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Dec 9

STARC-9: A Large-scale Dataset for Multi-Class Tissue Classification for CRC Histopathology

Multi-class tissue-type classification of colorectal cancer (CRC) histopathologic images is a significant step in the development of downstream machine learning models for diagnosis and treatment planning. However, existing public CRC datasets often lack morphologic diversity, suffer from class imbalance, and contain low-quality image tiles, limiting model performance and generalizability. To address these issues, we introduce STARC-9 (STAnford coloRectal Cancer), a large-scale dataset for multi-class tissue classification. STARC-9 contains 630,000 hematoxylin and eosin-stained image tiles uniformly sampled across nine clinically relevant tissue classes (70,000 tiles per class) from 200 CRC patients at the Stanford University School of Medicine. The dataset was built using a novel framework, DeepCluster++, designed to ensure intra-class diversity and reduce manual curation. First, an encoder from a histopathology-specific autoencoder extracts feature vectors from tiles within each whole-slide image. Then, K-means clustering groups morphologically similar tiles, followed by equal-frequency binning to sample diverse morphologic patterns within each class. The selected tiles are subsequently verified by expert gastrointestinal pathologists to ensure accuracy. This semi-automated process significantly reduces manual effort while producing high-quality, diverse tiles. To evaluate STARC-9, we benchmarked convolutional neural networks, transformers, and pathology-specific foundation models on multi-class CRC tissue classification and segmentation tasks, showing superior generalizability compared to models trained on existing datasets. Although we demonstrate the utility of DeepCluster++ on CRC as a pilot use-case, it is a flexible framework that can be used for constructing high-quality datasets from large WSI repositories across a wide range of cancer and non-cancer applications.

  • 8 authors
·
Oct 31

STARC: A General Framework For Quantifying Differences Between Reward Functions

In order to solve a task using reinforcement learning, it is necessary to first formalise the goal of that task as a reward function. However, for many real-world tasks, it is very difficult to manually specify a reward function that never incentivises undesirable behaviour. As a result, it is increasingly popular to use reward learning algorithms, which attempt to learn a reward function from data. However, the theoretical foundations of reward learning are not yet well-developed. In particular, it is typically not known when a given reward learning algorithm with high probability will learn a reward function that is safe to optimise. This means that reward learning algorithms generally must be evaluated empirically, which is expensive, and that their failure modes are difficult to anticipate in advance. One of the roadblocks to deriving better theoretical guarantees is the lack of good methods for quantifying the difference between reward functions. In this paper we provide a solution to this problem, in the form of a class of pseudometrics on the space of all reward functions that we call STARC (STAndardised Reward Comparison) metrics. We show that STARC metrics induce both an upper and a lower bound on worst-case regret, which implies that our metrics are tight, and that any metric with the same properties must be bilipschitz equivalent to ours. Moreover, we also identify a number of issues with reward metrics proposed by earlier works. Finally, we evaluate our metrics empirically, to demonstrate their practical efficacy. STARC metrics can be used to make both theoretical and empirical analysis of reward learning algorithms both easier and more principled.

  • 6 authors
·
Sep 26, 2023

StarCoder 2 and The Stack v2: The Next Generation

The BigCode project, an open-scientific collaboration focused on the responsible development of Large Language Models for Code (Code LLMs), introduces StarCoder2. In partnership with Software Heritage (SWH), we build The Stack v2 on top of the digital commons of their source code archive. Alongside the SWH repositories spanning 619 programming languages, we carefully select other high-quality data sources, such as GitHub pull requests, Kaggle notebooks, and code documentation. This results in a training set that is 4x larger than the first StarCoder dataset. We train StarCoder2 models with 3B, 7B, and 15B parameters on 3.3 to 4.3 trillion tokens and thoroughly evaluate them on a comprehensive set of Code LLM benchmarks. We find that our small model, StarCoder2-3B, outperforms other Code LLMs of similar size on most benchmarks, and also outperforms StarCoderBase-15B. Our large model, StarCoder2- 15B, significantly outperforms other models of comparable size. In addition, it matches or outperforms CodeLlama-34B, a model more than twice its size. Although DeepSeekCoder- 33B is the best-performing model at code completion for high-resource languages, we find that StarCoder2-15B outperforms it on math and code reasoning benchmarks, as well as several low-resource languages. We make the model weights available under an OpenRAIL license and ensure full transparency regarding the training data by releasing the SoftWare Heritage persistent IDentifiers (SWHIDs) of the source code data.

