Protein structure modeling rests on a single computational primitive: the interaction between what a residue is (sequence content) and where it sits (three-dimensional geometry). What is the expressive limit of this layer class? We show that the complete bilinear operator over content-geometry outer products--the sufficient statistic of all second-order interactions--is the expressive ceiling, while the additive message passing of mainstream geometric GNNs is provably blind to content-geometry binding. We then introduce Hyper-Fold, a rank-K separable convolutional backbone approaching this ceiling at message-passing cost: each radius neighborhood is organized into a sequence hyperedge and a contact hyperedge, modulated by an edge-conditioned matrix-valued operator factorized into K learned basis operators with geometry-generated coefficients. Across enzyme function prediction, fold classification, and ligand binding site detection, Hyper-Fold and its hierarchical variant Hyper-Fold-Deep achieve the best results among protein-specific structure encoders; Hyper-Fold-Pocket, an anchored set-prediction head, surpasses UniSite-3D on UniSite-DS and two zero-shot benchmarks with no sequence language model features, 68x fewer parameters, and 4.8x lower latency--suggesting that a sufficiently expressive 3D backbone recovers information that fusion architectures previously borrowed from evolution-scale pretraining.
Yifan Feng, Guang Cheng, Shihui Ying et al.· 0 citations
The results indicate that subtraction-based input and ensembling support robust tumor segmentation under cross-site domain shift, whereas pCR prediction from baseline DCE-MRI alone remains limited.
We study the empirical Sinkhorn estimator of the entropic optimal transport potentials under the uniform loss. Since the potentials are only unique up to additive constants, we measure the error using the quotient supremum norm, defined as $d_\infty([u],[v]) = \inf_{a\in\mathbb{R}}\|u-v-a\|_\infty$. For a fixed regularization parameter $\varepsilon>0$, we establish a non-asymptotic statistical rate of $n^{-1/2}$. This is achieved by combining the Birkhoff-Hopf contraction theorem with entropy bounds on normalized kernel sections. However, the constant in this bound grows exponentially with $1/\epsilon$. To improve this, we isolate geometric conditions under which the empirical estimator maintains the $n^{-1/2}$ rate but features polynomial dependence on $1/\varepsilon$. The key requirement is a polynomial residual-stability estimate for the population Sinkhorn map. We provide sufficient criteria for this, including a polynomial contraction property and a local inverse estimate. Furthermore, we introduce two rigorously verifiable model classes an $\varepsilon$-weak residual-interaction class obtained after separable centering and another based on connected tight-edge graphs for fixed discrete costs where the polynomial rate is guaranteed without relying on abstract resolvent assumptions. Finally, we establish matching minimax lower bounds demonstrating that the $\varepsilon n^{-1/2}$ rate cannot be uniformly improved in the bounded-interaction regime.
APIFlow-Bench is introduced, a fully auditable benchmark for long-horizon, dependent REST-API workflows that decomposes performance into seven engineering capabilities and requires agents to produce answers supported by the actual call path.
Ze-Lin Wan, Arash Nourian, Xiao-Xiao Li et al.· 0 citations
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The EM generalization metric is extended from a scalar distance to a dataset-specific generalization direction, which robustly predicts EM models'evilness under semantics-preserving prompt perturbations including appending random tokens and paraphrasing, where other methods do not reliably generalize.
Ming-Xuan Li, Qirun Dai, Hesi Wang et al.· 0 citations
This paper develops a unified theoretical framework showing that a broad family of clustering methods, including k-means, fuzzy c-means, kernel k-means, kernel FCM, and spectral clustering, can all be expressed as structured low-rank projectors acting on a signal-derived matrix. By formulating each method as an instance of min over B in C of ||M - M P_B||_F^2, with different constraint sets C, we establish a common optimization template that clarifies the algebraic links among hard, fuzzy, kernel-induced, and orthonormal projections. Within this framework, we derive non-trivial theoretical results, including geodesic convexity properties on the projection manifold, perturbation bounds quantifying stability to matrix noise, and exact recovery guarantees under ideal block-model conditions. The analysis further explains when different clustering families collapse to the same optimal subspace and how deviations arise under small inter-cluster leakage. Overall, the work provides a coherent, theory-first foundation for understanding clustering through structured projectors.
