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Aug 7

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics

The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

  • 9 authors
·
Jul 15, 2025

HACHIMI: Scalable and Controllable Student Persona Generation via Orchestrated Agents

Student Personas (SPs) are emerging as infrastructure for educational LLMs, yet prior work often relies on ad-hoc prompting or hand-crafted profiles with limited control over educational theory and population distributions. We formalize this as Theory-Aligned and Distribution-Controllable Persona Generation (TAD-PG) and introduce HACHIMI, a multi-agent Propose-Validate-Revise framework that generates theory-aligned, quota-controlled personas. HACHIMI factorizes each persona into a theory-anchored educational schema, enforces developmental and psychological constraints via a neuro-symbolic validator, and combines stratified sampling with semantic deduplication to reduce mode collapse. The resulting HACHIMI-1M corpus comprises 1 million personas for Grades 1-12. Intrinsic evaluation shows near-perfect schema validity, accurate quotas, and substantial diversity, while external evaluation instantiates personas as student agents answering CEPS and PISA 2022 surveys; across 16 cohorts, math and curiosity/growth constructs align strongly between humans and agents, whereas classroom-climate and well-being constructs are only moderately aligned, revealing a fidelity gradient. All personas are generated with Qwen2.5-72B, and HACHIMI provides a standardized synthetic student population for group-level benchmarking and social-science simulations. Resources available at https://github.com/ZeroLoss-Lab/HACHIMI

  • 5 authors
·
Mar 5

Fantastic Generalization Measures are Nowhere to be Found

We study the notion of a generalization bound being uniformly tight, meaning that the difference between the bound and the population loss is small for all learning algorithms and all population distributions. Numerous generalization bounds have been proposed in the literature as potential explanations for the ability of neural networks to generalize in the overparameterized setting. However, in their paper ``Fantastic Generalization Measures and Where to Find Them,'' Jiang et al. (2020) examine more than a dozen generalization bounds, and show empirically that none of them are uniformly tight. This raises the question of whether uniformly-tight generalization bounds are at all possible in the overparameterized setting. We consider two types of generalization bounds: (1) bounds that may depend on the training set and the learned hypothesis (e.g., margin bounds). We prove mathematically that no such bound can be uniformly tight in the overparameterized setting; (2) bounds that may in addition also depend on the learning algorithm (e.g., stability bounds). For these bounds, we show a trade-off between the algorithm's performance and the bound's tightness. Namely, if the algorithm achieves good accuracy on certain distributions, then no generalization bound can be uniformly tight for it in the overparameterized setting. We explain how these formal results can, in our view, inform research on generalization bounds for neural networks, while stressing that other interpretations of these results are also possible.

  • 4 authors
·
Sep 24, 2023

Toward Real-world Text Image Forgery Localization: Structured and Interpretable Data Synthesis

Existing Text Image Forgery Localization (T-IFL) methods often suffer from poor generalization due to the limited scale of real-world datasets and the distribution gap caused by synthetic data that fails to capture the complexity of real-world tampering. To tackle this issue, we propose Fourier Series-based Tampering Synthesis (FSTS), a structured and interpretable framework for synthesizing tampered text images. FSTS first collects 16,750 real-world tampering instances from five representative tampering types, using a structured pipeline that records human-performed editing traces via multi-format logs (e.g., video, PSD, and editing logs). By analyzing these collected parameters and identifying recurring behavioral patterns at both individual and population levels, we formulate a hierarchical modeling framework. Specifically, each individual tampering parameter is represented as a compact combination of basis operation-parameter configurations, while the population-level distribution is constructed by aggregating these behaviors. Since this formulation draws inspiration from the Fourier series, it enables an interpretable approximation using basis functions and their learned weights. By sampling from this modeled distribution, FSTS synthesizes diverse and realistic training data that better reflect real-world forgery traces. Extensive experiments across four evaluation protocols demonstrate that models trained with FSTS data achieve significantly improved generalization on real-world datasets. Dataset is available at https://github.com/ZeqinYu/FSTS{Project Page}.

  • 6 authors
·
Nov 16, 2025

Structured Proper Loss Geometries for Multiclass Classification: Theory and Controlled Empirical Evaluation

Strictly proper scoring rules identify the true conditional class distribution at population level, but their curvature can alter optimization and finite-sample behavior. We study three multiclass objectives: a class-aware quadratic Bregman score (CAPM), a strongly convex generator with constrained log-cosh ridges (HPG), and an HPG objective with an annealed probability-margin penalty (APMS). CAPM is treated as a structured instance of established quadratic scoring-rule theory. We derive conditional-regret, curvature, range, and logit-gradient bounds for CAPM and HPG, and prove exact penalty-range and conditional-target displacement bounds for APMS. Controlled five-seed experiments use Digits, Wisconsin breast cancer, and synthetic confusion and long-tail problems under clean labels, symmetric and pair-flip corruption, class imbalance, calibration evaluation, input corruption, and first-order adversarial perturbations. The candidates are close to cross-entropy on clean data and show descriptive gains in some noisy-label cells, but the five-seed comparisons are interpreted descriptively rather than as significance evidence. The selected noisy-label baselines perform better on Digits with 40% symmetric label noise, and explicit prior-adjustment methods perform better in the 30:1 synthetic long-tail experiment. Ablations do not show a consistent benefit from the candidate-specific graph, ridge, or margin components. The mathematical analysis establishes the stated properties, and the experiments delimit the empirical evidence; together they do not support a claim of general superiority.

