) for harmonizing country wide labels. These declarations have only recently been made available as open data, allowing for the first time the labeling of satellite imagery from ground truth data. We proceed to propose and standardise a new crop type taxonomy across Europe that address Common Agriculture Policy (CAP) needs, based on the Food and Agriculture Organization (FAO) Indicative Crop Classification scheme. Sen4AgriNet is the only multi-country, multi-year dataset that includes all spectral information. It is constructed to cover the period 2016-2020 for Catalonia and France, while it can be extended to include additional countries. Currently, it contains 42.5 million parcels, which makes it significantly larger than other available archives. We extract two sub-datasets to highlight its value for diverse Deep Learning applications; the Object Aggregated Dataset (OAD) and the Patches Assembled Dataset (PAD). OAD capitalizes zonal statistics of each parcel, thus creating a powerful label-to-features instance for classification algorithms. On the other hand, PAD structure generalizes the classification problem to parcel extraction and semantic segmentation and labeling. The PAD and OAD are examined under three different scenarios to showcase and model the effects of spatial and temporal variability across different years and different countries.

  • 4 authors
·
Apr 2, 2022

Value of the Teaching Career and Factors in Its Path in Peru

The teaching career shares common global characteristics, such as internal promotion, performance evaluation, recruitment of top candidates, continuous training, specialization, and peer learning. This study aims to describe the factors associated with the value placed on the teaching career in Peru. A total of 28217 public school teachers were analyzed using data from the 2020 National Teacher Survey. A variable measuring the "value of the teaching career" was constructed using eight indicators and categorized as low, medium, or high. Another variable, vision of the future, was classified as pessimistic, conformist, or optimistic. This observational, cross-sectional, and analytical study included variables related to in-service training, working conditions, professional recognition, and sociodemographic characteristics. Among the teachers surveyed, 45.8 % expressed an optimistic outlook on the future of the profession, 48 % held a conformist view, and only 6.2 % reported a pessimistic perspective. A generalized linear model revealed that the value placed on the teaching career was significantly associated with male gender (p = 0.002), a professional career (p < 0.001), an optimistic outlook (p = 0.033), and working at the primary level (p < 0.001). It was concluded that Peruvian teachers predominantly hold conformist or optimistic views of their profession. This highlights the need to reinforce merit-based advancement, competency-based training, intrinsic motivation, and ongoing professional development

  • 5 authors
·
Aug 1

Benchmarking the Pedagogical Knowledge of Large Language Models

Benchmarks like Massive Multitask Language Understanding (MMLU) have played a pivotal role in evaluating AI's knowledge and abilities across diverse domains. However, existing benchmarks predominantly focus on content knowledge, leaving a critical gap in assessing models' understanding of pedagogy - the method and practice of teaching. This paper introduces The Pedagogy Benchmark, a novel dataset designed to evaluate large language models on their Cross-Domain Pedagogical Knowledge (CDPK) and Special Education Needs and Disability (SEND) pedagogical knowledge. These benchmarks are built on a carefully curated set of questions sourced from professional development exams for teachers, which cover a range of pedagogical subdomains such as teaching strategies and assessment methods. Here we outline the methodology and development of these benchmarks. We report results for 97 models, with accuracies spanning a range from 28% to 89% on the pedagogical knowledge questions. We consider the relationship between cost and accuracy and chart the progression of the Pareto value frontier over time. We provide online leaderboards at https://rebrand.ly/pedagogy which are updated with new models and allow interactive exploration and filtering based on various model properties, such as cost per token and open-vs-closed weights, as well as looking at performance in different subjects. LLMs and generative AI have tremendous potential to influence education and help to address the global learning crisis. Education-focused benchmarks are crucial to measure models' capacities to understand pedagogical concepts, respond appropriately to learners' needs, and support effective teaching practices across diverse contexts. They are needed for informing the responsible and evidence-based deployment of LLMs and LLM-based tools in educational settings, and for guiding both development and policy decisions.

