What would it mean to have a scientific understanding of AI? Language models are not static objects—they are snapshots of time-evolving processes shaped by data, objectives, and optimization dynamics. Yet the field predominantly treats models as fixed artifacts, analyzing behaviors after training rather than asking why they emerge. This position paper argues that AI research should move beyond post hoc fixes and study the learning dynamics of models. We envision a hierarchy of scientific maturity: first predict outcomes from early training signals, then intervene when trajectories go wrong, ultimately design training procedures that guarantee desired properties. Scaling laws have reached the first level for loss; the challenge is extending all three levels to general capabilities, biases, and safety. We articulate requirements for such theories, survey progress across mechanistic interpretability, fairness, memorization, and learning dynamics, and identify concrete open problems. The path forward requires treating models as processes to be understood, not just artifacts to be patched.

Scientific data annotation, such as tracking animals in video or proofreading neural reconstructions, remains bottlenecked by the “last mile” problem: even with strong automation, verification and correction consume substantial human effort. Standard approaches train models to directly predict annotations, discarding the rich supervision in how experts navigate, click, verify, and correct. We introduce a framework for studying behavioral cloning on scientific annotation: 9 synthetic tasks paired with synthetic annotations that simulate realistic human strategies including exploration, mistake correction, and strategic decision-making. Our experiments reveal several findings. First, skills emerge hierarchically: models learn GUI mechanics before task-critical decisions, and commit fewer mistakes than the training data while retaining the ability to correct errors when they occur. Second, scaling models on multi-task behavioral cloning shows that larger models are more data efficient within our scale range. Third, multi-task pretraining enables efficient fine-tuning to new tasks, while training from scratch fails entirely. Fourth, linear probes reveal that models internally represent latent variables of the annotation process such as task phase and data position; interestingly, we find a shared mistake representation that generalizes across different annotation tasks. Overall, our framework establishes systematic benchmarks and identifies key bottlenecks, providing a foundation for scaling behavioral cloning to real-world scientific data annotation.

Memory formation is fundamental to intelligence, yet whether deep neural networks preserve identifiable memory traces analogous to biological memory units remains an open question. This work introduces a geometric framework to identify such “AI engrams” by formalizing the neuroscientific criteria of specificity, reactivation, sufficiency, and necessity into a constrained inverse problem. We derive a closed-form estimator that isolates individual memory traces from globally entangled parameters, and show that this biologically-derived solution corresponds to a natural gradient update on the parameter manifold. AI engrams enable surgical manipulation of learned knowledge: any subset of memories can be composed or erased through linear arithmetic, without iterative optimization. Experiments ranging from simple MLPs to LLMs demonstrate the causal validity and substantial scalability of AI engrams. Together, these results bridge theories of biological memory and artificial representation learning and offer geometric insight into how deep networks simultaneously support functional specificity within distributed storage.

Compositional explanations are a family of methods that aim to describe the spatial alignment between neurons' receptive field activations and concepts through logical rules, typically computed via a search over all possible concept combinations. Since computing the spatial alignment over the entire state space is computationally infeasible, the literature commonly adopts assumptions related to the structure of the combinations and beam search to restrict the state space. However, beam search cannot provide any theoretical guarantees of optimality, and it remains unclear how close current explanations are to the true optimum. In this theoretical paper, we address this gap by introducing the first framework for computing guaranteed optimal compositional explanations over the entire state space spanned by the adopted assumptions. Specifically, we propose: (i) a decomposition that identifies the factors influencing the spatial alignment, (ii) a heuristic to estimate the alignment at any stage of the search, and (iii) the first algorithm that can compute optimal compositional explanations in a time comparable to exhaustive beam search. Using this framework, we demonstrate that 10-40\% of explanations previously obtained with beam search are suboptimal when overlapping concepts are involved. Finally, we evaluate a beam-search variant guided by our proposed decomposition and heuristic, showing that it matches or improves runtime over prior methods while offering greater flexibility in hyperparameters and computational resources.