  • 1 authors
·
Jun 27

Mycorrhiza: Genotype Assignment usingPhylogenetic Networks

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

  • 3 authors
·
Oct 13, 2020

I Am Aligned, But With Whom? MENA Values Benchmark for Evaluating Cultural Alignment and Multilingual Bias in LLMs

We introduce MENAValues, a novel benchmark designed to evaluate the cultural alignment and multilingual biases of large language models (LLMs) with respect to the beliefs and values of the Middle East and North Africa (MENA) region, an underrepresented area in current AI evaluation efforts. Drawing from large-scale, authoritative human surveys, we curate a structured dataset that captures the sociocultural landscape of MENA with population-level response distributions from 16 countries. To probe LLM behavior, we evaluate diverse models across multiple conditions formed by crossing three perspective framings (neutral, personalized, and third-person/cultural observer) with two language modes (English and localized native languages: Arabic, Persian, Turkish). Our analysis reveals three critical phenomena: "Cross-Lingual Value Shifts" where identical questions yield drastically different responses based on language, "Reasoning-Induced Degradation" where prompting models to explain their reasoning worsens cultural alignment, and "Logit Leakage" where models refuse sensitive questions while internal probabilities reveal strong hidden preferences. We further demonstrate that models collapse into simplistic linguistic categories when operating in native languages, treating diverse nations as monolithic entities. MENAValues offers a scalable framework for diagnosing cultural misalignment, providing both empirical insights and methodological tools for developing more culturally inclusive AI.

  • 2 authors
·
Oct 15, 2025

The Population of the Galactic Center Filaments: Position Angle Distribution Reveal a Degree-scale Collimated Outflow from Sgr A* along the Galactic Plane

We have examined the distribution of the position angle (PA) of the Galactic center filaments with lengths L > 66'' and < 66'' as well as their length distribution as a function of PA. We find bimodal PA distributions of the filaments, long and short populations of radio filaments. Our PA study shows the evidence for a distinct population of short filaments with PA close to the Galactic plane. Mainly thermal short radio filaments (<66'') have PAs concentrated close to the Galactic plane within 60^circ < rm PA <120^circ. Remarkably, the short filament PAs are radial with respect to the Galactic center at l <0^circ, and extend in the direction toward Sgr A*. On a smaller scale, the prominent Sgr E HII complex G358.7-0.0 provides a vivid example of the nearly radial distribution of short filaments. The bimodal PA distribution suggests different origin for two distinct filament populations. We argue that alignment of the short filament population results from the ram pressure of a degree-scale outflow from Sgr A* that exceeds the internal filament pressure, and aligns them along the Galactic plane. The ram pressure is estimated to be 2times10^6, cm^{-3}, K at a distance of 300pc, requiring biconical mass outflow rate 10^{-4} \msol\, yr^{-1} with an opening angle of sim40^circ. This outflow aligns not only the magnetized filaments along the Galactic plane but also accelerates thermal material associated with embedded or partially embedded clouds. This places an estimate of sim6 Myr as the age of the outflow.

  • 4 authors
·
Jun 1, 2023

Population Aware Diffusion for Time Series Generation

Diffusion models have shown promising ability in generating high-quality time series (TS) data. Despite the initial success, existing works mostly focus on the authenticity of data at the individual level, but pay less attention to preserving the population-level properties on the entire dataset. Such population-level properties include value distributions for each dimension and distributions of certain functional dependencies (e.g., cross-correlation, CC) between different dimensions. For instance, when generating house energy consumption TS data, the value distributions of the outside temperature and the kitchen temperature should be preserved, as well as the distribution of CC between them. Preserving such TS population-level properties is critical in maintaining the statistical insights of the datasets, mitigating model bias, and augmenting downstream tasks like TS prediction. Yet, it is often overlooked by existing models. Hence, data generated by existing models often bear distribution shifts from the original data. We propose Population-aware Diffusion for Time Series (PaD-TS), a new TS generation model that better preserves the population-level properties. The key novelties of PaD-TS include 1) a new training method explicitly incorporating TS population-level property preservation, and 2) a new dual-channel encoder model architecture that better captures the TS data structure. Empirical results in major benchmark datasets show that PaD-TS can improve the average CC distribution shift score between real and synthetic data by 5.9x while maintaining a performance comparable to state-of-the-art models on individual-level authenticity.

  • 5 authors
·
Jan 1, 2025 2

scDFM: Distributional Flow Matching Model for Robust Single-Cell Perturbation Prediction

A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that perturbations often induce population-level shifts rather than changes in individual cells. Existing deep learning methods typically assume cell-level correspondences, limiting their ability to capture such global effects. We present scDFM, a generative framework based on conditional flow matching that models the full distribution of perturbed cells conditioned on control states. By incorporating a maximum mean discrepancy (MMD) objective, our method aligns perturbed and control populations beyond cell-level correspondences. To further improve robustness to sparsity and noise, we introduce the Perturbation-Aware Differential Transformer (PAD-Transformer), a backbone architecture that leverages gene interaction graphs and differential attention to capture context-specific expression changes. Across multiple genetic and drug perturbation benchmarks, scDFM consistently outperforms prior methods, demonstrating strong generalization in both unseen and combinatorial settings. In the combinatorial setting, it reduces mean squared error by 19.6% relative to the strongest baseline. These results highlight the importance of distribution-level generative modeling for robust in silico perturbation prediction. The code is available at https://github.com/AI4Science-WestlakeU/scDFM

  • 4 authors
·
Feb 5

Accelerometry-Derived Digital Biomarkers for Cardiometabolic Risk: A Population-Representative Tabular Benchmark with Uncertainty Quantification