  • 10 authors
·
Jun 23

A Large Dataset of Spontaneous Speech with the Accent Spoken in São Paulo for Automatic Speech Recognition Evaluation

We present a freely available spontaneous speech corpus for the Brazilian Portuguese language and report preliminary automatic speech recognition (ASR) results, using both the Wav2Vec2-XLSR-53 and Distil-Whisper models fine-tuned and trained on our corpus. The NURC-SP Audio Corpus comprises 401 different speakers (204 females, 197 males) with a total of 239.30 hours of transcribed audio recordings. To the best of our knowledge, this is the first large Paulistano accented spontaneous speech corpus dedicated to the ASR task in Portuguese. We first present the design and development procedures of the NURC-SP Audio Corpus, and then describe four ASR experiments in detail. The experiments demonstrated promising results for the applicability of the corpus for ASR. Specifically, we fine-tuned two versions of Wav2Vec2-XLSR-53 model, trained a Distil-Whisper model using our dataset with labels determined by Whisper Large-V3 model, and fine-tuned this Distil-Whisper model with our corpus. Our best results were the Distil-Whisper fine-tuned over NURC-SP Audio Corpus with a WER of 24.22% followed by a fine-tuned versions of Wav2Vec2-XLSR-53 model with a WER of 33.73%, that is almost 10% point worse than Distil-Whisper's. To enable experiment reproducibility, we share the NURC-SP Audio Corpus dataset, pre-trained models, and training recipes in Hugging-Face and Github repositories.

  • 4 authors
·
Sep 10, 2024

Galaxy Spectra neural Network (GaSNet). II. Using Deep Learning for Spectral Classification and Redshift Predictions

Large sky spectroscopic surveys have reached the scale of photometric surveys in terms of sample sizes and data complexity. These huge datasets require efficient, accurate, and flexible automated tools for data analysis and science exploitation. We present the Galaxy Spectra Network/GaSNet-II, a supervised multi-network deep learning tool for spectra classification and redshift prediction. GaSNet-II can be trained to identify a customized number of classes and optimize the redshift predictions for classified objects in each of them. It also provides redshift errors, using a network-of-networks that reproduces a Monte Carlo test on each spectrum, by randomizing their weight initialization. As a demonstration of the capability of the deep learning pipeline, we use 260k Sloan Digital Sky Survey spectra from Data Release 16, separated into 13 classes including 140k galactic, and 120k extragalactic objects. GaSNet-II achieves 92.4% average classification accuracy over the 13 classes (larger than 90% for the majority of them), and an average redshift error of approximately 0.23% for galaxies and 2.1% for quasars. We further train/test the same pipeline to classify spectra and predict redshifts for a sample of 200k 4MOST mock spectra and 21k publicly released DESI spectra. On 4MOST mock data, we reach 93.4% accuracy in 10-class classification and an average redshift error of 0.55% for galaxies and 0.3% for active galactic nuclei. On DESI data, we reach 96% accuracy in (star/galaxy/quasar only) classification and an average redshift error of 2.8% for galaxies and 4.8% for quasars, despite the small sample size available. GaSNet-II can process ~40k spectra in less than one minute, on a normal Desktop GPU. This makes the pipeline particularly suitable for real-time analyses of Stage-IV survey observations and an ideal tool for feedback loops aimed at night-by-night survey strategy optimization.

  • 28 authors
·
Nov 7, 2023

When Visualizing is the First Step to Reasoning: MIRA, a Benchmark for Visual Chain-of-Thought

We propose MIRA, a new benchmark designed to evaluate models in scenarios where generating intermediate visual images is essential for successful reasoning. Unlike traditional CoT methods that rely solely on text, tasks in MIRA require models to generate and utilize intermediate images - such as sketches, structural diagrams, or path drawings - to guide their reasoning process. This setup closely mirrors how humans solve complex problems through "drawing to think". To solve this, MIRA focuses on tasks that are intrinsically challenging and involve complex structures, spatial relationships, or reasoning steps that are difficult to express through language alone. To ensure that our evaluation data is of high-quality, we include 546 multimodal problems, annotated with intermediate visual images and final answers. We also propose a unified evaluation protocol for MIRA that spans three levels of evaluation input: direct input with image and question only, text-only CoT input with image and thinking prompts, and Visual-CoT input with both annotated image clues and textual thinking prompts. To probe the upper bound of model capacity on our benchmark, we also report pass@k and majority voting accuracies under different k settings. Experimental results show that existing multimodal large language models, including strongest private models as well as strong open-weight models, perform poorly when relying solely on textual prompts. However, when intermediate visual cues are provided, model performance improves consistently, yielding an average relative gain of 33.7% across all models and tasks. We also probe the upper bound by expanding the search space and designing textual prompts aligned with Visual-CoT, but both yield only limited improvements compared to our Visual-CoT setting. These results underscore the critical role of imagined visual information in enabling successful reasoning on MIRA.

