Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and selection remains a major challenge. A key barrier to developing effective machine learning-based EMA methods is the lack of large, diverse, and well-annotated datasets for training and evaluation. To address this gap, we introduce PSBench, a benchmark suite comprising five large-scale, labeled datasets, four of which were generated during the 15th and 16th community-wide Critical Assessment of Protein Structure Prediction (CASP15 and CASP16), and one curated for new Protein Data Bank (PDB) entries deposited between July 2024 and August 2025. PSBench includes over 1.4 million structural models covering a wide range of protein sequence lengths, complex stoichiometries, functional classes, and modeling difficulties. Each model is annotated with multiple complementary quality scores at the global, local, and interface levels. PSBench also provides multiple evaluation metrics and baseline EMA methods to facilitate rigorous comparisons. To demonstrate PSBench's utility, we trained and evaluated GATE, a graph transformer-based EMA method, on the CASP15 data. GATE was blindly tested in CASP16 (2024), where it ranked among the top-performing EMA methods.

Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and selection remains a major challenge. A key barrier to developing effective machine learning-based EMA methods is the lack of large, diverse, and well-annotated datasets for training and evaluation. To address this gap, we introduce PSBench, a benchmark suite comprising five large-scale, labeled datasets, four of which were generated during the 15th and 16th community-wide Critical Assessment of Protein Structure Prediction (CASP15 and CASP16), and one curated for new Protein Data Bank (PDB) entries deposited between July 2024 and August 2025. PSBench includes over 1.4 million structural models covering a wide range of protein sequence lengths, complex stoichiometries, functional classes, and modeling difficulties. Each model is annotated with multiple complementary quality scores at the global, local, and interface levels. PSBench also provides multiple evaluation metrics and baseline EMA methods to facilitate rigorous comparisons. To demonstrate PSBench's utility, we trained and evaluated GATE, a graph transformer-based EMA method, on the CASP15 data. GATE was blindly tested in CASP16 (2024), where it ranked among the top-performing EMA methods.

Neural Information Processing Systems http://nips.cc/

The aim of this paper is to make clear and precise the relationship between the Rubin causal model (RCM) and structural causal model (SCM) frameworks for causal inference. Adopting a neutral logical perspective, and drawing on previous work, we show what is required for an RCM to be representable by an SCM. A key result then shows that every RCM---including those that violate algebraic principles implied by the SCM framework---emerges as an abstraction of some representable RCM. Finally, we illustrate the power of this ameliorative perspective by pinpointing an important role for SCM principles in classic applications of RCMs; conversely, we offer a characterization of the algebraic constraints implied by a graph, helping to substantiate further comparisons between the two frameworks.

We develop pre-trained estimators for structural econometric models. The estimator uses a neural net to recognize the structural model's parameter from data patterns. Once trained, the estimator can be shared and applied to different datasets at negligible cost and effort. Under sufficient training, the estimator converges to the Bayesian posterior given the data patterns. As an illustration, we construct a pretrained estimator for a sequential search model (available at pnnehome.github.io). Estimation takes only seconds and achieves high accuracy on 12 real datasets. More broadly, pretrained estimators can make structural models much easier to use and more accessible.

Electronic health records provide a rich source of data for machine learning methods to learn dynamic treatment responses over time.

Deep neural networks has been increasingly applied in fault diagnostics, where it uses historical data to capture systems behavior, bypassing the need for high-fidelity physical models. However, despite their competence in prediction tasks, these models often struggle with the evaluation of their confidence. This matter is particularly important in consistency-based diagnosis where decision logic is highly sensitive to false alarms. To address this challenge, this work presents a diagnostic framework that uses ensemble probabilistic machine learning to improve diagnostic characteristics of data driven consistency based diagnosis by quantifying and automating the prediction uncertainty. The proposed method is evaluated across several case studies using both ablation and comparative analyses, showing consistent improvements across a range of diagnostic metrics.

Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the quality of these predicted models (estimation of model accuracy, or EMA) for model ranking and selection remains a major challenge. A key barrier to developing effective machine learning-based EMA methods is the lack of large, diverse, and well-annotated datasets for training and evaluation. To address this gap, we introduce PSBench, a benchmark suite comprising four large-scale, labeled datasets generated during the 15th and 16th community-wide Critical Assessment of Protein Structure Prediction (CASP15 and CASP16). PSBench includes over one million structural models covering a wide range of protein sequence lengths, complex stoichiometries, functional classes, and modeling difficulties. Each model is annotated with multiple complementary quality scores at the global, local, and interface levels. PSBench also provides multiple evaluation metrics and baseline EMA methods to facilitate rigorous comparisons. To demonstrate PSBench's utility, we trained and evaluated GATE, a graph transformer-based EMA method, on the CASP15 data. GATE was blindly tested in CASP16 (2024), where it ranked among the top-performing EMA methods. These results highlight PSBench as a valuable resource for advancing EMA research in protein complex modeling. PSBench is publicly available at: https://github.com/BioinfoMachineLearning/PSBench.

This paper presents R-CAGE (Rhythmic Control Architecture for Guarding Ego), a theoretical framework for restructuring emotional output in long-term human-AI interaction. While prior affective computing approaches emphasized expressiveness, immersion, and responsiveness, they often neglected the cognitive and structural consequences of repeated emotional engagement. R-CAGE instead conceptualizes emotional output not as reactive expression but as ethical design structure requiring architectural intervention. The model is grounded in experiential observations of subtle affective symptoms such as localized head tension, interpretive fixation, and emotional lag arising from prolonged interaction with affective AI systems. These indicate a mismatch between system-driven emotion and user interpretation that cannot be fully explained by biometric data or observable behavior. R-CAGE adopts a user-centered stance prioritizing psychological recovery, interpretive autonomy, and identity continuity. The framework consists of four control blocks: (1) Control of Rhythmic Expression regulates output pacing to reduce fatigue; (2) Architecture of Sensory Structuring adjusts intensity and timing of affective stimuli; (3) Guarding of Cognitive Framing reduces semantic pressure to allow flexible interpretation; (4) Ego-Aligned Response Design supports self-reference recovery during interpretive lag. By structurally regulating emotional rhythm, sensory intensity, and interpretive affordances, R-CAGE frames emotion not as performative output but as sustainable design unit. The goal is to protect users from oversaturation and cognitive overload while sustaining long-term interpretive agency in AI-mediated environments.

The aim of this paper is to make clear and precise the relationship between the Rubin causal model (RCM) and structural causal model (SCM) frameworks for causal inference. Adopting a neutral logical perspective, and drawing on previous work, we show what is required for an RCM to be representable by an SCM. A key result then shows that every RCM---including those that violate algebraic principles implied by the SCM framework---emerges as an abstraction of some representable RCM. Finally, we illustrate the power of this ameliorative perspective by pinpointing an important role for SCM principles in classic applications of RCMs; conversely, we offer a characterization of the algebraic constraints implied by a graph, helping to substantiate further comparisons between the two frameworks.