  • 66 authors
·
Feb 29, 2024 5

StarCraftImage: A Dataset For Prototyping Spatial Reasoning Methods For Multi-Agent Environments

Spatial reasoning tasks in multi-agent environments such as event prediction, agent type identification, or missing data imputation are important for multiple applications (e.g., autonomous surveillance over sensor networks and subtasks for reinforcement learning (RL)). StarCraft II game replays encode intelligent (and adversarial) multi-agent behavior and could provide a testbed for these tasks; however, extracting simple and standardized representations for prototyping these tasks is laborious and hinders reproducibility. In contrast, MNIST and CIFAR10, despite their extreme simplicity, have enabled rapid prototyping and reproducibility of ML methods. Following the simplicity of these datasets, we construct a benchmark spatial reasoning dataset based on StarCraft II replays that exhibit complex multi-agent behaviors, while still being as easy to use as MNIST and CIFAR10. Specifically, we carefully summarize a window of 255 consecutive game states to create 3.6 million summary images from 60,000 replays, including all relevant metadata such as game outcome and player races. We develop three formats of decreasing complexity: Hyperspectral images that include one channel for every unit type (similar to multispectral geospatial images), RGB images that mimic CIFAR10, and grayscale images that mimic MNIST. We show how this dataset can be used for prototyping spatial reasoning methods. All datasets, code for extraction, and code for dataset loading can be found at https://starcraftdata.davidinouye.com

  • 4 authors
·
Jan 8, 2024

Large Language Models Play StarCraft II: Benchmarks and A Chain of Summarization Approach

StarCraft II is a challenging benchmark for AI agents due to the necessity of both precise micro level operations and strategic macro awareness. Previous works, such as Alphastar and SCC, achieve impressive performance on tackling StarCraft II , however, still exhibit deficiencies in long term strategic planning and strategy interpretability. Emerging large language model (LLM) agents, such as Voyage and MetaGPT, presents the immense potential in solving intricate tasks. Motivated by this, we aim to validate the capabilities of LLMs on StarCraft II, a highly complex RTS game.To conveniently take full advantage of LLMs` reasoning abilities, we first develop textual StratCraft II environment, called TextStarCraft II, which LLM agent can interact. Secondly, we propose a Chain of Summarization method, including single frame summarization for processing raw observations and multi frame summarization for analyzing game information, providing command recommendations, and generating strategic decisions. Our experiment consists of two parts: first, an evaluation by human experts, which includes assessing the LLMs`s mastery of StarCraft II knowledge and the performance of LLM agents in the game; second, the in game performance of LLM agents, encompassing aspects like win rate and the impact of Chain of Summarization.Experiment results demonstrate that: 1. LLMs possess the relevant knowledge and complex planning abilities needed to address StarCraft II scenarios; 2. Human experts consider the performance of LLM agents to be close to that of an average player who has played StarCraft II for eight years; 3. LLM agents are capable of defeating the built in AI at the Harder(Lv5) difficulty level. We have open sourced the code and released demo videos of LLM agent playing StarCraft II.

