Articles across AI, biotech, forecasting, and emerging tech.
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arXiv:2605.00925v1 Announce Type: new Abstract: Integrating molecular, morphological, and clinical data is essential for basic and translational biomedical research, yet systematic frameworks for jointly modeling these modalities remain limited. Here we present Haiku, a tri-modal contrastive learning model trained on multiplexed immunofluorescence (mIF). It comprises 26.7 million spatial proteomics patches from 3,218 tissue sections across 1,606 patients spanning 11 organ types, with matched hem...
arXiv:2605.00933v1 Announce Type: new Abstract: Continuous Glucose Monitoring (CGM) can detect early metabolic subphenotypes (insulin resistance, IR; $\beta$-cell dysfunction), but population-scale deployment faces two coupled problems. First, the same physiological state appears through multiple views (CGM time series, venous OGTT, Glucodensity summaries), so single-view representations fail to transfer when deployment shifts the modality or setting. Second, baselines perform inconsistently acr...
arXiv:2605.00930v1 Announce Type: new Abstract: In this work, we introduce CellxPert, a scalable multimodal foundation model that unifies single-cell and spatial multi-omics within a common representation space. CellxPert jointly encodes transcriptomic (scRNA-seq), chromatin-accessibility (ATAC-seq), and surface-proteomic (CITE-seq) measurements, while directly incorporating MERFISH and imaging mass-cytometry data as 2D or 3D spatial-visual layers. CellxPert facilitates four key downstream tasks...
arXiv:2605.00948v1 Announce Type: new Abstract: De novo functional protein design aims to generate protein sequences that realize specified biochemical functions without relying on evolutionary templates, enabling broad applications in biotechnology and medicine. Existing approaches adopt either direct function-to-sequence mapping or decoupled structure-sequence generation strategies but often fail to achieve functionality and foldability simultaneously. To address this, we propose CodeFP, a Co-...
arXiv:2605.01056v1 Announce Type: new Abstract: Hill functions, the standard tool for modelling gene regulatory networks, carry three structural flaws when the cooperativity exponent is non-integer: loss of global smoothness, silent complex-valued arithmetic corruption of ODE trajectories, and an identically zero basal production rate that traps bistable models in off-states. Logistic functions $f^\pm$, being globally $C^\infty$, real-valued for all arguments, and strictly positive at zero, reso...
arXiv:2605.01083v1 Announce Type: new Abstract: Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are a promising therapy for regenerating myocardium after infarction, but their use is limited by graft-related arrhythmias that frequently occur shortly after transplantation. Experimental studies indicate that these arrhythmias can originate within the graft, which may act as an ectopic pacemaker, yet the mechanisms governing successful excitation of host tissue remain poorly understoo...
arXiv:2605.01109v1 Announce Type: new Abstract: Phylogenetic trees are the primary framework for conveying evolutionary relationships. While many tools exist for visualizing phylogenetic trees, most are limited to static graphics, require coding expertise, or are developed for a specific website and not easily reusable or extensible. To address these limitations, we developed heat-tree, a collection of software packages in JavaScript, R, and Python for interactive visualization, manipulation, an...
arXiv:2605.01378v1 Announce Type: new Abstract: Identifying phenotype-associated genes is a common first step in polygenic risk score construction, enrichment testing, target prioritisation and variant interpretation, but relevant evidence is distributed across heterogeneous databases with different interfaces, formats and evidence models. Here, we present PhenotypeToGeneDownloaderR, a phenotype-guided R/Python pipeline for automated gene retrieval, harmonisation, symbol validation and cross-sou...
arXiv:2605.01656v1 Announce Type: new Abstract: Human cognition emerges from coordinated spiking dynamics in distributed neural circuits, where information is encoded via both firing rates and precise spike timing determined by brain rhythms. Inspired by this notion, we propose a brain-inspired learning primitive in which cognition-level neural synchrony emerges through iterative bottom-up and top-down interactions between micro-scale dynamics of spiking neurons and a macro-scale mechanism of os...