Structured tabular data dominates clinical medicine, yet existing benchmarks fail to reflect real-world properties like complex survey sampling, demographic oversampling, and subgroup fairness. We introduce the NHANES Accelerometry Cardiometabolic Benchmark, derived from NHANES 2003-2006, comprising 1,381 adults with hip-worn accelerometry, fasting laboratory biomarkers, dietary intake, and anthropometrics. We evaluate three tabular learning methods -- ridge regression, XGBoost, and the foundation model TabPFN v2 -- to predict glycated haemoglobin (HbA1c), fasting triglycerides, and C-reactive protein (CRP) from activity phenotypes and lifestyle covariates. TabPFN v2 achieves the best overall performance (HbA1c R^2=0.156, CRP R^2=0.383), while triglycerides remain largely unpredictable (R^2 < 0.05), consistent with known genetic dominance. We apply split conformal prediction to generate distribution-free 90% prediction intervals and evaluate demographic coverage equity across sex and race/ethnicity subgroups. Marginal coverage aligns with the 90% target for CRP and HbA1c but falls below for triglycerides. At the subgroup level, we observe localized undercoverage (e.g., HbA1c for Mexican American participants), illustrating the gap between marginal guarantees and the conditional coverage required for clinical fairness. Code and data are at https://github.com/felizzi/nhanes-accel-cardiometabolic-benchmark.

  • 1 authors
·
Jun 28

Identifying Connectivity Distributions from Neural Dynamics Using Flows

Connectivity structure shapes neural computation, but inferring this structure from population recordings is degenerate: multiple connectivity structures can generate identical dynamics. Recent work uses low-rank recurrent neural networks (lrRNNs) to infer low-dimensional latent dynamics and connectivity from observed activity, enabling a mechanistic interpretation of the dynamics. However, standard approaches for training lrRNNs can recover spurious structures irrelevant to the underlying dynamics. We first characterize the identifiability of connectivity structures in lrRNNs and determine conditions under which a unique solution exists. To find such solutions, we develop an inference framework based on maximum entropy and continuous normalizing flows (CNFs), trained via flow matching. Instead of estimating a single connectivity matrix, our method learns a distribution over connection weights that is maximally unbiased over unidentifiable components while matching the observed dynamics. This approach captures complex yet necessary distributions such as heavy-tailed connectivity found in empirical data. We validate our method on synthetic datasets with connectivity structures that generate multistable attractors, limit cycles, and ring attractors, and demonstrate its applicability in recordings from rat frontal cortex during decision-making. Our framework shifts circuit inference from recovering connectivity to identifying which connectivity structures are computationally required, and which are artifacts of underconstrained inference.

  • 5 authors
·
May 28

Estimating Tail Risks in Language Model Output Distributions

Language models are increasingly capable and are being rapidly deployed on a population-level scale. As a result, the safety of these models is increasingly high-stakes. Fortunately, advances in alignment have significantly reduced the likelihood of harmful model outputs. However, when models are queried billions of times in a day, even rare worst-case behaviors will occur. Current safety evaluations focus on capturing the distribution of inputs that yield harmful outputs. These evaluations disregard the probabilistic nature of models and their tail output behavior. To measure this tail risk, we propose a method to efficiently estimate the probability of harmful outputs for any input query. Instead of naive brute-force sampling from the target model, where harmful outputs could be rare, we operationalize importance sampling by creating unsafe versions of the target model. These unsafe versions enable sample-efficient estimation by making harmful outputs more probable. On benchmarks measuring misuse and misalignment, these estimates match brute-force Monte Carlo estimates using 10-20x fewer samples. For example, we can estimate probability of harmful outputs on the order of 10^-4 with just 500 samples. Additionally, we find that these harmfulness estimates can reveal the sensitivity of models to perturbations in model input and predict deployment risks. Our work demonstrates that accurate rare-event estimation is both critical and feasible for safety evaluations. Code is available at https://github.com/rangell/LMTailRisk

  • 7 authors
·
Apr 23

GWKokab: An Implementation to Identify the Properties of Multiple Population of Gravitational Wave Sources

The rapidly increasing sensitivity of gravitational wave detectors is enabling the detection of a growing number of compact binary mergers. These events are crucial for understanding the population properties of compact binaries. However, many previous studies rely on computationally expensive inference frameworks, limiting their scalability. In this work, we present GWKokab, a JAX-based framework that enables modular model building with independent rate for each subpopulation such as BBH, BNS, and NSBH binaries. It provides accelerated inference using the normalizing flow based sampler called flowMC and is also compatible with NumPyro samplers. To validate our framework, we generated two synthetic populations, one comprising spinning eccentric binaries and the other circular binaries using a multi-source model. We then recovered their injected parameters at significantly reduced computational cost and demonstrated that eccentricity distribution can be recovered even in spinning eccentric populations. We also reproduced results from two prior studies: one on non-spinning eccentric populations, and another on the BBH mass distribution using the third Gravitational Wave Transient Catalog (GWTC-3). We anticipate that GWKokab will not only reduce computational costs but also enable more detailed subpopulation analyses such as their mass, spin, eccentricity, and redshift distributions in gravitational wave events, offering deeper insights into compact binary formation and evolution.

Understanding the Neutron Star Population with the SKA

Since their discovery in the late 1960's the population of known neutron stars (NSs) has grown to ~2500. The last five decades of observations have yielded many surprises and demonstrated that the observational properties of NSs are remarkably diverse. The surveys that will be performed with SKA (the Square Kilometre Array) will produce a further tenfold increase in the number of Galactic NSs known. Moreover, the SKA's broad spectral coverage, sub-arraying and multi-beaming capabilities will allow us to characterise these sources with unprecedented efficiency, in turn enabling a giant leap in the understanding of their properties. Here we review the NS population and outline our strategies for studying each of the growing number of diverse classes that are populating the "NS zoo". Some of the main scientific questions that will be addressed by the much larger statistical samples and vastly improved timing efficiency provided by SKA include: (i) the spin period and spin-down rate distributions (and thus magnetic fields) at birth, and the associated information about the SNe wherein they are formed; (ii) the radio pulsar-magnetar connection; (iii) the link between normal radio pulsars, intermittent pulsars and rotating radio transients; (iv) the slowest possible spin period for a radio pulsar (revealing the conditions at the pulsar death-line); (v) proper motions of pulsars (revealing SN kick physics); (vi) the mass distribution of NSs (vii) the fastest possible spin period for a recycled pulsar (constraining magnetosphere-accretion disc interactions, gravitational wave radiation and the equation-of-state); (viii) the origin of high eccentricity millisecond pulsars (MSPs); (ix) the formation channels for recently identified triple systems; and finally (x) how isolated MSPs are formed. We expect that the SKA will break new ground unveiling exotic systems that will challenge... [abridged]