  • 7 authors
·
Dec 19, 2023

StarCraft II: A New Challenge for Reinforcement Learning

This paper introduces SC2LE (StarCraft II Learning Environment), a reinforcement learning environment based on the StarCraft II game. This domain poses a new grand challenge for reinforcement learning, representing a more difficult class of problems than considered in most prior work. It is a multi-agent problem with multiple players interacting; there is imperfect information due to a partially observed map; it has a large action space involving the selection and control of hundreds of units; it has a large state space that must be observed solely from raw input feature planes; and it has delayed credit assignment requiring long-term strategies over thousands of steps. We describe the observation, action, and reward specification for the StarCraft II domain and provide an open source Python-based interface for communicating with the game engine. In addition to the main game maps, we provide a suite of mini-games focusing on different elements of StarCraft II gameplay. For the main game maps, we also provide an accompanying dataset of game replay data from human expert players. We give initial baseline results for neural networks trained from this data to predict game outcomes and player actions. Finally, we present initial baseline results for canonical deep reinforcement learning agents applied to the StarCraft II domain. On the mini-games, these agents learn to achieve a level of play that is comparable to a novice player. However, when trained on the main game, these agents are unable to make significant progress. Thus, SC2LE offers a new and challenging environment for exploring deep reinforcement learning algorithms and architectures.

  • 25 authors
·
Aug 16, 2017

SC2EGSet: StarCraft II Esport Replay and Game-state Dataset

As a relatively new form of sport, esports offers unparalleled data availability. Despite the vast amounts of data that are generated by game engines, it can be challenging to extract them and verify their integrity for the purposes of practical and scientific use. Our work aims to open esports to a broader scientific community by supplying raw and pre-processed files from StarCraft II esports tournaments. These files can be used in statistical and machine learning modeling tasks and related to various laboratory-based measurements (e.g., behavioral tests, brain imaging). We have gathered publicly available game-engine generated "replays" of tournament matches and performed data extraction and cleanup using a low-level application programming interface (API) parser library. Additionally, we open-sourced and published all the custom tools that were developed in the process of creating our dataset. These tools include PyTorch and PyTorch Lightning API abstractions to load and model the data. Our dataset contains replays from major and premiere StarCraft II tournaments since 2016. To prepare the dataset, we processed 55 tournament "replaypacks" that contained 17930 files with game-state information. Based on initial investigation of available StarCraft II datasets, we observed that our dataset is the largest publicly available source of StarCraft II esports data upon its publication. Analysis of the extracted data holds promise for further Artificial Intelligence (AI), Machine Learning (ML), psychological, Human-Computer Interaction (HCI), and sports-related studies in a variety of supervised and self-supervised tasks.

  • 8 authors
·
Jul 7, 2022

LLM-PySC2: Starcraft II learning environment for Large Language Models

This paper introduces a new environment LLM-PySC2 (the Large Language Model StarCraft II Learning Environment), a platform derived from DeepMind's StarCraft II Learning Environment that serves to develop Large Language Models (LLMs) based decision-making methodologies. This environment is the first to offer the complete StarCraft II action space, multi-modal observation interfaces, and a structured game knowledge database, which are seamlessly connected with various LLMs to facilitate the research of LLMs-based decision-making. To further support multi-agent research, we developed an LLM collaborative framework that supports multi-agent concurrent queries and multi-agent communication. In our experiments, the LLM-PySC2 environment is adapted to be compatible with the StarCraft Multi-Agent Challenge (SMAC) task group and provided eight new scenarios focused on macro-decision abilities. We evaluated nine mainstream LLMs in the experiments, and results show that sufficient parameters are necessary for LLMs to make decisions, but improving reasoning ability does not directly lead to better decision-making outcomes. Our findings further indicate the importance of enabling large models to learn autonomously in the deployment environment through parameter training or train-free learning techniques. Ultimately, we expect that the LLM-PySC2 environment can promote research on learning methods for LLMs, helping LLM-based methods better adapt to task scenarios.

