Despite recent advances in molecular foundation models, several limitations remain, such as chemically invalid augmentations, modality collapse, and incomplete representation of biochemical environments. To address these challenges, we present \textbf{Mol-JEPA}, a scalable framework for learning molecular world models. Rather than relying on suboptimal molecular perturbations, our model uses modality masking to exploit information from molecular structures, cellular phenotypes, binding affinities, ADMET profiles, quantum chemistry simulations and other drug discovery data. Across various benchmarks, we show that the representations learned by Mol-JEPA deliver strong performance, demonstrating the value of incorporating biochemical context through latent space prediction.
Florian Rottach, Sebastian Schieferdecker, William Rudman et al.· 0 citations
Text-Attributed Graphs (TAGs) integrate graph structures and node-associated textual attributes, and recent studies have increasingly leveraged Large Language Models (LLMs) to improve TAG learning in few-shot settings. However, existing approaches typically utilize LLM-derived information uniformly across all nodes, despite substantial variations in its reliability, while also incurring considerable monetary costs. We argue that the most appropriate source of supervision may differ across nodes, as Graph Neural Networks (GNNs) and LLMs exhibit complementary strengths in exploiting structural and semantic information, respectively. To this end, we propose CoTeach, a Confidence-aware dual-teacher learning framework that dynamically selects the more reliable teacher for each node. Experimental results demonstrate that CoTeach consistently improves few-shot node classification performance while reducing unnecessary LLM utilization and associated monetary costs.
Hojin Kim, Sujin Yoon, Sungsu Lim et al.· 0 citations
Reinforcement learning with verifiable rewards (RLVR) is deployed to make models better at reasoning tasks, but its side effect on what models will divulge is under studied. Here we show that RLVR on facts increases extraction of personally identifiable information (PII) the instruct model had already memorized. We first confirm that instruct models have already memorized PII but leave them latent, rarely surfacing one when asked. We then apply RL on benign factual data that contains no PII of any kind, and re-probe: a targeted probe over name->email pairs, and an untargeted free-recall prompt that simply asks the model to list the addresses it knows. PII extraction rises sharply under both: on DeepSeek-V3.1, verbatim recall@k increases from 0.155 to 0.370, a 2.4x gain. The effect scales with model size: across three models spanning 8B to 671B parameters, absolute leakage is largest in the biggest model. Meanwhile model's reasoning abilities and refusal rates are retained, indicating that RL selectively changes which memorized information is accessible rather than broadly altering the model. In summary, memorized private data can be made markedly more extractable by training that never touches it. This gives an adversary a route to memorized data that requires no privacy-relevant training signal and no access to the data itself -- only the ability to fine-tune on something innocuous.
A 4-bit quantized weight specifies a rounding cell rather than a single full-precision value. We introduce in-cell learning, a paradigm for writing new knowledge only within these cells, so that re-quantizing the served weights reproduces the released integer codes and scales exactly. CellFill implements this idea with bounded trainable positions inside frozen quantization cells and ships the update as a separate, subtractively revocable file. Across published NF4 and W4A16 releases of Qwen3 and Gemma from 1.7B to 32B parameters, CellFill writes 83-99% of a real-fact corpus while returning the stored code on every constrained weight. The injected facts generalize to paraphrases and composition, and answer 78-88% of selected PopQA questions that the released model misses. Sequential experiments show that rehearsal preserves earlier knowledge, whereas available room and new-task plasticity decline across updates. Consolidation re-quantizes the learned weights to produce a declared major version, restoring room at a measured capability cost. A six-task write-rehearse-consolidate cycle retains at least 92.8% of first learning in two 8B runs and records zero code violations over 6.9 billion constrained weights at every fold. These results define a version-management protocol in which minor updates preserve the released quantized artifact bitwise and major updates are explicit, measurable, and verifiable.
Zifeng Liu, Yaxin Lu, Xuanhan Wu et al.· 0 citations
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Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs. Generative models such as large language models (LLMs) provide expressive priors over such spaces, but their likelihoods and self-assessments are unreliable proxies for the objectives and calibrated epistemic uncertainty, especially for novel candidates outside the observed data distribution. We introduce the Large Discovery Model (LDM), an empirically grounded recurrent architecture that couples a generative model with a Bayesian non-parametric reward surrogate model. The generative model proposes and refines candidate designs, while the surrogate predicts their performance and quantifies uncertainty, yielding an uncertainty-aware value that guides candidate generation, refinement, and selection. The discovery memory and the surrogate model are continually updated as each new experimental observation arrives. We evaluate LDM on three scenarios spanning different design modalities and objectives, including neural-network training, antibody design, and molecular optimisation. Compared to LLM-only reflection or traditional statistical search across these domains, LDM achieves a $2.4\times$ greater reduction in validation BPB, an $18.2\%$ relative decrease in binding energy, and more than $60\%$ relative gains in molecular multi-objective performance. These results suggests that LDM could serve as a general-purpose discovery engine for effective search over open-ended hypothesis spaces.
