Technology
When Does Gene Regulatory Network Inference Break? A Controlled Diagnostic Study of Causal and Correlational Methods on Single-Cell Data
Fernandez-de-Retana, Miguel, Sanchez-Corcuera, Ruben, Zulaika, Unai, Bilbao-Jayo, Aritz, Almeida, Aitor
Despite theoretical advantages, causal methods for Gene Regulatory Network (GRN) inference from single-cell RNA-seq data consistently fail to match or outperform correlation-based baselines in many realistic benchmarks, a persistent puzzle which casts doubt on the value of causality for this task. We argue that existing benchmarks are insufficiently controlled to answer this question because they evaluate on real or semi-real data where multiple pathologies co-occur, confounding failure modes, and obscuring the specific conditions under which different inference methods excel or fail. To address this gap, we introduce a controlled diagnostic framework that isolates seven biologically motivated pathologies (dropout, latent confounders, cell-type mixing, feedback loops, network density, sample size, and pseudotime drift) and measure how six representative methods spanning three inference paradigms degrade as each pathology intensifies. Across 6,120 controlled experiments, we find that causal methods genuinely dominate in clean and structurally favorable regimes, but specific pathologies (notably dropout and latent confounders) selectively neutralize their advantages. We further introduce an errortype decomposition that reveals methods with similar aggregate accuracy commit qualitatively different errors. To probe whether single-pathology effects persist when multiple stressors co-occur, we perform an interaction sweep over the three most impactful pathologies and find that their joint effects are sub-additive, while also exposing density-conditional cross-overs invisible to single-dial analysis. Our findings offer a nuanced understanding of when and why different methods succeed or fail for GRN inference, providing actionable insights for method development and practical guidance for practitioners.3
Jacobian-Velocity Bounds for Deployment Risk Under Covariate Drift
We study long-horizon deployment of a frozen predictor under dynamic covariate shift. A time-domain Poincaré inequality reduces temporal risk volatility to derivative energy, and a Jacobian-velocity theorem identifies directional tangent energy along the deployment path as the governing quantity under explicit along-path regularity and domination assumptions. Under low-rank drift, that quantity reduces to directional Jacobian energy in the drift subspace, motivating drift-aligned tangent regularization (DTR) and a matched monitoring proxy. Rather than smoothing the network isotropically, DTR penalizes sensitivity only along estimated drift directions. We validate the theorem-to-method pipeline in four experiments: a synthetic benchmark for the time-domain inequality, a controlled synthetic comparison against isotropic Jacobian regularization, and two frozen-deployment studies on the UCI Air Quality and Tetouan power-consumption datasets. DTR reduces risk volatility and directional gain in the controlled low-rank regime, beats isotropic smoothing there, and gives validation-selected deployment gains on both real datasets when the Air Quality drift subspace is estimated from target-orthogonal sensor motion. Moderate drift-subspace misspecification is tolerable while orthogonal misspecification largely removes the benefit.
Adaptivity Under Realizability Constraints: Comparing In-Context and Agentic Learning
Kratsios, Anastasis, Neuman, A. Martina, Petersen, Philipp
We compare in-context learning with fixed queries and agentic learning with adaptive queries for uniform approximation of task families. We consider two settings: an unrestricted regime, where querying and approximation are arbitrary functions, and a realizable regime, where we require these operations to be implemented by ReLU neural networks. In both settings, adaptivity never hinders approximation performance. However, this advantage can change when one passes from the unrestricted regime to the realizable regime. We identify four distinct approximation scenarios, each witnessed by an explicit task family: (a) no advantage of adaptivity; (b) an advantage in the unrestricted regime that persists under ReLU realizability; (c) an advantage that arises only under realizability; and (d) an advantage that disappears under realizability. This demonstrates that representational constraints interact profoundly with the effect of adaptivity.
Scalable inference of spatial regions and temporal signatures from time series
Regionalization aims to partition a spatial domain into contiguous regions that share similar characteristics, enabling more effective spatial analysis, policy making, and resource management. Existing approaches for spatial regionalization typically rely on static spatial snapshots rather than evolving time series. Meanwhile, most time series clustering methods ignore spatial structure or enforce spatial continuity through ad hoc regularization, constraining the number of inferred regions a priori either explicitly or implicitly. Utilizing the minimum description length principle from information theory, here we propose an efficient and fully nonparametric framework for the regionalization of spatial time series. Our method jointly infers a spatial partition along with a set of representative time series archetypes ("drivers") that best compress a spatiotemporal dataset, with a runtime log-linear in the number of time series. We demonstrate that this method can accurately recover planted regional structure and drivers in synthetic time series, and can extract meaningful structural regularities in large-scale empirical air quality and vegetation index records. Our method provides a principled and scalable framework for spatially contiguous partitioning, allowing interpretable temporal patterns and homogeneous regions to emerge directly from the data itself.
Hypergraph Generation via Structured Stochastic Diffusion
Hypergraphs model higher-order interactions, but realistic hypergraph generation remains difficult because incidence, hyperedge-size heterogeneity, and overlap structure are not faithfully captured by pairwise reductions. We propose \HEDGE, a generative model defined directly on relaxed incidence matrices via a structured stochastic diffusion. The forward process combines a hypergraph-specific two-sided heat operator with an Ornstein--Uhlenbeck component, preserving structure-aware noising near the data while yielding an explicit Gaussian terminal law. Conditional on an observed hypergraph, this forward process is linear-Gaussian, so conditional means, covariances, scores, and reverse-drift targets are available in closed form. We therefore learn a permutation-equivariant state-only reverse-drift field in incidence space by regressing onto exact conditional targets, and generate samples by simulating a learned reverse-time SDE from the Gaussian base law. We establish exactness in the ideal state-only setting together with finite-horizon stability guarantees, and empirically show improved hypergraph generation quality relative to strong baselines.