  • 13 authors
·
Nov 8, 2024

SwarmBrain: Embodied agent for real-time strategy game StarCraft II via large language models

Large language models (LLMs) have recently garnered significant accomplishments in various exploratory tasks, even surpassing the performance of traditional reinforcement learning-based methods that have historically dominated the agent-based field. The purpose of this paper is to investigate the efficacy of LLMs in executing real-time strategy war tasks within the StarCraft II gaming environment. In this paper, we introduce SwarmBrain, an embodied agent leveraging LLM for real-time strategy implementation in the StarCraft II game environment. The SwarmBrain comprises two key components: 1) a Overmind Intelligence Matrix, powered by state-of-the-art LLMs, is designed to orchestrate macro-level strategies from a high-level perspective. This matrix emulates the overarching consciousness of the Zerg intelligence brain, synthesizing strategic foresight with the aim of allocating resources, directing expansion, and coordinating multi-pronged assaults. 2) a Swarm ReflexNet, which is agile counterpart to the calculated deliberation of the Overmind Intelligence Matrix. Due to the inherent latency in LLM reasoning, the Swarm ReflexNet employs a condition-response state machine framework, enabling expedited tactical responses for fundamental Zerg unit maneuvers. In the experimental setup, SwarmBrain is in control of the Zerg race in confrontation with an Computer-controlled Terran adversary. Experimental results show the capacity of SwarmBrain to conduct economic augmentation, territorial expansion, and tactical formulation, and it shows the SwarmBrain is capable of achieving victory against Computer players set at different difficulty levels.

  • 4 authors
·
Jan 31, 2024

Ground-based image deconvolution with Swin Transformer UNet

As ground-based all-sky astronomical surveys will gather millions of images in the coming years, a critical requirement emerges for the development of fast deconvolution algorithms capable of efficiently improving the spatial resolution of these images. By successfully recovering clean and high-resolution images from these surveys, the objective is to deepen the understanding of galaxy formation and evolution through accurate photometric measurements. We introduce a two-step deconvolution framework using a Swin Transformer architecture. Our study reveals that the deep learning-based solution introduces a bias, constraining the scope of scientific analysis. To address this limitation, we propose a novel third step relying on the active coefficients in the sparsity wavelet framework. We conducted a performance comparison between our deep learning-based method and Firedec, a classical deconvolution algorithm, based on an analysis of a subset of the EDisCS cluster samples. We demonstrate the advantage of our method in terms of resolution recovery, generalisation to different noise properties, and computational efficiency. The analysis of this cluster sample not only allowed us to assess the efficiency of our method, but it also enabled us to quantify the number of clumps within these galaxies in relation to their disc colour. This robust technique that we propose holds promise for identifying structures in the distant universe through ground-based images.

  • 4 authors
·
May 13, 2024

Joint multiband deconvolution for Euclid and Vera C. Rubin images

With the advent of surveys like Euclid and Vera C. Rubin, astrophysicists will have access to both deep, high-resolution images and multiband images. However, these two types are not simultaneously available in any single dataset. It is therefore vital to devise image deconvolution algorithms that exploit the best of both worlds and that can jointly analyze datasets spanning a range of resolutions and wavelengths. In this work we introduce a novel multiband deconvolution technique aimed at improving the resolution of ground-based astronomical images by leveraging higher-resolution space-based observations. The method capitalizes on the fortunate fact that the Rubin r, i, and z bands lie within the Euclid VIS band. The algorithm jointly de-convolves all the data to convert the r-, i-, and z-band Rubin images to the resolution of Euclid by leveraging the correlations between the different bands. We also investigate the performance of deep-learning-based denoising with DRUNet to further improve the results. We illustrate the effectiveness of our method in terms of resolution and morphology recovery, flux preservation, and generalization to different noise levels. This approach extends beyond the specific Euclid-Rubin combination, offering a versatile solution to improving the resolution of ground-based images in multiple photometric bands by jointly using any space-based images with overlapping filters.