Zhongwei Yu, Yan Song, Xue Yan et al.· 0 citations
Momentum-based optimizers are widely used in modern deep learning, yet the relations among momentum recursion, update geometry, and acceleration remain only partially understood. We develop an $\textbf{A}$DMM-$\textbf{I}$nspired $\textbf{M}$omentum (AIM) framework based on residual-penalty variable splitting, which interprets momentum as a multiplier-like correction driven by the splitting residual. AIM recovers the exponential moving average of gradients from an ADMM-style multiplier update and separates two mechanisms that are usually intertwined in practical optimizers: the residual penalty determines the update geometry, whereas the approximation of the objective-related subproblem determines the acceleration form. Building on AIM, we propose $\textbf{R}$elativistic $\textbf{A}$daptive gradient $\textbf{D}$escent with $\textbf{A}$ccelerated $\textbf{R}$esidual (RADAR), which combines relativistic adaptive geometry, decoupled residual correction, and second-order momentum filtering to improve the update direction and momentum estimation. We establish stochastic convergence through a variance-perturbed Lyapunov drift analysis. Experiments on supervised vision learning, language modeling, and reinforcement learning show that RADAR achieves consistent improvements over strong adaptive optimizer baselines.
Zhixin Ren, Yao Lyu, Congrong Li et al.· 0 citations
Automating empirical research is a long-standing direction of AI. Recent automatic research (AutoResearch) agents bring this goal within reach, as modern LLMs show the capability to independently implement solutions and learn from the execution outcomes. Behind these gains, post-training (especially RL) plays a central role. In this paper, we identify a fundamental tension when scaling RL for these agents: the two components of every AutoResearch trajectory (agent generation and environment execution) scale in very different manners, since all generation shares compute through batching, while each execution occupies its exclusive sandbox and real machine time. As a result, the environment execution dominates the training cost and becomes the bottleneck as trajectories grow. To resolve this tension, we propose World Model RL (WMRL), which replaces environment execution with a world model to remove this bottleneck. Additionally, the world model can be imperfect, as its rewards are corrupted by bias and noise. Therefore, we further equip WMRL with two mitigations, Online Debiasing and Inverse-Variance Denoising, which offset the bias and suppress the noise respectively. Theoretically, we prove that both mitigations of WMRL strictly improve the convergence guarantee. Empirically, WMRL accelerates training by 3-4x on various tasks at different agent scales, while exceeding the performance of standard RL baselines. Moreover, our post-trained 4B and 9B agents outperform much larger open-weight agents of 48B and 120B on held-out benchmarks. Beyond AutoResearch, WMRL also transfers to post-training embodied VLA policies, which demonstrates the generalizability of our method.
Xiyuan Yang, Sheikh Sarwar, Jingru Cheng et al.· 0 citations
Many sequential construction tasks have exact terminal symmetries even though execution is directed and depends on history. Process evidence supplies order; terminal correspondence transports it between equivalent outcomes; the realized state updates relevance. These roles define a carrier framework: transport what the outcome preserves; refine what history changes. SymBuild combines transported process and state residual ranks by ordinal rank meet; its top-$k$ prefix exactly equals their top-$k$ union, yielding a tight worst-case verifier query bound under prefix information. We evaluate SymBuild in three construction domains: computer-aided design (CAD) assembly, Mini-Programs, and exact-fill packing, and test additional framework instantiations in all four domains. SymBuild improves the area under the anytime verified success curve by up to 6.77, 21.75, and 8.68 points over initial-static in the three construction domains. Refresh gains recur beyond SymBuild under alternative aggregation, planning, and learned scoring methods; on Geometric Reasoning Network (GRN) target removal, direct Combined refresh has the lowest mean capped verifier cost at all three scales and reduces learned state evaluations by factors of 6.57-12.20 relative to refreshed population-guided search. Together, these results support the carrier framework and demonstrate that SymBuild is an effective, analyzable method for anytime verified construction.
Task arithmetic composes skills by adding weight displacements, and merged models are then judged on benchmark suites. We measure when that composition is functionally additive, and find that the answer depends as much on how the model is prompted as on which tasks are merged. Across two-dimensional composition surfaces -- five model settings from 0.5B to 8B, two families, LoRA and full fine-tuning -- pairwise non-additivity is real, seed-stable, and transfers in coarse order to unseen task pairs: all eight preregistered sign predictions held. But it is input-conditioned everywhere we measured: the same merged model that shows a six-point interaction contrast on code prompts shows none on math prompts, and wrapping the identical code prompts in the instruction template the adapters were trained on collapses the contrast twenty-fold, from +6.9 to +0.3 points -- while re-serializing them in an untrained chat template leaves it intact (+12.5), falsifying our own preregistered prediction. Execution benchmarks (pass@1) inherit the training-format wrapper's blindness. Weight-space composition therefore supports coarse, input- and format-conditioned functional statements -- not a universal merging-performance predictor, and not one that training-format evaluations can see.