  • 12 authors
·
Dec 30, 2014

Detecting Machine-Generated Texts by Multi-Population Aware Optimization for Maximum Mean Discrepancy

Large language models (LLMs) such as ChatGPT have exhibited remarkable performance in generating human-like texts. However, machine-generated texts (MGTs) may carry critical risks, such as plagiarism issues, misleading information, or hallucination issues. Therefore, it is very urgent and important to detect MGTs in many situations. Unfortunately, it is challenging to distinguish MGTs and human-written texts because the distributional discrepancy between them is often very subtle due to the remarkable performance of LLMs. In this paper, we seek to exploit maximum mean discrepancy (MMD) to address this issue in the sense that MMD can well identify distributional discrepancies. However, directly training a detector with MMD using diverse MGTs will incur a significantly increased variance of MMD since MGTs may contain multiple text populations due to various LLMs. This will severely impair MMD's ability to measure the difference between two samples. To tackle this, we propose a novel multi-population aware optimization method for MMD called MMD-MP, which can avoid variance increases and thus improve the stability to measure the distributional discrepancy. Relying on MMD-MP, we develop two methods for paragraph-based and sentence-based detection, respectively. Extensive experiments on various LLMs, \eg, GPT2 and ChatGPT, show superior detection performance of our MMD-MP. The source code is available at https://github.com/ZSHsh98/MMD-MP.

  • 6 authors
·
Feb 25, 2024

Semi-Supervised Learning via Weight-aware Distillation under Class Distribution Mismatch

Semi-Supervised Learning (SSL) under class distribution mismatch aims to tackle a challenging problem wherein unlabeled data contain lots of unknown categories unseen in the labeled ones. In such mismatch scenarios, traditional SSL suffers severe performance damage due to the harmful invasion of the instances with unknown categories into the target classifier. In this study, by strict mathematical reasoning, we reveal that the SSL error under class distribution mismatch is composed of pseudo-labeling error and invasion error, both of which jointly bound the SSL population risk. To alleviate the SSL error, we propose a robust SSL framework called Weight-Aware Distillation (WAD) that, by weights, selectively transfers knowledge beneficial to the target task from unsupervised contrastive representation to the target classifier. Specifically, WAD captures adaptive weights and high-quality pseudo labels to target instances by exploring point mutual information (PMI) in representation space to maximize the role of unlabeled data and filter unknown categories. Theoretically, we prove that WAD has a tight upper bound of population risk under class distribution mismatch. Experimentally, extensive results demonstrate that WAD outperforms five state-of-the-art SSL approaches and one standard baseline on two benchmark datasets, CIFAR10 and CIFAR100, and an artificial cross-dataset. The code is available at https://github.com/RUC-DWBI-ML/research/tree/main/WAD-master.

  • 5 authors
·
Aug 22, 2023

Dust in the very metal-poor galaxy Sextans A with JWST. I: Characterizing the evolved stellar population of Sextans A based on JWST observations and stellar evolution models

The nearby star-forming dwarf galaxy Sextans A offers a unique window into galaxy evolution in the early Universe, owing to its extremely low metallicity (about 1-7% Zsun). Recent JWST imaging of Sextans A spanning 1-21 micron enables a detailed characterization of its dusty stellar populations and interstellar medium. In this work, we compare the observed JWST color-magnitude distributions of evolved stars with stellar evolution and dust-formation models to characterize the properties of the asymptotic giant branch (AGB) population, including progenitor mass, formation epoch, metallicity, and dust production. Evolutionary tracks for 0.8-7 Msun stars with metallicity Z=10^-3 provide good agreement with the overall distribution of AGB stars in Sextans A. More than 90% of the AGB population occupies a nearly vertical sequence in the color-magnitude diagrams, corresponding to stars spanning a wide range of masses and ages but exhibiting little or no circumstellar dust. This sequence appears to be dominated by oxygen-rich (M-type) AGB stars and reveals that the F444W flux is a robust luminosity diagnostic. A small subset of sources displays strong infrared excesses and is dominated by carbon stars descending from 1.25-1.5 Msun progenitors that formed about 2-3 Gyr ago and are currently in the final AGB phases. Their MIRI colors imply very low metallicities, consistent with estimates from the red giant branch morphology (about 1-2% Zsun). Finally, we show that the JWST/NIRCam F277W-F444W color serves as an effective proxy for the dust production rate, with models predicting rates up to 10^-7 Msun/yr for the reddest sources in Sextans A.