arXiv:2605.01767v1 Announce Type: new Abstract: Regeneration of the nervous system after injury remains an important therapeutic objective, especially in the central nervous system (CNS), in which regeneration is restricted by both neuronal limitations as well as adverse extracellular environments. Conversely, the peripheral nervous system (PNS) displays enhanced regenerative capability in the presence of supportive Schwann cells (SC) and pro-growth stimuli. While the structure and molecular mec...
arXiv:2605.01770v1 Announce Type: new Abstract: We extend the $N$ branching Brownian motions model of population invasion to higher-order asexual reproduction. Increasing reproduction order leads to qualitative changes: invasion fronts generically cease to exist beyond binary reproduction; and in the binary case itself, their speed becomes diffusion-independent. Ternary reproduction shows critical behavior, with collapse into a strongly localized `invasion bullet' in the supercritical regime, di...
arXiv:2605.01819v1 Announce Type: new Abstract: Quantitative susceptibility mapping (QSM) has been increasingly applied in longitudinal studies of neurodegenerative diseases and aging to assess temporal alterations in brain iron and myelin. The accuracy of such investigations depends on the repeatability and sensitivity of measurements. However, the ill-posed nature of the QSM processing steps makes the reconstruction vulnerable to background field changes, head orientation changes, noise, and i...
arXiv:2605.02142v1 Announce Type: new Abstract: Gene programs co-activate within cells, but existing single-cell methods either treat programs independently or require experimental perturbation data to model their interactions. We introduce ORBIT, a self-supervised transformer that learns asymmetric dependencies among gene programs from observational single-cell RNA-sequencing data alone, quantifying how strongly each program influences every other program. The key mechanism is an intervention-c...
arXiv:2605.02852v1 Announce Type: new Abstract: In biological systems, neural circuits compute through directed, short-latency interactions whose effects unfold across multiple time scales and behavioral contexts. We address the problem of inferring these local, lag-specific interactions from sampled neural population activity under varying stimuli, without assuming a parametric form for the underlying dynamics. Our approach leverages denoising score models by estimating joint-window scores over...
arXiv:2605.00857v1 Announce Type: cross Abstract: Source-free domain adaptation (SFDA) provides a practical solution to cross-subject EEG decoding by adapting source-pretrained models to unlabeled target domains without accessing source data. However, existing SFDA methods rely solely on the limited internal knowledge of source-pretrained models, leading to inferior cross-domain generalization and unreliable pseudo-labels. Although EEG Foundation Models (FMs) pretrained on large-scale data exhib...
arXiv:2605.00865v1 Announce Type: cross Abstract: EEG based phoneme decoding is promising for brain computer interfaces, but many prior studies rely on within subject evaluation, small cohorts, or weak leakage control. We present a reproducible cross subject benchmark for five class vowel decoding (a, e, i, o, u) from auditory EEG using OpenNeuro ds006104 (16 subjects, 61 channels, 256 Hz). Under strict leave one subject out evaluation with training only normalization and explicit anti leakage c...
arXiv:2605.00966v1 Announce Type: cross Abstract: Hierarchical Gaussian Filtering (HGF) networks allow for efficient updating of posterior distributions (beliefs) about hidden states of an agent's environment. HGF parent nodes can target the mean or variance of their children. New information entering at input nodes leads to a cascade of belief updates across the network according to one-step update equations for each node's mean and precision (inverse variance). However, the original form of th...
arXiv:2605.01472v1 Announce Type: cross Abstract: Molecular dipoles near interfaces emit highly directional radiation due to near-field interactions, making surface-bound fluorophores sensitive probes of local physicochemical changes. We introduce smart coverslips, stably coated with uniform, brightly fluorescent nanobead films, that exploit refractive-index-dependent emission shifts for sensitive micro-refractometry in small volumes. Supercritical-angle fluorescence refractometry uses single ba...
Maternal health is a known crisis in the U.S., where pregnant women and new mothers die at a rate several times higher than in comparable countries. In recent years, increased awareness of the problem has led to interventions at the federal and state level and a strengthening of surveillance and data collection. Even as sizable improvements continue to be elusive, the picture of how many new mothers are dying, and why, is becoming clearer. A research letter published on Monday in JAMA Pediatric...
