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A PMP-inspired Evaluation Framework for Assessing Deep-Learning Earth System Models
arXiv:2604.06567v3 Announce Type: replace Abstract: In recent years, Deep-Learning Earth System Models (DL-ESMs) have emerged as promising, computationally efficient complements to traditional Earth system models. Here, we present an evaluation framework for testing DL-ESMs from an Earth system model-development perspective using standardized diagnostics from the PCMDI Metrics Package (PMP). This framework allows DL-ESMs, including Ai2's ACE2 and Google's NeuralGCM, to be assessed with...
Greece gets green light to repay €6.95bn of bailout loans early
Greece has been cleared to repay almost €7bn of bailout loans ahead of schedule, in a move European officials say will improve the country's debt position. The European Stability Mechanism (ESM) has approved Greece's request to repay €6.95 billion of loans early under the first bailout programme through the Greek Loan Facility (GLF). The loans were part of the international rescue packages agreed during Greece's debt crisis in 2010.
Robust Multi-Mutant Protein Stability Prediction from a Fine-Tuned Evolutionary Scale Model
Recently, high-throughput experimental techniques have propelled improvements in deep learning-based prediction of mutation effects on protein stability. However, leading stability predictors still struggle to predict the combined effect of multiple mutations and prefer mutations that negatively impact other properties, including expressibility. To mitigate these limitations, we apply Low-Rank Adaptation (LoRA) to specialize ESM3 for stability prediction by fine-tuning on the Megascale...
When Does Structure Help? The Information Bonus of AlphaFold2 Representations over Protein Language Models
arXiv:2606.04228v1 Announce Type: new Abstract: AI scientist systems increasingly choose biological foundation models before they choose experiments. In protein pipelines, this creates a concrete engineering and scientific question: when is the cost of structural inference worth paying over a cheaper sequence-only model? We introduce the information bonus (IB), a task-level metric that measures the linearly accessible advantage of frozen single-sequence AlphaFold2 Evoformer representations...
Polynomial Trajectory Compression for Protein Language Model Embeddings
Protein language models (PLMs) generate rich, layer-wise embeddings that capture diverse biological information but are expensive in terms of storage and computation at scale. In this work, we propose a compact surrogate representation for PLM embeddings across transformer layers using low-dimensional PCA projections and cubic polynomial trajectories. This approach enables efficient storage and on-demand reconstruction of these protein-level embeddings at any layer without rerunning the PLM.
Climate network characterization of the AMOC edge state
arXiv:2606.08623v1 Announce Type: new Abstract: The Atlantic Meridional Overturning Circulation (AMOC) has been identified as a tipping element in the Earth system. Under the current climate change scenarios, it is urgent to develop robust methods for determining the probability of future AMOC transitions. Recent studies using an Earth System Model of Intermediate Complexity (EMIC) have revealed the importance of an AMOC edge state, located on the boundary of the attraction basin of the...
HonestAffinity: Leak-Aware Evaluation of Protein and Pocket Priors for Binding Affinity Prediction
arXiv:2606.03422v1 Announce Type: new Abstract: Sequence-based deep learning offers a scalable alternative to structure-based scoring for protein-ligand binding affinity prediction. However, progress is hard to interpret when architectural priors are evaluated on canonical PDBbind-style splits that leak similarity classes across folds.
Show HN: Solving complex optimization problems with Google OR-Tools in browser
Solve complex optimization models from TypeScript with Google OR-Tools running as multithreaded WebAssembly. Used in PragmaPlanner Run the local test site: npm install npm run dev Install from npm: npm install or-tools-wasm Import the solver API you need from its subpath: import { CpSat } from 'or-tools-wasm/cp-sat'; Public solver APIs live under solver-scoped subpaths: import { CpModel, CpSolver } from 'or-tools-wasm/cp-sat'; import { RoutingIndexManager, RoutingModel } from...
TaxoFormer: Hierarchical Transformer for Predicting the Full Taxonomic Lineage of Protein Sequences
Predicting labels in massive, hierarchically structured output spaces is a core challenge in machine learning. In this work, we use the problem of predicting the full taxonomic lineage of a protein from its sequence as a case study for this challenge. We introduce TaxoFormer, an architecture whose primary contribution is a structured tokenization scheme that losslessly represents the entire NCBI phylogenetic tree, a graph with over 1.3 million nodes using a compact vocabulary of just 15,000...
Structure-Aware Prediction of PROTAC-Mediated Protein Degradability via Graph Neural Networks
Announce Type: cross Abstract: Proteolysis-targeting chimeras (PROTACs) can selectively degrade disease-causing proteins, yet predicting which targets are amenable to degradation remains a critical bottleneck: existing computational methods require the complete PROTAC molecular structure, information unavailable before synthesis. We present DegradoMap, a graph neural network that predicts PROTAC-mediated degradability from protein structure and E3 ligase identity alone -- the minimal...