  • 25 authors
·
Jun 4

Euclid Quick Data Release (Q1). Active galactic nuclei identification using diffusion-based inpainting of Euclid VIS images

Light emission from galaxies exhibit diverse brightness profiles, influenced by factors such as galaxy type, structural features and interactions with other galaxies. Elliptical galaxies feature more uniform light distributions, while spiral and irregular galaxies have complex, varied light profiles due to their structural heterogeneity and star-forming activity. In addition, galaxies with an active galactic nucleus (AGN) feature intense, concentrated emission from gas accretion around supermassive black holes, superimposed on regular galactic light, while quasi-stellar objects (QSO) are the extreme case of the AGN emission dominating the galaxy. The challenge of identifying AGN and QSO has been discussed many times in the literature, often requiring multi-wavelength observations. This paper introduces a novel approach to identify AGN and QSO from a single image. Diffusion models have been recently developed in the machine-learning literature to generate realistic-looking images of everyday objects. Utilising the spatial resolving power of the Euclid VIS images, we created a diffusion model trained on one million sources, without using any source pre-selection or labels. The model learns to reconstruct light distributions of normal galaxies, since the population is dominated by them. We condition the prediction of the central light distribution by masking the central few pixels of each source and reconstruct the light according to the diffusion model. We further use this prediction to identify sources that deviate from this profile by examining the reconstruction error of the few central pixels regenerated in each source's core. Our approach, solely using VIS imaging, features high completeness compared to traditional methods of AGN and QSO selection, including optical, near-infrared, mid-infrared, and X-rays.

  • 274 authors
·
Mar 19, 2025

PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

  • 6 authors
·
Feb 22

Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

  • 8 authors
·
Aug 26, 2024 2

JWST observations of photodissociation regions III. Dust modelling at the illuminated edge of the Horsehead PDR

Carbonaceous nano-grains are a significant component of interstellar dust and dominate the mid-infrared emission of photodissociation regions (PDRs). We study the evolution of nano-grains across the illuminated edge of the Horsehead PDR, especially their abundance and size properties. This work is part of the Physics and Chemistry of PDR Fronts program studying dust and gas in PDRs with JWST. We use NIRCam+MIRI photometric bands and NIRSpec+MRS spectroscopy to map the illuminated edge. We model dust emission using the THEMIS dust model with the SOC radiative transfer code. Detailed modeling of high angular resolution JWST data allows us to obtain constraints on nano-grain properties. We find that diffuse ISM dust cannot account for the observed data, requiring evolved grains. A sharp density increase is observed at the illuminated edge, consistent with ALMA observations revealing a sharp transition between molecular and ionized gas. Although the PDR length could not be directly determined, we estimate an upper limit of approximately 0.015 pc. This implies a lower limit on small grain abundance (greater than 0.003), showing small grains are not depleted at the Horsehead edge, unlike in the Orion Bar. Our findings indicate a high-density environment and less steep size distribution for nano-grains at the illuminated edge versus the diffuse ISM. This implies nano-grain destruction mechanisms might be less efficient in the Horsehead's moderate-UV field than in more intense PDRs. These results support a model where nano-grain population recovery is slower in moderate-UV environments, leading to a unique dust size distribution at the edge of the Horsehead Nebula.

  • 22 authors
·
Oct 28, 2025

EgoAdapt: A multi-stream evaluation study of adaptation to real-world egocentric user video

In egocentric action recognition a single population model is typically trained and subsequently embodied on a head-mounted device, such as an augmented reality headset. While this model remains static for new users and environments, we introduce an adaptive paradigm of two phases, where after pretraining a population model, the model adapts on-device and online to the user's experience. This setting is highly challenging due to the change from population to user domain and the distribution shifts in the user's data stream. Coping with the latter in-stream distribution shifts is the focus of continual learning, where progress has been rooted in controlled benchmarks but challenges faced in real-world applications often remain unaddressed. We introduce EgoAdapt, a benchmark for real-world egocentric action recognition that facilitates our two-phased adaptive paradigm, and real-world challenges naturally occur in the egocentric video streams from Ego4d, such as long-tailed action distributions and large-scale classification over 2740 actions. We introduce an evaluation framework that directly exploits the user's data stream with new metrics to measure the adaptation gain over the population model, online generalization, and hindsight performance. In contrast to single-stream evaluation in existing works, our framework proposes a meta-evaluation that aggregates the results from 50 independent user streams. We provide an extensive empirical study for finetuning and experience replay.

  • 6 authors
·
Jul 10, 2023

Searching For Anisotropic Gravitational-wave Backgrounds Using Pulsar Timing Arrays

We present the results of simulated injections testing the first Bayesian search-pipeline capable of investigating the angular-structure of a gravitational-wave (GW) background influencing pulsar signals. A stochastic background of GWs from the incoherent superposition of many inspiraling supermassive black hole binaries at nHz frequencies is likely to be the dominant GW signal detectable by pulsar timing arrays (PTAs). Even though one might expect a background composed of a high-redshift cosmological population of sources to be fairly isotropic, deviations from isotropy may be indicative of local GW hotspots or some form of continuous anisotropy in the angular-distribution of GW-power. A GWB induces time-of-arrival deviations in pulsar signals which are correlated between separated pulsars. In an isotropic background this cross-correlation follows a distinctive relationship, known as the Hellings and Downs curve, that depends only on the angular separation of the pulsars. If the background is anisotropic, the cross-correlation is different, but predictable, and also depends on the absolute position of the pulsars. By simulating datasets containing GWBs with various anisotropic configurations, we have explored the prospects for constraining anisotropy using near future data. We find that at moderate to high signal to noise ratio the assumption of isotropy is no longer an appropriate description of the simulated background. Furthermore, we can recover the nature of the injected anisotropy in a Bayesian parameter-estimation search, and propose a prior on the anisotropy search-space motivated by the physicality of the implied distribution of sources.