  • 4 authors
·
Feb 24

Whole Heart 3D+T Representation Learning Through Sparse 2D Cardiac MR Images

Cardiac Magnetic Resonance (CMR) imaging serves as the gold-standard for evaluating cardiac morphology and function. Typically, a multi-view CMR stack, covering short-axis (SA) and 2/3/4-chamber long-axis (LA) views, is acquired for a thorough cardiac assessment. However, efficiently streamlining the complex, high-dimensional 3D+T CMR data and distilling compact, coherent representation remains a challenge. In this work, we introduce a whole-heart self-supervised learning framework that utilizes masked imaging modeling to automatically uncover the correlations between spatial and temporal patches throughout the cardiac stacks. This process facilitates the generation of meaningful and well-clustered heart representations without relying on the traditionally required, and often costly, labeled data. The learned heart representation can be directly used for various downstream tasks. Furthermore, our method demonstrates remarkable robustness, ensuring consistent representations even when certain CMR planes are missing/flawed. We train our model on 14,000 unlabeled CMR data from UK BioBank and evaluate it on 1,000 annotated data. The proposed method demonstrates superior performance to baselines in tasks that demand comprehensive 3D+T cardiac information, e.g. cardiac phenotype (ejection fraction and ventricle volume) prediction and multi-plane/multi-frame CMR segmentation, highlighting its effectiveness in extracting comprehensive cardiac features that are both anatomically and pathologically relevant.

  • 6 authors
·
Jun 1, 2024

UNIONS: The Ultraviolet Near-Infrared Optical Northern Survey

The Ultraviolet Near-Infrared Optical Northern Survey (UNIONS) is a "collaboration of collaborations" that is using the Canada-France-Hawai'i Telescope, the Pan-STARRS telescopes, and the Subaru Observatory to obtain ugriz images of a core survey region of 6250 deg^2 of the northern sky. The 10sigma point source depth of the data, as measured within a 2-arcsecond diameter aperture, are [u,g,r,i,z] = [23.7, 24.5, 24.2, 23.8, 23.3]\ in AB magnitudes. UNIONS is addressing some of the most fundamental questions in astronomy, including the properties of dark matter, the growth of structure in the Universe from the very smallest galaxies to large-scale structure, and the assembly of the Milky Way. It is set to become the major ground-based legacy survey for the northern hemisphere for the next decade and provides an essential northern complement to the static-sky science of the Vera C. Rubin Observatory's Legacy Survey of Space and Time. UNIONS supports the core science mission of the {\it Euclid} space mission by providing the data necessary in the northern hemisphere for the calibration of the wavelength dependence of the {\it Euclid} point-spread function and derivation of photometric redshifts in the North Galactic Cap. This region contains the highest quality sky for {\it Euclid}, with low backgrounds from the zodiacal light, stellar density, extinction, and emission from Galactic cirrus. Here, we describe the UNIONS survey components, science goals, data products, and the current status of the overall program.

  • 89 authors
·
Mar 17

Euclid. II. The VIS Instrument

This paper presents the specification, design, and development of the Visible Camera (VIS) on the ESA Euclid mission. VIS is a large optical-band imager with a field of view of 0.54 deg^2 sampled at 0.1" with an array of 609 Megapixels and spatial resolution of 0.18". It will be used to survey approximately 14,000 deg^2 of extragalactic sky to measure the distortion of galaxies in the redshift range z=0.1-1.5 resulting from weak gravitational lensing, one of the two principal cosmology probes of Euclid. With photometric redshifts, the distribution of dark matter can be mapped in three dimensions, and, from how this has changed with look-back time, the nature of dark energy and theories of gravity can be constrained. The entire VIS focal plane will be transmitted to provide the largest images of the Universe from space to date, reaching m_AB>24.5 with S/N >10 in a single broad I_E~(r+i+z) band over a six year survey. The particularly challenging aspects of the instrument are the control and calibration of observational biases, which lead to stringent performance requirements and calibration regimes. With its combination of spatial resolution, calibration knowledge, depth, and area covering most of the extra-Galactic sky, VIS will also provide a legacy data set for many other fields. This paper discusses the rationale behind the VIS concept and describes the instrument design and development before reporting the pre-launch performance derived from ground calibrations and brief results from the in-orbit commissioning. VIS should reach fainter than m_AB=25 with S/N>10 for galaxies of full-width half-maximum of 0.3" in a 1.3" diameter aperture over the Wide Survey, and m_AB>26.4 for a Deep Survey that will cover more than 50 deg^2. The paper also describes how VIS works with the other Euclid components of survey, telescope, and science data processing to extract the cosmological information.

  • 435 authors
·
May 22, 2024