It is shown that this lower bound is tight and that a clustering in the $2$-Droop core always exists, and that such a clustering can be achieved by only selecting centers from locations in the metric space where an agent resides.
Operator-learning surrogates have been benchmarked largely on single-field, single-interface problems, leaving unclear whether architectural choices validated in those settings transfer to constrained, multiphase flows. We introduce a three-phase interfacial-flow benchmark to examine whether the trunk coordinate representation matters for a multi-channel, interface-dominated target. The configuration consists of an air bubble rising through water, piercing a water-oil interface, and entraining a water plume into the oil within a bounded, wall-confined domain. Reference data are generated using a structure-preserving ternary Cahn-Hilliard-Navier-Stokes solver that algebraically preserves the simplex constraint. From 1,024 Sobol-sampled simulations spanning a nine-dimensional parameter space, we learn the mapping from physical parameters to five-channel space-time fields. We compare three parameter-matched DeepONet variants differing only in trunk representation: raw coordinates (DeepONet), random Fourier features (FEDONet), and a fixed tensor-product Chebyshev dictionary (SEDONet). SEDONet reduces the test relative L2 error by 16.8% compared with FEDONet and by 24.0% compared with DeepONet, while improving all five output channels. Spatial and temporal error analyses localize the principal gains near the diffuse interfaces and after bubble breakthrough. The results indicate that the Chebyshev representation is particularly effective for the strongly non-periodic wall-normal and temporal structure of this three-phase flow.
We determine the sharp restricted isometry threshold for recovery at global minima of the rank-restricted matrix LASSO. For target rank $r_{\star}$, if the rank-$k$ RIP constant satisfies $\delta<\delta_{\mathrm{sharp}}(k/r_{\star})$, where $\delta_{\mathrm{sharp}}(t)=t/(4-t)$ for $0<t<4/3$ and $\delta_{\mathrm{sharp}}(t)=\sqrt{(t-1)/t}$ for $t\ge4/3$, then every global minimizer has Frobenius error $\lesssim\sqrt{r_{\star}}\lambda$ for all $\lambda\gtrsim\|\mathcal{A}^{*}(\xi)\|_{\mathrm{op}}$ and at every search rank $r\ge r_{\star}$. The constants depend only on the RIP constant and $t=k/r_{\star}$, and in particular are independent of the search rank. When the rank restriction is inactive, the result specializes to the ordinary convex matrix LASSO. We also obtain the analogous results for sparsity-restricted vector LASSO. Conversely, we show that the threshold $\delta<\delta_{\mathrm{sharp}}(k/r_{\star})$ cannot be improved, due to the existence of counterexamples whose global minimizers fail to recover the ground truth.
This work proposes Jigsaw-CRL, a framework for recovering global latent causal order from a fragmented multi-client setting, where multiple clients interact with the same global latent causal system but each client only accesses and intervenes on a subset of the latent variables.
Although performance of language-based models is improved by scaling, whether the gap to a structure-aware architecture can eventually be eliminated remains untested.
A policy-aligned retrieval framework that improves offline relevance over a matched-capacity baseline, with gains broadly distributed across facet combinations, and serves this framework with a two-stage GPU architecture.
Dhritiman Das, Chujie Zheng, Ronak Kaoshik et al.· 0 citations
A weeklong summer workshop brought higher education faculty to campus to explore how AI and machine learning materials can be adapted for their classrooms.
Adaptive AI agents can help make BIM data more machine-readable by navigating IFC models, interpreting inconsistent information, and mapping it to defined standards. In this blog, Alok Rawat shares findings from a real-world pilot in construction workflows. The post Adaptive AI Agents in Construction Workflows appeared first on GPT-Lab.