MaIR: A Locality- and Continuity-Preserving Mamba for Image Restoration

Recent advancements in Mamba have shown promising results in image restoration. These methods typically flatten 2D images into multiple distinct 1D sequences along rows and columns, process each sequence independently using selective scan operation, and recombine them to form the outputs. However, such a paradigm overlooks two vital aspects: i) the local relationships and spatial continuity inherent in natural images, and ii) the discrepancies among sequences unfolded through totally different ways. To overcome the drawbacks, we explore two problems in Mamba-based restoration methods: i) how to design a scanning strategy preserving both locality and continuity while facilitating restoration, and ii) how to aggregate the distinct sequences unfolded in totally different ways. To address these problems, we propose a novel Mamba-based Image Restoration model (MaIR), which consists of Nested S-shaped Scanning strategy (NSS) and Sequence Shuffle Attention block (SSA). Specifically, NSS preserves locality and continuity of the input images through the stripe-based scanning region and the S-shaped scanning path, respectively. SSA aggregates sequences through calculating attention weights within the corresponding channels of different sequences. Thanks to NSS and SSA, MaIR surpasses 40 baselines across 14 challenging datasets, achieving state-of-the-art performance on the tasks of image super-resolution, denoising, deblurring and dehazing. The code is available at https://github.com/XLearning-SCU/2025-CVPR-MaIR.

  • 6 authors
·
Dec 28, 2024

MIRA: Medical Time Series Foundation Model for Real-World Health Data

A unified foundation model for medical time series -- pretrained on open access and ethics board-approved medical corpora -- offers the potential to reduce annotation burdens, minimize model customization, and enable robust transfer across clinical institutions, modalities, and tasks, particularly in data-scarce or privacy-constrained environments. However, existing generalist time series foundation models struggle to handle medical time series data due to their inherent challenges, including irregular intervals, heterogeneous sampling rates, and frequent missing values. To address these challenges, we introduce MIRA, a unified foundation model specifically designed for medical time series forecasting. MIRA incorporates a Continuous-Time Rotary Positional Encoding that enables fine-grained modeling of variable time intervals, a frequency-specific mixture-of-experts layer that routes computation across latent frequency regimes to further promote temporal specialization, and a Continuous Dynamics Extrapolation Block based on Neural ODE that models the continuous trajectory of latent states, enabling accurate forecasting at arbitrary target timestamps. Pretrained on a large-scale and diverse medical corpus comprising over 454 billion time points collect from publicly available datasets, MIRA achieves reductions in forecasting errors by an average of 10% and 7% in out-of-distribution and in-distribution scenarios, respectively, when compared to other zero-shot and fine-tuned baselines. We also introduce a comprehensive benchmark spanning multiple downstream clinical tasks, establishing a foundation for future research in medical time series modeling.

  • 11 authors
·
Jun 9

MAIR++: Improving Multi-view Attention Inverse Rendering with Implicit Lighting Representation

In this paper, we propose a scene-level inverse rendering framework that uses multi-view images to decompose the scene into geometry, SVBRDF, and 3D spatially-varying lighting. While multi-view images have been widely used for object-level inverse rendering, scene-level inverse rendering has primarily been studied using single-view images due to the lack of a dataset containing high dynamic range multi-view images with ground-truth geometry, material, and spatially-varying lighting. To improve the quality of scene-level inverse rendering, a novel framework called Multi-view Attention Inverse Rendering (MAIR) was recently introduced. MAIR performs scene-level multi-view inverse rendering by expanding the OpenRooms dataset, designing efficient pipelines to handle multi-view images, and splitting spatially-varying lighting. Although MAIR showed impressive results, its lighting representation is fixed to spherical Gaussians, which limits its ability to render images realistically. Consequently, MAIR cannot be directly used in applications such as material editing. Moreover, its multi-view aggregation networks have difficulties extracting rich features because they only focus on the mean and variance between multi-view features. In this paper, we propose its extended version, called MAIR++. MAIR++ addresses the aforementioned limitations by introducing an implicit lighting representation that accurately captures the lighting conditions of an image while facilitating realistic rendering. Furthermore, we design a directional attention-based multi-view aggregation network to infer more intricate relationships between views. Experimental results show that MAIR++ not only achieves better performance than MAIR and single-view-based methods, but also displays robust performance on unseen real-world scenes.

