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Stochastic gradient descent estimation of generalized matrix factorization models with application to single-cell RNA sequencing data
Castiglione, Cristian, Segers, Alexandre, Clement, Lieven, Risso, Davide
Single-cell RNA sequencing allows the quantitation of gene expression at the individual cell level, enabling the study of cellular heterogeneity and gene expression dynamics. Dimensionality reduction is a common preprocessing step to simplify the visualization, clustering, and phenotypic characterization of samples. This step, often performed using principal component analysis or closely related methods, is challenging because of the size and complexity of the data. In this work, we present a generalized matrix factorization model assuming a general exponential dispersion family distribution and we show that many of the proposed approaches in the single-cell dimensionality reduction literature can be seen as special cases of this model. Furthermore, we propose a scalable adaptive stochastic gradient descent algorithm that allows us to estimate the model efficiently, enabling the analysis of millions of cells. Our contribution extends to introducing a novel warm start initialization method, designed to accelerate algorithm convergence and increase the precision of final estimates. Moreover, we discuss strategies for dealing with missing values and model selection. We benchmark the proposed algorithm through extensive numerical experiments against state-of-the-art methods and showcase its use in real-world biological applications. The proposed method systematically outperforms existing methods of both generalized and non-negative matrix factorization, demonstrating faster execution times while maintaining, or even enhancing, matrix reconstruction fidelity and accuracy in biological signal extraction. Finally, all the methods discussed here are implemented in an efficient open-source R package, sgdGMF, available at github/CristianCastiglione/sgdGMF
Elon Musk vs. Laura Loomer: MAGA Clashes Over Immigration
Less than a month before Donald Trump returns to office, two of his most ardent allies have plunged into a fierce online debate over immigration, specifically the government's visa program that allows American companies to hire so-called "highly skilled" foreign workers. The clash started on Monday with Laura Loomer, the far-right social media character known for her virulent racism, condemning Trump's decision to name Sriram Krishnan, a tech investor who was born in India, as a senior adviser on artificial intelligence. Tech leaders, including Elon Musk, weighed in to defend the practice of hiring foreign workers, specifically through the government's H-1B visa program. The debate has since devolved into a relentless string of petty insults--Loomer likened tech billionaires to "termites" at Mar-a-Lago; Musk called Loomer a troll--as well as accusations of censorship on X as retaliation. At a different point, Vivek Ramaswamy chimed in to register his support for hiring foreign workers.
2025 in SPACEFLIGHT: The incredible missions set to take off next year, revealed - from China's daring asteroid retrieval to the first private trip to Venus
From NASA's mission to study Jupiter's icy moon Europa to Elon Musk's SpaceX catching its Starship rocket mid-air, there's no doubt 2024 saw some incredible space feats. 'In 2024, NASA made leap after giant leap to explore, discover, and inspire โ all while bringing real, tangible, and substantial benefits to the American people and to all of humanity,' said NASA Administrator Bill Nelson. And 2025 is set to be an even more remarkable year for space agencies and companies around the world, who have an assortment of exciting missions lined up. Among them are NASA, which is sending two twin spacecraft to Mars โ although its upcoming return to the moon has been delayed yet again. There's also the European Space Agency, which is set to launch its futuristic'Space Rider' spaceplane โ described as a'robotic laboratory the size of two minivans'.
Putin apologises to Azerbaijan's president over 'tragic' plane crash
Russian President Vladimir Putin has apologised to his Azerbaijani counterpart Ilham Aliyev for what he called a "tragic incident" following the deadly crash of an Azerbaijan Airlines plane this week in Kazakhstan. The plane was flying on Wednesday from Azerbaijan's capital of Baku to Grozny, the regional capital of the Russian republic of Chechnya, when it turned towards Kazakhstan and crashed while attempting to land. In a statement on Saturday, the Kremlin said Russian air defence systems were firing near Grozny due to a Ukrainian drone strike, but stopped short of saying one of these hit the plane. "Vladimir Putin apologised for the tragic incident that occurred in Russian airspace and once again expressed his deep and sincere condolences to the families of the victims and wished a speedy recovery to the injured," the Kremlin said. "At that time, Grozny, Mozdok and Vladikavkaz were being attacked by Ukrainian unmanned aerial vehicles, and Russian air defence systems repelled these attacks."