Enterprise AI coding assistants incur substantial inference spend, and naive token-cost minimization often fails to reduce end-to-end cost once retries, escalations, and developer wait time are included. We present Task-to-Model Optimization (T2MO), a data-driven methodology for optimizing model selection in production coding workflows. We treat each developer session as a task that can be discovered, classified, graded for difficulty, benchmarked in a production-like harness, and routed to the cheapest model able to complete it within quality and latency constraints. The framework is a nine-stage pipeline spanning telemetry instrumentation, taxonomy discovery, difficulty grading, benchmark construction, candidate evaluation, optimal mix derivation, forecasting and version planning, staged routing deployment, and continuous governance. Unlike token-centric routing rules, our objective is cost per completed task, with failure escalation priced in explicitly. We show that this expected-completion-cost objective weakly dominates token-cost minimization under escalation, and we derive the routing boundary, the minimum pass rate a cheaper model must reach on a given cell to be worth deploying. Decisions are organized as a two-level hierarchy of task category difficulty tier, and per-cell displacement opportunities are aggregated into a traffic-weighted savings waterfall that ranks replacement candidates by realized dollar impact. The framework supports developer guidance, spend forecasting, and a staged transition from static policies to shadow-mode classifiers, verified cascades, and ultimately an intelligent router. We describe the methodology, optimization objective, evaluation protocol, and governance loop in a form suitable for production deployment and future empirical study.
Srinivasan Manoharan, Junhua Zhao, Fangbo Tu et al.· 0 citations
The initialization of deep neural networks determines whether information and gradients can propagate across depth, yet a unified theory connecting these properties to learning dynamics remains elusive. Combining mean-field theory and random matrix theory, we establish a direct link between correlation propagation and the Neural Tangent Kernel (NTK) that governs learning in the sequential limit of infinitely wide, infinitely deep networks. Correlation propagation to infinite depth is possible only at a single, critical point in the weight-bias variance plane. At this point, we leverage the algebraic decay of the end-to-end Jacobian with depth to prove that the NTK becomes exactly proportional to the output correlation at infinite depth, tying together information propagation and learning dynamics. We further show that orthogonal initialization suppresses the leading finite-size corrections present under Gaussian initialization, clarifying the respective roles of the two initialization ensembles in this limit. These theoretical predictions are validated quantitatively on finite-width, finite-depth networks. Together, these results demonstrate that orthogonal initialization and criticality are required to control the asymptotic dynamics of deep learning.
Andrea Combette, Nelly Pustelnik, Antoine Venaille· 0 citations
Smooth acyclicity constraints answer whether a weighted support is a DAG, whereas structure learning asks which support change should be made. Existing analyses establish degeneracy for particular constraint formulas but do not isolate what follows from smooth exactness itself. At a DAG boundary, we show that minimal cycle completions generate a squarefree monomial ideal containing every restricted Taylor jet of an exact representation. If the smallest completion has $q$ edges, the first possible response has order $q$ for a vector residual and $2q$ for a nonnegative scalar. Exponentially many constant-scale cyclic manifolds exhibit the same lack of ranking away from the boundary for NOTEARS and DAGMA. We derive the exact selection time for an isolated cycle. When $\Psi'(h)\asymp h^\nu$, the feasibility-only time is $T_0(\varepsilon)=\Theta(\varepsilon^{-(2\nu+1)})$; a score margin changes the leading dynamics at scale $T_0^{-1}$ for $\nu>0$, while $\nu=0$ has a logarithmic boundary layer requiring $\gamma T_0\log(1/\varepsilon)\to0$. Experiments verify this law, and a truth-free separation statistic predicts selection time on 320 official NOTEARS/DAGMA trajectories (Spearman $-0.52$ and $-0.66$, permutation $p<10^{-4}$). For finite samples, a parent-set confidence family and forced-opposite queries certify skeleton and unshielded-collider labels shared by every population optimum of a frozen score. Across 320 runs, every regret bound covers an independent oracle-score audit. None of 3,042 certified skeleton or 2,396 collider labels disagrees with the oracle-score optimum, although 4.4% and 5.5%, respectively, disagree with the generating graph. These results separate DAG feasibility, score-based support selection, and causal identification.
Rui Wu, Zongyuan Chen, Hong Xie et al.· 0 citations
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
MIT News · Artificial Intelligence· news.mit.eduAug 24, 2026
A new method for surgically removing training examples from a model reveals that as datasets grow, the link between what a model learns and what it produces dissolves.
