Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier to adoption because biologists cannot assess whether predictions reflect genuine biochemical insight or spurious correlations. We present \textbf{Protein Thoughts}, a framework that reformulates PPI discovery as an interpretable search problem with explicit reasoning. The system decomposes binding evidence into four biologically meaningful signals: sequence similarity reflecting evolutionary relationships, structural complementarity capturing geometric fit, interface balance, and chemical compatibility encoding residue-level interactions. Rather than collapsing these signals into an opaque score, we preserve their individual contributions through a transparent value function that enables both ranking and auditing. To navigate large candidate spaces efficiently, we introduce hypothesis-guided entropy-regularized Tree-of-Thoughts search. A fine-tuned language model generates search directives from embedding-derived features, classifying candidates as high-priority, exploratory, or skippable. These directives condition a Boltzmann policy that balances exploitation with entropy-driven exploration, while hypothesis-aware pruning prevents premature abandonment of promising candidates. For candidates exhibiting score disagreement, hypothesis-conditioned embedding-space flow matching transports protein embeddings toward the binder manifold. On the SHS148k benchmark, Protein Thoughts achieves mean best-binder rank of 11.2 versus 47.7 for an entropic tree search baseline, a 76% improvement, and for binding prediction the trained value function achieves $91.08 \pm 0.19$ Micro-F1, outperforming existing PPI methods on the same dataset.

It is a classical result in rational approximation theory that certain non-smooth or singular functions, such as $|x|$ and $x^{1/p}$, can be efficiently approximated using rational functions with root-exponential convergence in terms of degrees of freedom \cite{Sta, GN}. In contrast, polynomial approximations admit only algebraic convergence by Jackson's theorem \cite{Lub2}. Recent work shows that composite polynomial architectures can recover exponential approximation rates even without smoothness \cite{KY}. In this work, we introduce and analyze a class of weighted deep polynomial approximants tailored for functions with asymmetric behavior-growing unbounded on one side and decaying on the other. By multiplying a learnable deep polynomial with a one-sided weight, we capture both local non-smoothness and global growth. We show numerically that this framework outperforms Taylor, Chebyshev, and standard deep polynomial approximants, even when all use the same number of parameters. To optimize these approximants in practice, we propose a stable graph-based parameterization strategy building on \cite{Jar}.