  • 6 authors
·
Aug 13, 2024

SR-CACO-2: A Dataset for Confocal Fluorescence Microscopy Image Super-Resolution

Confocal fluorescence microscopy is one of the most accessible and widely used imaging techniques for the study of biological processes. Scanning confocal microscopy allows the capture of high-quality images from 3D samples, yet suffers from well-known limitations such as photobleaching and phototoxicity of specimens caused by intense light exposure, which limits its use in some applications, especially for living cells. Cellular damage can be alleviated by changing imaging parameters to reduce light exposure, often at the expense of image quality. Machine/deep learning methods for single-image super-resolution (SISR) can be applied to restore image quality by upscaling lower-resolution (LR) images to produce high-resolution images (HR). These SISR methods have been successfully applied to photo-realistic images due partly to the abundance of publicly available data. In contrast, the lack of publicly available data partly limits their application and success in scanning confocal microscopy. In this paper, we introduce a large scanning confocal microscopy dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs marked for three different fluorescent markers. It allows the evaluation of performance of SISR methods on three different upscaling levels (X2, X4, X8). SR-CACO-2 contains the human epithelial cell line Caco-2 (ATCC HTB-37), and it is composed of 22 tiles that have been translated in the form of 9,937 image patches for experiments with SISR methods. Given the new SR-CACO-2 dataset, we also provide benchmarking results for 15 state-of-the-art methods that are representative of the main SISR families. Results show that these methods have limited success in producing high-resolution textures, indicating that SR-CACO-2 represents a challenging problem. Our dataset, code and pretrained weights are available: https://github.com/sbelharbi/sr-caco-2.

  • 6 authors
·
Jun 13, 2024

ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

  • 25 authors
·
Jun 14, 2022

ISLES 2024: The first longitudinal multimodal multi-center real-world dataset in (sub-)acute stroke

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

  • 18 authors
·
Aug 20, 2024

PaccMann$^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models

With the fast development of COVID-19 into a global pandemic, scientists around the globe are desperately searching for effective antiviral therapeutic agents. Bridging systems biology and drug discovery, we propose a deep learning framework for conditional de novo design of antiviral candidate drugs tailored against given protein targets. First, we train a multimodal ligand--protein binding affinity model on predicting affinities of antiviral compounds to target proteins and couple this model with pharmacological toxicity predictors. Exploiting this multi-objective as a reward function of a conditional molecular generator (consisting of two VAEs), we showcase a framework that navigates the chemical space toward regions with more antiviral molecules. Specifically, we explore a challenging setting of generating ligands against unseen protein targets by performing a leave-one-out-cross-validation on 41 SARS-CoV-2-related target proteins. Using deep RL, it is demonstrated that in 35 out of 41 cases, the generation is biased towards sampling more binding ligands, with an average increase of 83% comparing to an unbiased VAE. We present a case-study on a potential Envelope-protein inhibitor and perform a synthetic accessibility assessment of the best generated molecules is performed that resembles a viable roadmap towards a rapid in-vitro evaluation of potential SARS-CoV-2 inhibitors.

  • 7 authors
·
May 27, 2020

Discord Unveiled: A Comprehensive Dataset of Public Communication (2015-2024)

Discord has evolved from a gaming-focused communication tool into a versatile platform supporting diverse online communities. Despite its large user base and active public servers, academic research on Discord remains limited due to data accessibility challenges. This paper introduces Discord Unveiled: A Comprehensive Dataset of Public Communication (2015-2024), the most extensive Discord public server's data to date. The dataset comprises over 2.05 billion messages from 4.74 million users across 3,167 public servers, representing approximately 10% of servers listed in Discord's Discovery feature. Spanning from Discord's launch in 2015 to the end of 2024, it offers a robust temporal and thematic framework for analyzing decentralized moderation, community governance, information dissemination, and social dynamics. Data was collected through Discord's public API, adhering to ethical guidelines and privacy standards via anonymization techniques. Organized into structured JSON files, the dataset facilitates seamless integration with computational social science methodologies. Preliminary analyses reveal significant trends in user engagement, bot utilization, and linguistic diversity, with English predominating alongside substantial representations of Spanish, French, and Portuguese. Additionally, prevalent community themes such as social, art, music, and memes highlight Discord's expansion beyond its gaming origins.