'All people could do was hope the nerds would fix it': the global panic over the millennium bug, 25 years on
Just before midnight on New Year's Eve, 25 years ago, Queen Elizabeth II stepped off a private barge to arrive at London's Millennium Dome for its grand opening ceremony. Dressed in a pumpkin-orange coat, she entered the venue with Prince Philip, taking her place alongside Tony and Cherie Blair and 12,000 guests to celebrate the dawn of a new millennium. At the stroke of midnight, Big Ben began to chime and 40 tonnes of fireworks were launched from 16 barges lined along the river. The crowd joined hands, preparing to sing Auld Lang Syne. For a few long moments, the Queen was neglected โ she flapped her arms out like a toddler wanting to be lifted up, before Blair and Philip noticed her, took a hand each, and the singing began. A new century was born. One politician who wasn't in attendance at the glitzy celebration was Paddy Tipping, a Labour MP who spent the night in the Cabinet Office.
Putin apologises for plane crash, without saying Russia at fault
The Kremlin released a statement on Saturday noting Putin had spoken to Azerbaijan's president Ilham Aliyev by phone. "(President) Vladimir Putin apologised for the tragic incident that occurred in Russian airspace and once again expressed his deep and sincere condolences to the families of the victims and wished a speedy recovery to the injured," the statement said. Prior to Saturday, the Kremlin had not yet commented on the crash. But Russian aviation authorities had said the situation in the region was "very complicated" due to Ukrainian drone strikes on Chechnya. Aviation experts and others in Azerbaijan believe the plane's GPS systems were affected by electronic jamming and it was then damaged by shrapnel from Russian air defence missile blasts.
North Koreans die in droves even as Russia unleashes firepower on Ukraine
Ukrainian forces have killed or wounded more than 1,000 North Korean troops Russia has sent to fight them, according to Kyiv and officials in South Korea. "According to preliminary data, the number of killed and wounded North Korean soldiers in the Kursk region already exceeds 3,000 people," Ukrainian President Volodymyr Zelenskyy said in his evening address on December 23. South Korean intelligence put the North Korean dead and wounded at 1,100, and said the North was preparing to send more troops. North Korea sent 11,000 troops to fight in the Russian region of Kursk, which Ukraine counter-invaded in August. North Korean troops were evidently untrained in dealing with Ukrainian drones, which took a high toll.
FAA places restrictions on drone company after Florida boy injured at holiday airshow, underwent heart surgery
The Federal Aviation Administration (FAA) has suspended certain operations by a Texas-based drone company after a Florida boy was injured during a holiday airshow last week and had to undergo heart surgery. The FAA confirmed to Fox News Digital that it suspended the Part 107 Waiver for Sky Elements Drones. The waiver allows drone operators to fly at night, fly over people, and operate drones outside the line of sight. Thus, with this waiver suspended, Sky Elements Drones legally cannot perform its shows. It's not clear how long the pause will remain in place.
A survey on pioneering metaheuristic algorithms between 2019 and 2024
Dokeroglu, Tansel, Canturk, Deniz, Kucukyilmaz, Tayfun
With innovation accelerating, selecting the most effective algorithms has become increasingly demanding for researchers and practitioners alike. Recognizing this, we conducted an in-depth review of metaheuristics introduced in the past six years, focusing on their influence and effectiveness. We evaluated these algorithms across essential criteria: citation frequency, diversity in tackled problem types, code availability, ease of parameter tuning, introduction of novel mechanisms, and resilience to issues like stagnation and early convergence. Out of 158 algorithms, we identified 23 that set themselves apart, each contributing unique solutions to long-standing optimization challenges. These algorithms stand out for their versatility and innovation, positioning them as valuable assets for advancing research and addressing complex real-world problems. Our review offers a detailed analysis of these algorithms, comparing their strengths, limitations, similarities, and applications, while highlighting promising trends and future pathways in metaheuristic research.
An Anomaly Detection System Based on Generative Classifiers for Controller Area Network
Zhao, Chunheng, Longari, Stefano, Carminati, Michele, Pisu, Pierluigi
As electronic systems become increasingly complex and prevalent in modern vehicles, securing onboard networks is crucial, particularly as many of these systems are safety-critical. Researchers have demonstrated that modern vehicles are susceptible to various types of attacks, enabling attackers to gain control and compromise safety-critical electronic systems. Consequently, several Intrusion Detection Systems (IDSs) have been proposed in the literature to detect such cyber-attacks on vehicles. This paper introduces a novel generative classifier-based Intrusion Detection System (IDS) designed for anomaly detection in automotive networks, specifically focusing on the Controller Area Network (CAN). Leveraging variational Bayes, our proposed IDS utilizes a deep latent variable model to construct a causal graph for conditional probabilities. An auto-encoder architecture is utilized to build the classifier to estimate conditional probabilities, which contribute to the final prediction probabilities through Bayesian inference. Comparative evaluations against state-of-the-art IDSs on a public Car-hacking dataset highlight our proposed classifier's superior performance in improving detection accuracy and F1-score. The proposed IDS demonstrates its efficacy by outperforming existing models with limited training data, providing enhanced security assurance for automotive systems.