Proximal Projection for Doubly Sparse Regularized Models
He, Jia Wei, Ali, R. Ayesha, Darlington, Gerarda
Regularization is often used in high-dimensional regression settings to generate a sparse model, which can save tremendous computing resources and identify predictors that are most strongly associated with the response. When the predictors can be represented by a Gaussian graphical model, the structure of the predictor graph can be exploited during regularization. Our proposed model exploits this underlying predictor graph structure by decomposing the estimated coefficient vector into a sum of latent variables that correspond to the sum of each node contribution to the coefficient vector. Regularization is then performed on the latent variables rather than on the coefficient vector directly. We use a penalty function that permits a clear user-defined trade-off between the L1 and L2 penalties and propose a novel proximal projection during optimization. Further, our implementation computes the projection operator for the intersection of selected groups, which conserves more computing resources compared to predictor duplication methods, especially for high-dimensional data. Through simulation, we evaluate the performance of our approach under different graph structures and node counts, and present results on real-world data. Results suggest that our method exhibits stable performance relative to other singly or doubly sparse graphical regression models.
A Bayesian Approach for Task-Specific Next-Best-View Selection with Uncertain Geometry
Zhu, Jingsen, Sellán, Silvia, Terenin, Alexander
We develop a framework for task-specific active next-best-view selection in 3D reconstruction from point clouds, by casting the problem in the language of Bayesian decision theory. Our framework works by (a) placing a prior distribution over the space of implicit surfaces, (b) using recently-developed stochastic surface reconstruction methods to calculate the resulting posterior distribution, then (c) using the posterior distribution to carefully reason about which view to scan next. This enables us to perform camera selection in a manner that is directly optimized for the intended use of the reconstructed data - meaning, we reduce uncertainty only in those regions that make a difference in the task at hand, as opposed to prior approaches that reduce it uniformly across space. We evaluate our method across three distinct downstream tasks: semantic classification, segmentation, and PDE-guided physics simulation. Experimental results demonstrate that our framework achieves superior task performance with fewer views compared to commonly used baselines and prior general uncertainty-reduction techniques.
Sharp Capacity Thresholds in Linear Associative Memory: From Winner-Take-All to Listwise Retrieval
Barnfield, Nicholas, Kim, Juno, Nichani, Eshaan, Lee, Jason D., Lu, Yue M.
How many key-value associations can a $d\times d$ linear memory store? We show that the answer depends not only on the $d^2$ degrees of freedom in the memory matrix, but also on the retrieval criterion. In an isotropic Gaussian model for the stored pairs, we show that top-1 retrieval, where every signal must beat its largest distractor, requires the logarithmic model-size scale $d^2\asymp n\log n$. We prove that the correlation matrix memory construction, which stores associations by superposing key-target outer products, achieves this scale through a sharp phase transition, and that the same scaling is necessary for any linear memory. Thus the logarithm is the intrinsic extreme-value price of winner-take-all decoding. We next consider listwise retrieval, where the correct target need not be the unique top-scoring item but should remain among the strongest candidates. To formalize this regime, we propose the Tail-Average Margin (TAM), a convex upper-tail criterion that certifies inclusion of the correct target in a controlled candidate list. Under this listwise retrieval criterion, the capacity follows the quadratic scale $d^2\asymp n$. At load $n/d^2\toα$, we develop an exact asymptotic theory for the TAM empirical-risk minimizer through a two-parameter scalar variational principle. The theory has a rich phenomenology: in the ridgeless limit it yields a closed-form critical load separating satisfiable and unsatisfiable phases, and it predicts the limiting laws of true scores, competitor scores, margins, and percentile profiles. Finally, a small-tail extrapolation further leads to the conjectural sharp top-1 threshold $d^2\sim 2n\log n$.
Elon Musk's Last-Ditch Effort to Control OpenAI: Recruit Sam Altman to Tesla
Messages between Shivon Zilis and Tesla executives reveal plans in 2017 to start a rival AI lab, potentially led by Altman or Demis Hassabis. A few months before Elon Musk left OpenAI's board of directors in February 2018, he tried to recruit Sam Altman to join a "world-class AI lab" within Tesla. Musk went as far as offering the OpenAI CEO a Tesla board seat, according to emails and testimony presented in federal court on Wednesday during the trial . The emails were shown to a jury during the cross examination of Shivon Zilis, a former OpenAI adviser and board member who is also the mother of four of Musk's children. Musk's core claim in this lawsuit is that Altman and OpenAI president Greg Brockman effectively stole a nonprofit, using the $38 million Musk invested to create a private company worth more than $800 billion today.
'We had people come just to see it': Amazon delivers its first UK parcels by drone
'We had people come just to see it': Amazon delivers its first UK parcels by drone Amazon has become the first retailer in the UK to start a drone delivery service with a limited launch in Darlington, County Durham. Packages weighing less than 5lb (2.2kg) and containing everyday items such as beauty products, batteries and cables are now being delivered within a 7.5 mile (12km) radius of Amazon's fulfilment centre. The tech giant is convinced there is demand for ultra-fast deliveries and hopes to slowly expand the service. Rob Shield let Amazon use an Airbnb on his farm for its first test runs. Initially it was a novelty, so we were ordering everything under the sun, he says.