  • 15 authors
·
Feb 1

Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

  • 141 authors
·
Nov 20, 2024 2

Robust Binding Energy Distribution Sampling on Amorphous Solid Water Models. Method testing and validation with NH3, CO and CH4

This work aims to develop a method based on a structurally reliable ice model and a statistically and physico-chemically robust approach for BE distribution inference, with the aim to be applicable to various relevant interstellar species. A multiscale computational approach is presented, with a Molecular Dynamics (MD) Heat & Quench protocol for the amorphous water ice model, and an ONIOM(B3LYP-D3(BJ)/6-311+G**:GFN2-xtb) scheme for the BE inference, with a prime emphasis onto the BE/real system size convergence. The sampling of the binding configurations is twofold, exploring both regularly spaced binding sites, as well as various adsorbate-to-substrate orientations on each locally distinct site. This second source of BE diversity accounts for the local roughness of the potential energy landscape of the substrate. Three different adsorbate test cases are considered, i.e. NH3, CO and CH4, owing to their significance in dust icy mantles, and their distinct binding behavior with water ices. The BE distributions for NH3, CO and CH4 have been inferred, with converged statistics. The distribution for NH3 is better represented by a double Gaussian component profile. Three starting adsorbate orientations per site are required to reach convergence for both Gaussian components of NH3, while 2 orientations are sufficient for CO, and one unique for CH4 (symmetric). Further geometrical and molecular surrounding insights have been provided. These results encompass previously reported results.

  • 4 authors
·
Apr 25

VacancySBERT: the approach for representation of titles and skills for semantic similarity search in the recruitment domain

The paper focuses on deep learning semantic search algorithms applied in the HR domain. The aim of the article is developing a novel approach to training a Siamese network to link the skills mentioned in the job ad with the title. It has been shown that the title normalization process can be based either on classification or similarity comparison approaches. While classification algorithms strive to classify a sample into predefined set of categories, similarity search algorithms take a more flexible approach, since they are designed to find samples that are similar to a given query sample, without requiring pre-defined classes and labels. In this article semantic similarity search to find candidates for title normalization has been used. A pre-trained language model has been adapted while teaching it to match titles and skills based on co-occurrence information. For the purpose of this research fifty billion title-descriptions pairs had been collected for training the model and thirty three thousand title-description-normalized title triplets, where normalized job title was picked up manually by job ad creator for testing purposes. As baselines FastText, BERT, SentenceBert and JobBert have been used. As a metric of the accuracy of the designed algorithm is Recall in top one, five and ten model's suggestions. It has been shown that the novel training objective lets it achieve significant improvement in comparison to other generic and specific text encoders. Two settings with treating titles as standalone strings, and with included skills as additional features during inference have been used and the results have been compared in this article. Improvements by 10% and 21.5% have been achieved using VacancySBERT and VacancySBERT (with skills) respectively. The benchmark has been developed as open-source to foster further research in the area.

  • 3 authors
·
Jul 31, 2023

The illusion of a perfect metric: Why evaluating AI's words is harder than it looks

Evaluating Natural Language Generation (NLG) is crucial for the practical adoption of AI, but has been a longstanding research challenge. While human evaluation is considered the de-facto standard, it is expensive and lacks scalability. Practical applications have driven the development of various automatic evaluation metrics (AEM), designed to compare the model output with human-written references, generating a score which approximates human judgment. Over time, AEMs have evolved from simple lexical comparisons, to semantic similarity models and, more recently, to LLM-based evaluators. However, it seems that no single metric has emerged as a definitive solution, resulting in studies using different ones without fully considering the implications. This paper aims to show this by conducting a thorough examination of the methodologies of existing metrics, their documented strengths and limitations, validation methods, and correlations with human judgment. We identify several key challenges: metrics often capture only specific aspects of text quality, their effectiveness varies by task and dataset, validation practices remain unstructured, and correlations with human judgment are inconsistent. Importantly, we find that these challenges persist in the most recent type of metric, LLM-as-a-Judge, as well as in the evaluation of Retrieval Augmented Generation (RAG), an increasingly relevant task in academia and industry. Our findings challenge the quest for the 'perfect metric'. We propose selecting metrics based on task-specific needs and leveraging complementary evaluations and advocate that new metrics should focus on enhanced validation methodologies.