  • 2 authors
·
Jun 23, 2013

Partition, Prompt, Aggregate: Statistical Self-Consistency in Language Models

In-context learning is commonly interpreted as a form of conditional inference, in which the prompt specifies a context and the model's output is treated as an estimate of the corresponding conditional distribution. If this interpretation holds, then LLM estimates should satisfy basic probabilistic identities. In particular, the law of total probability asserts that prior-weighted conditional distributions aggregate into population-level marginals over any valid partition of the population. In this work, we investigate to what extent LLM estimates adhere to this self-consistency principle. We use binary trees as an evaluation scaffold to recursively partition a population into increasingly fine-grained subpopulations. We then prompt LLMs with verbalized subpopulation descriptions in context, aggregate the resulting estimates back into population-level estimates, and compare them across partitions of varying granularity. Applying this protocol across problem domains and state-of-the-art frontier models, we show widespread violations of basic consistency properties. An in-depth study of persona prompting reveals a pattern we call the macro fallacy: estimates reconstructed from more fine-grained subpopulation responses are often better aligned with human reference data than direct population-level estimates. This effect persists across variations in tree structure and estimation task, and can be partially recovered through implicit prompting. Together, these findings suggest that models possess relevant subpopulation knowledge but do not reliably propagate it into aggregate estimates. This gap establishes statistical self-consistency as an unsaturated, reference-free criterion for evaluating LLMs.

  • 4 authors
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Jul 15 2

BioAnalyst: A Foundation Model for Biodiversity

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

  • 7 authors
·
Jul 11, 2025

Neon: Negative Extrapolation From Self-Training Improves Image Generation

Scaling generative AI models is bottlenecked by the scarcity of high-quality training data. The ease of synthesizing from a generative model suggests using (unverified) synthetic data to augment a limited corpus of real data for the purpose of fine-tuning in the hope of improving performance. Unfortunately, however, the resulting positive feedback loop leads to model autophagy disorder (MAD, aka model collapse) that results in a rapid degradation in sample quality and/or diversity. In this paper, we introduce Neon (for Negative Extrapolation frOm self-traiNing), a new learning method that turns the degradation from self-training into a powerful signal for self-improvement. Given a base model, Neon first fine-tunes it on its own self-synthesized data but then, counterintuitively, reverses its gradient updates to extrapolate away from the degraded weights. We prove that Neon works because typical inference samplers that favor high-probability regions create a predictable anti-alignment between the synthetic and real data population gradients, which negative extrapolation corrects to better align the model with the true data distribution. Neon is remarkably easy to implement via a simple post-hoc merge that requires no new real data, works effectively with as few as 1k synthetic samples, and typically uses less than 1% additional training compute. We demonstrate Neon's universality across a range of architectures (diffusion, flow matching, autoregressive, and inductive moment matching models) and datasets (ImageNet, CIFAR-10, and FFHQ). In particular, on ImageNet 256x256, Neon elevates the xAR-L model to a new state-of-the-art FID of 1.02 with only 0.36% additional training compute. Code is available at https://github.com/SinaAlemohammad/Neon

  • 3 authors
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Oct 3, 2025

LLM as Dataset Analyst: Subpopulation Structure Discovery with Large Language Model

The distribution of subpopulations is an important property hidden within a dataset. Uncovering and analyzing the subpopulation distribution within datasets provides a comprehensive understanding of the datasets, standing as a powerful tool beneficial to various downstream tasks, including Dataset Subpopulation Organization, Subpopulation Shift, and Slice Discovery. Despite its importance, there has been no work that systematically explores the subpopulation distribution of datasets to our knowledge. To address the limitation and solve all the mentioned tasks in a unified way, we introduce a novel concept of subpopulation structures to represent, analyze, and utilize subpopulation distributions within datasets. To characterize the structures in an interpretable manner, we propose the Subpopulation Structure Discovery with Large Language Models (SSD-LLM) framework, which employs world knowledge and instruction-following capabilities of Large Language Models (LLMs) to linguistically analyze informative image captions and summarize the structures. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery.

  • 6 authors
·
May 3, 2024

Impulsive mixing of stellar populations in dwarf spheroidal galaxies

We study the response of mono-energetic stellar populations with initially isotropic kinematics to impulsive and adiabatic changes to an underlying dark matter potential. Half-light radii expand and velocity dispersions decrease as enclosed dark matter is removed. The details of this expansion and cooling depend on the time scale on which the underlying potential changes. In the adiabatic regime, the product of half-light radius and average velocity dispersion is conserved. We show that the stellar populations maintain centrally isotropic kinematics throughout their adiabatic evolution, and their densities can be approximated by a family of analytical radial profiles. Metallicity gradients within the galaxy flatten as dark matter is slowly removed. In the case of strong impulsive perturbations, stellar populations develop power-law-like density tails with radially biased kinematics. We show that the distribution of stellar binding energies within the dark matter halo substantially widens after an impulsive perturbation, no matter the sign of the perturbation. This allows initially energetically separated stellar populations to mix, to the extent that previously chemo-dynamically distinct populations may masquerade as a single population with large metallicity and energy spread. Finally, we show that in response to an impulsive perturbation, stellar populations that are deeply embedded in cored dark matter halos undergo a series of damped oscillations before reaching a virialised equilibrium state, driven by inefficient phase mixing in the harmonic potentials of cored halos. This slow return to equilibrium adds substantial systematic uncertainty to dynamical masses estimated from Jeans modeling or the virial theorem.

  • 5 authors
·
Feb 26, 2025

Generative Distribution Embeddings

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the W_2 distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning representations of cell populations from lineage-tracing data (150K cells), predicting perturbation effects on single-cell transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), modeling tissue-specific DNA methylation patterns (253M sequences), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).