Want to stay on top of the science and politics driving biotech today? Sign up to get our biotech newsletter in your inbox. The U.S. is starting to feel the downstream effects of tighter immigration policies, as visa delays and uncertainty push international scientists away. Also, new funding for gene therapy startup Latus Bio, China’s tightening the reins on its supply chain, and more.Read the rest…
Gene therapy startup Latus Bio has raised another $42 million to start its first clinical trials, where it will try to sidestep issues that have set back a more advanced competitor. Latus is moving two treatments through clinical trials this year. The first is for a form of Batten disease called CLN2 disease, a fatal genetic condition that causes seizures, vision loss, and cognitive problems. The company anticipates having initial clinical data by the end of the year. Now, Latus — founded by B...
arXiv:2605.00014v1 Announce Type: new Abstract: The analyses presented herein demonstrate that neuronal electrical activity can be consistently interpreted as a manifestation of murburn redox-mediated electronic dynamics rather than as a process fundamentally driven by transmembrane ionic flux. By integrating comparison with established models, quantitative predictions, and diverse experimental observations, the murburn framework emerges as a unified and chemically grounded description of excita...
arXiv:2605.00025v1 Announce Type: new Abstract: Speech neuroprosthesis systems decode intended speech from neural activity in the absence of audible output, offering a path to restoring communication for individuals with speech-impairing conditions. Current approaches decode predominantly from motor cortical areas, discarding others -- such as area 44, part of Broca's area -- that may encode complementary linguistic information. We introduce MoDAl (Modality Decorrelation and Alignment), a framew...
arXiv:2605.00033v1 Announce Type: new Abstract: Remote and webcam-based eye tracking in multi-line reading suffers from various noise factors and layout ambiguity, precisely where real-time reading support needs reliable, per-fixation line assignment. Prior work largely addresses this challenge post hoc or by restricting behavior (e.g., disallowing re-reading), undermining interactive use. We propose CONF-LA (Confidence-score-based Online Fixation-to-Line Assignment), a principled, low-latency a...
arXiv:2605.00067v1 Announce Type: new Abstract: We present EPITIME (EPidemic Integral models TIMe profile Explorer), a computational framework for the simulation of two classes of integral epidemic models: an age of infection model and an information dependent behavioural model. The framework combines structure preserving Non-Standard Finite Difference discretizations with modular implementations in MATLAB and Python, together with routines for parameter handling, input validation, performance a...
arXiv:2605.00085v1 Announce Type: new Abstract: Percolation theory from statistical physics has been applied to several aspects of tumor progression. Tumor growth on percolation clusters has been used to model spatial expansion, vascular percolation to describe nutrient supply and transport related percolation to investigate drug and gene delivery. At the molecular level, mutational percolation has been employed to account for the emergence of malignant phenotypes, while inverse percolation to r...
arXiv:2605.00272v1 Announce Type: new Abstract: We introduce LNODE, a mechanism-based phenomenological model for amyloid beta (A$\beta$) dynamics, calibrated using positron emission tomography (PET) imaging. A$\beta$ is a key biomarker of Alzheimer's disease. LNODE is designed to support the fusion, harmonization, quantitative analysis, and interpretation of Abeta PET scans. We evaluate LNODE on 1461 subjects in the ADNI cohort and 1070 subjects in the A4 Study, using MUSE and DKT anatomical atl...
arXiv:2605.00479v1 Announce Type: new Abstract: The stochastic simulation algorithm (SSA) is widely used to perform exact forward simulation of discrete stochastic processes in biology. However, the computational cost, driven by sequential event-by-event sampling across large ensembles, remains a computational barrier. We investigate whether reduced-precision floating-point arithmetic can accelerate SSA without degrading statistical fidelity, drawing on the success of reduced-precision methods i...