  • 4 authors
·
Aug 19

Sample complexity of data-driven tuning of model hyperparameters in neural networks with structured parameter-dependent dual function

Modern machine learning algorithms, especially deep learning based techniques, typically involve careful hyperparameter tuning to achieve the best performance. Despite the surge of intense interest in practical techniques like Bayesian optimization and random search based approaches to automating this laborious and compute intensive task, the fundamental learning theoretic complexity of tuning hyperparameters for deep neural networks is poorly understood. Inspired by this glaring gap, we initiate the formal study of hyperparameter tuning complexity in deep learning through a recently introduced data driven setting. We assume that we have a series of deep learning tasks, and we have to tune hyperparameters to do well on average over the distribution of tasks. A major difficulty is that the utility function as a function of the hyperparameter is very volatile and furthermore, it is given implicitly by an optimization problem over the model parameters. To tackle this challenge, we introduce a new technique to characterize the discontinuities and oscillations of the utility function on any fixed problem instance as we vary the hyperparameter; our analysis relies on subtle concepts including tools from differential/algebraic geometry and constrained optimization. This can be used to show that the learning theoretic complexity of the corresponding family of utility functions is bounded. We instantiate our results and provide sample complexity bounds for concrete applications tuning a hyperparameter that interpolates neural activation functions and setting the kernel parameter in graph neural networks.

  • 3 authors
·
Jan 23

Holistic Understanding of 3D Scenes as Universal Scene Description

3D scene understanding is a long-standing challenge in computer vision and a key component in enabling mixed reality, wearable computing, and embodied AI. Providing a solution to these applications requires a multifaceted approach that covers scene-centric, object-centric, as well as interaction-centric capabilities. While there exist numerous datasets approaching the former two problems, the task of understanding interactable and articulated objects is underrepresented and only partly covered by current works. In this work, we address this shortcoming and introduce (1) an expertly curated dataset in the Universal Scene Description (USD) format, featuring high-quality manual annotations, for instance, segmentation and articulation on 280 indoor scenes; (2) a learning-based model together with a novel baseline capable of predicting part segmentation along with a full specification of motion attributes, including motion type, articulated and interactable parts, and motion parameters; (3) a benchmark serving to compare upcoming methods for the task at hand. Overall, our dataset provides 8 types of annotations - object and part segmentations, motion types, movable and interactable parts, motion parameters, connectivity, and object mass annotations. With its broad and high-quality annotations, the data provides the basis for holistic 3D scene understanding models. All data is provided in the USD format, allowing interoperability and easy integration with downstream tasks. We provide open access to our dataset, benchmark, and method's source code.

  • 6 authors
·
Dec 2, 2024

Towards Automation of Human Stage of Decay Identification: An Artificial Intelligence Approach

Determining the stage of decomposition (SOD) is crucial for estimating the postmortem interval and identifying human remains. Currently, labor-intensive manual scoring methods are used for this purpose, but they are subjective and do not scale for the emerging large-scale archival collections of human decomposition photos. This study explores the feasibility of automating two common human decomposition scoring methods proposed by Megyesi and Gelderman using artificial intelligence (AI). We evaluated two popular deep learning models, Inception V3 and Xception, by training them on a large dataset of human decomposition images to classify the SOD for different anatomical regions, including the head, torso, and limbs. Additionally, an interrater study was conducted to assess the reliability of the AI models compared to human forensic examiners for SOD identification. The Xception model achieved the best classification performance, with macro-averaged F1 scores of .878, .881, and .702 for the head, torso, and limbs when predicting Megyesi's SODs, and .872, .875, and .76 for the head, torso, and limbs when predicting Gelderman's SODs. The interrater study results supported AI's ability to determine the SOD at a reliability level comparable to a human expert. This work demonstrates the potential of AI models trained on a large dataset of human decomposition images to automate SOD identification.

  • 4 authors
·
Aug 19, 2024

All You Need Is Sex for Diversity

Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to some form of self-adaptive selection mechanism. In nature, genetic diversity can be the consequence of many different factors, but when considering reproduction Sexual Selection can have an impact on promoting variety within a species. Specifically, Mate Choice often results in different selective pressures between sexes, which in turn may trigger evolutionary differences among them. Although some mechanisms of Sexual Selection have been applied to Genetic Programming in the past, the literature is scarce when it comes to mate choice. Recently, a way of modelling mating preferences by ideal mate representations was proposed, achieving good results when compared to a standard approach. These mating preferences evolve freely in a self-adaptive fashion, creating an evolutionary driving force of its own alongside fitness pressure. The inner mechanisms of this approach operate from personal choice, as each individual has its own representation of a perfect mate which affects the mate to be selected. In this paper, we compare this method against a random mate choice to assess whether there are advantages in evolving personal preferences. We conducted experiments using three symbolic regression problems and different mutation rates. The results show that self-adaptive mating preferences are able to create a more diverse set of solutions when compared to the traditional approach and a random mate approach (with statistically significant differences) and have a higher success rate in three of the six instances tested.

  • 3 authors
·
Mar 30, 2023