  • 5 authors
·
May 23, 2025

Fair and Explainable Credit-Scoring under Concept Drift: Adaptive Explanation Frameworks for Evolving Populations

Evolving borrower behaviors, shifting economic conditions, and changing regulatory landscapes continuously reshape the data distributions underlying modern credit-scoring systems. Conventional explainability techniques, such as SHAP, assume static data and fixed background distributions, making their explanations unstable and potentially unfair when concept drift occurs. This study addresses that challenge by developing adaptive explanation frameworks that recalibrate interpretability and fairness in dynamically evolving credit models. Using a multi-year credit dataset, we integrate predictive modeling via XGBoost with three adaptive SHAP variants: (A) per-slice explanation reweighting that adjusts for feature distribution shifts, (B) drift-aware SHAP rebaselining with sliding-window background samples, and (C) online surrogate calibration using incremental Ridge regression. Each method is benchmarked against static SHAP explanations using metrics of predictive performance (AUC, F1), directional and rank stability (cosine, Kendall tau), and fairness (demographic parity and recalibration). Results show that adaptive methods, particularly rebaselined and surrogate-based explanations, substantially improve temporal stability and reduce disparate impact across demographic groups without degrading predictive accuracy. Robustness tests, including counterfactual perturbations, background sensitivity analysis, and proxy-variable detection, confirm the resilience of adaptive explanations under real-world drift conditions. These findings establish adaptive explainability as a practical mechanism for sustaining transparency, accountability, and ethical reliability in data-driven credit systems, and more broadly, in any domain where decision models evolve with population change.

  • 1 authors
·
Nov 4, 2025

SymptomAI: Towards a Conversational AI Agent for Everyday Symptom Assessment

Language models excel at diagnostic assessments on currated medical case-studies and vignettes, performing on par with, or better than, clinical professionals. However, existing studies focus on complex scenarios with rich context making it difficult to draw conclusions about how these systems perform for patients reporting symptoms in everyday life. We deployed SymptomAI, a set of conversational AI agents for end-to-end patient interviewing and differential diagnosis (DDx), via the Fitbit app in a study that randomized participants (N=13,917) to interact with five AI agents. This corpus captures diverse communication and a realistic distribution of illnesses from a real world population. A subset of 1,228 participants reported a clinician-provided diagnosis, and 517 of these were further evaluated by a panel of clinicians during over 250 hours of annotation. SymptomAI DDx were significantly more accurate (OR = 2.47, p < 0.001) than those from independent clinicians given the same dialogue in a blinded randomized comparison. Moreover, agentic strategies which conduct a dedicated symptom interview that elicit additional symptom information before providing a diagnosis, perform substantially better than baseline, user-guided conversations (p < 0.001). An auxiliary analysis on 1,509 conversations from a general US population panel validated that these results generalize beyond wearable device users. We used SymptomAI diagnoses as labels for all 13,917 participants to analyze over 500,000 days of wearable metrics across nearly 400 unique conditions. We identified strong associations between acute infections and physiological shifts (e.g., OR > 7 for influenza). While limited by self-reported ground truth, these results demonstrate the benefits of a dedicated and complete symptom interview compared to a user-guided symptom discussion, which is the default of most consumer LLMs.

  • 33 authors
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May 4 1

Dark Matter Subhalos and Higher Order Catastrophes in Gravitational Wave Lensing

Gravitational lensing is an invaluable probe of the nature of dark matter, and the structures it forms. Lensed gravitational waves in particular allow for unparalleled sensitivity to small scale structures within the lenses, due to the precise time resolution in combination with the continuous monitoring of the entire sky. In this work, we show two distinct ways of using strongly lensed gravitational waves to identify the presence of dark matter subhalos: {i)} through higher order caustics generating high relative magnification (mu_r > 2), short time delay image pairs that break the caustic universality relations of single dark matter halos, which occur for sim 1-10 percent of strongly lensed events in our cold dark matter models, and ii) through the presence of more than three highly magnified images, which occur for sim 0.01-1 percent of the same simulated events. We find that these results are highly sensitive to the concentrations of subhalos in our simulations, and more mildly to their number densities. The presence of low-mass subhalos increases the probability of observing wave-optics lensing in lensed gravitational waves, which is studied by solving the diffraction integral with the stationary phase approximation, as well as numerically. We also report distinct quantitative and qualitative differences in the distributions of relative magnifications and time delays for subhalo populations with increased number densities or concentrations. With the upcoming detection of strongly lensed events by ground- and space- based detectors, comparisons against these simulated distributions will provide insight into the nature of dark matter.

  • 5 authors
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Oct 16, 2025

Galaxy properties from the outskirts to the core of a protocluster at z=3.699

We present follow-up spectroscopy on a protocluster candidate selected from the wide-field imaging of the Hyper SuprimeCam Subaru Strategic Programme. The target protocluster candidate was identified as a 4.5σ overdense region of g-dropout galaxies, and the redshifts of g-dropout galaxies are determined by detecting their Lyα emission. Thirteen galaxies, at least, are found to be clustering in the narrow redshift range of Δz<0.05 at z=3.699. This is clear evidence of the presence of a protocluster in the target region. Following the discovery of the protocluster at z=3.699, the physical properties and three-dimensional distribution of its member galaxies are investigated. Based on spectroscopically-confirmed g-dropout galaxies, we find an overabundance of rest-frame ultraviolet (UV) bright galaxies in the protocluster. The UV brightest protocluster member turns out to be an active galactic nucleus, and the other UV brighter members tend to show smaller Lyα equivalent widths than field counterparts. The member galaxies tend to densely populate near the centre of the protocluster, but the separation from the nearest neighbour rather than the distance from the centre of the protocluster is more tightly correlated to galaxy properties, implying that the protocluster is still in an early phase of cluster formation and only close neighbours have a significant impact on the physical properties of protocluster members. The number density of massive galaxies, selected from an archival photometric-redshift catalogue, is higher near the centre of the protocluster, while dusty starburst galaxies are distributed on the outskirts. These observational results suggest that the protocluster consists of multiple galaxy populations, whose spatial distributions may hint at the developmental phase of the galaxy cluster.

