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Detecting Batch Heterogeneity via Likelihood Clustering

arXiv.org Machine Learning

Batch effects represent a major confounder in genomic diagnostics. In copy number variant (CNV) detection from NGS, many algorithms compare read depth between test samples and a reference sample, assuming they are process-matched. When this assumption is violated, with causes ranging from reagent lot changes to multi-site processing, the reference becomes inappropriate, introducing false CNV calls or masking true pathogenic variants. Detecting such heterogeneity before downstream analysis is critical for reliable clinical interpretation. Existing batch effect detection methods either cluster samples based on raw features, risking conflation of biological signal with technical variation, or require known batch labels that are frequently unavailable. We introduce a method that addresses both limitations by clustering samples according to their Bayesian model evidence. The central insight is that evidence quantifies compatibility between data and model assumptions, technical artifacts violate assumptions and reduce evidence, whereas biological variation, including CNV status, is anticipated by the model and yields high evidence. This asymmetry provides a discriminative signal that separates batch effects from biology. We formalize heterogeneity detection as a likelihood ratio test for mixture structure in evidence space, using parametric bootstrap calibration to ensure conservative false positive rates. We validate our approach on synthetic data demonstrating proper Type I error control, three clinical targeted sequencing panels (liquid biopsy, BRCA, and thalassemia) exhibiting distinct batch effect mechanisms, and mouse electrophysiology recordings demonstrating cross-modality generalization. Our method achieves superior clustering accuracy compared to standard correlation-based and dimensionality-reduction approaches while maintaining the conservativeness required for clinical usage.


Random Walk Learning and the Pac-Man Attack

arXiv.org Machine Learning

Random walk (RW)-based algorithms have long been popular in distributed systems due to low overheads and scalability, with recent growing applications in decentralized learning. However, their reliance on local interactions makes them inherently vulnerable to malicious behavior. In this work, we investigate an adversarial threat that we term the ``Pac-Man'' attack, in which a malicious node probabilistically terminates any RW that visits it. This stealthy behavior gradually eliminates active RWs from the network, effectively halting the learning process without triggering failure alarms. To counter this threat, we propose the Average Crossing (AC) algorithm--a fully decentralized mechanism for duplicating RWs to prevent RW extinction in the presence of Pac-Man. Our theoretical analysis establishes that (i) the RW population remains almost surely bounded under AC and (ii) RW-based stochastic gradient descent remains convergent under AC, even in the presence of Pac-Man, with a quantifiable deviation from the true optimum. Our extensive empirical results on both synthetic and real-world datasets corroborate our theoretical findings. Furthermore, they uncover a phase transition in the extinction probability as a function of the duplication threshold. We offer theoretical insights by analyzing a simplified variant of the AC, which sheds light on the observed phase transition.


Meta's Layoffs Leave Supernatural Fitness Users in Mourning

WIRED

Meta's Layoffs Leave Supernatural Fitness Users in Mourning Users of the VR fitness service are distraught that Supernatural has had its staff cut and won't receive any more content updates. I hear a stranger's heavy breathing through the rollicking dude-bro anthem blasting my eardrums, courtesy of the pop-rock band Imagine Dragons. Me and two people I just met are punching digital blocks that fly at our heads in the VR workout platform Supernatural . My new friends have nameplates floating above their heads that say Chip and Alisa. That's all I know about them.


Trump admin relaunches key council after Biden admin shuttered it: 'Ignorance and arrogance'

FOX News

Trump officials reboot coal council Biden admin shut down, calling previous administration's move 'ignorance and arrogance' as industry fights red tape.


Signal's Founder Built a Chatbot That Can't Spy on You

TIME - Tech

Signal's Founder Built a Chatbot That Can't Spy on You Welcome back to, TIME's new twice-weekly newsletter about AI. If you're reading this in your browser, why not subscribe to have the next one delivered straight to your inbox? What to Know: Signal's founder is working on encrypted chatbots Moxie Marlinspike, the cryptographic prodigy who wrote the code that underpins Signal and WhatsApp, has a new project--and it could be one of the most important things happening in AI right now. The tool, named Confer, is an end-to-end encrypted AI assistant. It uses smart math to ensure that even though the compute-intensive process of running the AI still happens on a server in the cloud, the only person who can access the unscrambled details of that computation is you, the user.


Take an Extra 50 Off My Favorite Mattress With This Code

WIRED

Life's Too Short to Put Up With a Bad Mattress--My Favorite Is on Sale Nolah's Evolution is the mattress I personally sleep on as a certified sleep coach, and it's on sale pre-Presidents' Day. I'm a picky person when it comes to mattresses. Of the hundreds I've tested over my career as a certified sleep coach and mattress tester, I have a short list of ones that have exceeded my expectations. At the top of my list is the Nolah Evolution, with the distinct honor of being the mattress I personally own. Given my job, that's got to be like the equivalent of a Grammy or Emmy in the mattress world.


Inside OpenAI's Raid on Thinking Machines Lab

WIRED

OpenAI is planning to bring over more researchers from Thinking Machines Lab after nabbing two cofounders, a source familiar with the situation says. If someone ever makes an HBO Max series about the AI industry, the events of this week will make quite the episode. On Wednesday, OpenAI's CEO of applications, Fidji Simo, announced the company had rehired Barret Zoph and Luke Metz, cofounders of Mira Murati's AI startup, Thinking Machines Lab. We reported last night on two narratives forming around what led to the departures, and have since learned new information. A source with direct knowledge says that Thinking Machines leadership believed Zoph engaged in an incident of serious misconduct while at the company last year.



Toxic 'forever chemicals' linked to cancer now associated with major pregnancy complication

Daily Mail - Science & tech

Senator accused of steamy affair with her bodyguard in bombshell lawsuit from his WIFE: 'Bring MDMA so I can guide you' Socialite who accused playboy twins of sex attack at Hamptons'castle' is found dead in unexplained circumstances Amy Schumer's friends reveal true meaning of thin bikini pictures and why they're'monitoring her'... as depth of ex Chris Fischer's heartbreak is laid bare Hunter Biden's stripper baby mama asks for him to be ARRESTED over claims he is still failing to pay her child support Ellen Greenberg's fiancé Sam Goldberg breaks cover as feds reopen probe into her'suicide'... and late teacher's mother shares incredible sign sent from beyond the grave Nicole Richie addresses her daughter's new identity after unveiling transformation on her 18th birthday '90s Vogue model Niki Taylor looks amazing as she sizzles at age 50 for new campaign Karoline Leavitt reveals the thinking behind Trump's call to cancel elections Family of Tyler Robinson's transgender lover speaks ...


Netflix's expanded Sony deal includes streaming rights to the Legend of Zelda movie

Engadget

Apple's Siri AI will be powered by Gemini Netflix's expanded Sony deal includes streaming rights to the Legend of Zelda movie It will also be the first streaming service to get Sony's films worldwide. As part of a new agreement, films from Sony Pictures Entertainment will stream on Netflix first, the companies announced via a joint statement . The new deal expands on the exclusive rights Netflix had to Sony films in the US, and means the service will be the first place people will be able to stream upcoming projects like the live-action adaptation of The Legend of Zelda, and a quartet of biopics about The Beatles . Sony's films will stream worldwide on Netflix in what's called Pay-1, the first window of availability after a movie's theatrical and VOD releases. As part of the deal, Netflix is also licensing an undisclosed number of films and television shows from the Sony Pictures back catalog to help fill out its library.