arXiv:2605.00746v1 Announce Type: new Abstract: Reliable control in motor imagery brain-computer interfaces (MI-BCIs) requires the precise decoding of user-specific neural rhythms, which vary significantly across individuals. The Common Spatial Pattern (CSP) algorithm is a cornerstone of MI-BCI decoding, yet its performance depends strongly on the spectral range of the input EEG data. Although Filter Bank CSP (FBCSP) extends this as a data-driven decoding framework, its frequency sub-bands are p...
arXiv:2605.00225v1 Announce Type: cross Abstract: We show that pretrained acoustic embeddings classify elephant vocalisations at a level approaching that of end-to-end supervised neural networks, without any fine-tuning of the embedding model. This result is of practical importance because annotated bioacoustic data are scarce and costly to obtain, leaving conventional supervised approaches prone to overfitting and to poor generalisation under domain shift. A broad range of embedding models draw...
arXiv:2605.00401v1 Announce Type: cross Abstract: Recent EEG-to-image retrieval methods leverage pretrained vision encoders and foveation-inspired priors, but typically assume a fixed, center-focused view. This center bias conflicts with content-driven human attention, creating a geometric-semantic dissociation between visual features and EEG responses. We propose SIMON, a saliency-aware multi-view framework for zero-shot EEG-to-image retrieval. SIMON combines foreground segmentation and salienc...
arXiv:2605.00545v1 Announce Type: cross Abstract: Inferring cellular trajectories from destructive snapshots is complicated by the challenges of stochasticity and non-conservative mass dynamics such as cell proliferation and apoptosis. Existing unbalanced Optimal Transport (OT) methods treat mass as a continuous fluid, performing inference at the population level. However, this macroscopic view often fails to capture the discrete, jump-like nature of birth-death events at single-cell resolution,...
arXiv:2605.00730v1 Announce Type: cross Abstract: The reconstruction of physically valid transport fields from subject-specific imaging data is a fundamental challenge in image-based computational modeling due to measurement noise, modeling uncertainties and discretization errors. Without a methodology to construct models that faithfully reflect the underlying physics, mechanistic understanding of complex biological systems is inherently limited. In this work, we address this challenge in the gl...
arXiv:2605.00778v1 Announce Type: cross Abstract: In biomechanical systems, observable performance is often used as a proxy for underlying system organization. However, this assumption implicitly presumes a correspondence between output metrics and internal system states that may not hold in adaptive systems. In this study, the vertical dimension of occlusion (VDO) is considered as a constraint applied to an adaptive neuromechanical system, enabling the exploration of system-level responses unde...
arXiv:2406.02522v4 Announce Type: replace Abstract: Long-duration human missions to Mars will require autonomous systems capable of converting in situ resources into structural materials, tools, and functional components. More broadly, such systems represent a class of resource-limited bioprocesses relevant to extreme-environment manufacturing. Here, we investigate engineered autotrophic-heterotrophic consortia, inspired by lichen biology, as a platform for autonomous biofabrication from granula...
arXiv:2507.01946v2 Announce Type: replace Abstract: Biological function arises through the dynamical interactions of multiple subsystems, including those between brain areas, within gene regulatory networks, and more. A common approach to understanding these systems is to model the dynamics of each subsystem and characterize communication between them. An alternative approach is through the lens of control theory: how the subsystems control one another. This approach involves inferring the direc...
arXiv:2511.06140v3 Announce Type: replace Abstract: Forces transmitted by bones are routinely studied in human biomechanics, but it is challenging to measure them non-invasively, especially outside of laboratory settings. We introduce a technique for non-invasive, in vivo measurement of tibial compressive force using flexural waves propagating in the tibia. Modelling the tibia as an axially compressed Euler-Bernoulli beam, we show that tibial flexural waves have load-dependent frequency spectra....
From soil-welfare research to the New World Screwworm: a practical portfolio for wild-invertebrate welfare.This is part 3 of a five-part sequence on welfare ecology. Part 1 introduces the ethical premises. Part 2 covers the empirical landscape. Part 4 explores a model of invertebrate suffering. Part 5 covers AI.In part 2, I argued that land use is a key lever for wild-invertebrate welfare and that pesticides applied at constant net primary productivity (NPP) c...