  • 9 authors
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Apr 24, 2024

SynGP500: A Clinically-Grounded Synthetic Dataset of Australian General Practice Medical Notes

We introduce SynGP500, a clinician-curated collection of 500 synthetic Australian general practice medical notes. The dataset integrates curriculum-based clinical breadth (RACGP 2022 Curriculum), epidemiologically-calibrated prevalence (BEACH study), and diverse consultation contexts. This approach systematically includes both common presentations and less-common curriculum-specified conditions that GPs must recognize but appear infrequently in single practice populations, potentially supporting more generalizable model training than datasets constrained by naturally occurring case distributions. SynGP500 is messy by design, reflecting the authentic complexity of healthcare delivery: telegraphic documentation, typos, patient non-adherence, socioeconomic barriers, and clinician-patient disagreements, unlike sanitized synthetic datasets that obscure clinical realities. Multi-faceted validation demonstrates dataset quality through epidemiological alignment with real Australian GP consultation patterns (BEACH study), stylometric analysis confirming high linguistic variation, semantic diversity analysis demonstrating broad coverage, and exploratory downstream evaluation using self-supervised medical concept extraction, showing F1 improvements. SynGP500 addresses a critical national gap, providing researchers and educators with a resource for developing and evaluating clinical NLP methods for Australian general practice while inherently protecting patient privacy.

  • 1 authors
·
Dec 17, 2025

Optimizing Brain Tumor Segmentation with MedNeXt: BraTS 2024 SSA and Pediatrics

Identifying key pathological features in brain MRIs is crucial for the long-term survival of glioma patients. However, manual segmentation is time-consuming, requiring expert intervention and is susceptible to human error. Therefore, significant research has been devoted to developing machine learning methods that can accurately segment tumors in 3D multimodal brain MRI scans. Despite their progress, state-of-the-art models are often limited by the data they are trained on, raising concerns about their reliability when applied to diverse populations that may introduce distribution shifts. Such shifts can stem from lower quality MRI technology (e.g., in sub-Saharan Africa) or variations in patient demographics (e.g., children). The BraTS-2024 challenge provides a platform to address these issues. This study presents our methodology for segmenting tumors in the BraTS-2024 SSA and Pediatric Tumors tasks using MedNeXt, comprehensive model ensembling, and thorough postprocessing. Our approach demonstrated strong performance on the unseen validation set, achieving an average Dice Similarity Coefficient (DSC) of 0.896 on the BraTS-2024 SSA dataset and an average DSC of 0.830 on the BraTS Pediatric Tumor dataset. Additionally, our method achieved an average Hausdorff Distance (HD95) of 14.682 on the BraTS-2024 SSA dataset and an average HD95 of 37.508 on the BraTS Pediatric dataset. Our GitHub repository can be accessed here: Project Repository : https://github.com/python-arch/BioMbz-Optimizing-Brain-Tumor-Segmentation-with-MedNeXt-BraTS-2024-SSA-and-Pediatrics

  • 9 authors
·
Nov 24, 2024 2

GeoPlant: Spatial Plant Species Prediction Dataset

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10-50 m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) that are traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time-series of climatic variables, and satellite time-series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

  • 10 authors
·
Aug 25, 2024

Predicting integers from continuous parameters

We study the problem of predicting numeric labels that are constrained to the integers or to a subrange of the integers. For example, the number of up-votes on social media posts, or the number of bicycles available at a public rental station. While it is possible to model these as continuous values, and to apply traditional regression, this approach changes the underlying distribution on the labels from discrete to continuous. Discrete distributions have certain benefits, which leads us to the question whether such integer labels can be modeled directly by a discrete distribution, whose parameters are predicted from the features of a given instance. Moreover, we focus on the use case of output distributions of neural networks, which adds the requirement that the parameters of the distribution be continuous so that backpropagation and gradient descent may be used to learn the weights of the network. We investigate several options for such distributions, some existing and some novel, and test them on a range of tasks, including tabular learning, sequential prediction and image generation. We find that overall the best performance comes from two distributions: Bitwise, which represents the target integer in bits and places a Bernoulli distribution on each, and a discrete analogue of the Laplace distribution, which uses a distribution with exponentially decaying tails around a continuous mean.

Simulating Brown Dwarf Observations for Various Mass Functions, Birthrates, and Low-mass Cutoffs

After decades of brown dwarf discovery and follow-up, we can now infer the functional form of the mass distribution within 20 parsecs, which serves as a constraint on star formation theory at the lowest masses. Unlike objects on the main sequence that have a clear luminosity-to-mass correlation, brown dwarfs lack a correlation between an observable parameter (luminosity, spectral type, or color) and mass. A measurement of the brown dwarf mass function must therefore be procured through proxy measurements and theoretical models. We utilize various assumed forms of the mass function, together with a variety of birthrate functions, low-mass cutoffs, and theoretical evolutionary models, to build predicted forms of the effective temperature distribution. We then determine the best fit of the observed effective temperature distribution to these predictions, which in turn reveals the most likely mass function. We find that a simple power law (dN/dM propto M^{-α}) with αapprox 0.5 is optimal. Additionally, we conclude that the low-mass cutoff for star formation is lesssim0.005M_{odot}. We corroborate the findings of Burgasser (2004) which state that the birthrate has a far lesser impact than the mass function on the form of the temperature distribution, but we note that our alternate birthrates tend to favor slightly smaller values of α than the constant birthrate. Our code for simulating these distributions is publicly available. As another use case for this code, we present findings on the width and location of the subdwarf temperature gap by simulating distributions of very old (8-10 Gyr) brown dwarfs.

  • 14 authors
·
Jun 13, 2024

A Flexible Parametric Modelling Framework for Survival Analysis

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

  • 3 authors
·
Jan 10, 2019