Want to stay on top of the science and politics driving biotech today? Sign up to get our biotech newsletter in your inbox. The FDA named Katherine Szarama acting head of CBER as it continues to search for a permanent leader. Julia Vitarello is launching a new effort to scale bespoke medicines after her first startup faltered. And Matt Herper reflects on the legacy of genomics pioneer J. Craig Venter, whose vision helped shape modern biotech.Continue to STAT+ to read the full story…
AI-powered mental health apps have attracted growing interest as a low-cost way to expand care. Yet questions remain about their effectiveness, safety, and whether they may crowd out psychotherapy. We evaluate one such app in a randomized controlled trial among 1,964 Mexican women with mild to severe psychological distress. Over six months, app access improved mental health by 0.3 standard deviations with no evidence of harm, improved sleep quality, increased healthful behaviors, and reduced mis...
Teen fertility collapsed globally starting around 2007. This affected countries across the income and policy spectrum. This paper argues that smartphones changed how teens spend time with each other, and that this change in turn drove the collapse in teen fertility. Once enough teens are on the phone, being on the phone is where the peer network is; in-person time falls sharply, and with it the unstructured contact in which most unintended teen conceptions occur. A coordination model formalizes ...
Michael Halassa: Did John Nash Really Have Schizophrenia? is a good article on the genetics of psychosis. Previous research found that schizophrenia genes decreased IQ but increased educational attainment. Usually IQ and education are correlated, so this was surprising. The new research finds two components to schizophrenia genetic risk. The first component, shared with bipolar, increases educational attainment. The second component, not shared with bipolar, decreases IQ. They average out to the...
Welcome to Decoding Bio’s BioByte: each week our writing collective highlight notable news—from the latest scientific papers to the latest funding rounds—and everything in between. All in one place.Subscribe nowRenée Stout, Circuit Board No. 2 (2014)What we readBlogsEngineering Cell Fate: Towards a Foundation Model for Virtual Cell Signaling [Cellular Intelligence, January 2026]Although there are only about 20 known fundamental molecular signaling pathways that cells utilize to communicate with ...
It’s been an incredibly exciting year in metascience at large, and for us at Convergent. Last week, the National Science Foundation announced their Tech Labs Initiative. The week before, we joined teams from our UK FRO Founder Residency (powered by ) in London as they presented the proposals they’ve been working on since June. All year, our existing Focused Research Organizations (we’ve launched almost a dozen) have been sharing the fruits of their labor, and we’re hard at work on many more new ...
As an editorial in Nature put it, “On 2 July, a science initiative was born in a lecture hall in London.” That morning, the Metascience Alliance, a collaboration of dozens of organizations in the metascience community, was announced onstage at the Metascience 2025 conference.We were honored to be invited to join the coalition at its launch and to speak at the conference, which brought together 830 participants from around 65 countries.Thanks for reading Essential Technology! Subscribe to get not...
Today we’re releasing v1.0 of our Fundamental Development Gap Map, a new web portal for exploring the landscape of bottlenecks holding back science and the fundamental technologies to solve them. You can jump in right away at gap-map.org, and read more about where this database came from below.Subscribe nowBridging gaps in fundamental R&DIn our first post, we set out a vision for accelerating beneficial scientific R&D:Humanity could increase its rate of scientific and technological advancement b...
Science needs more catalytic projects so that we can build essential technologies.How do we find those catalytic projects? One way is by surveying the landscape of science and creating roadmaps that show us how to navigate the tech tree before us.There are bottlenecks choking progress in virtually every scientific field, and you can identify these with a good roadmap. Once you know where they are, you can conduct research to break through these bottlenecks (or find clever ways to route around th...
Workers at the Naval Surface Warfare Center in Indian Head, Maryland, the only facility where torpedo fuel is produced for the U.S. NavyIn the event of a late-2020s Chinese attempt to invade Taiwan, leading to a US-China military conflict, what would be the most urgent bottlenecks in military equipment? Where is there the greatest need to scale up defense manufacturing?I am not an expert in military matters, so take all this with a grain of salt. But I looked into this question and it seems to h...