BioSight/docs/PURE_EQUATION_MAP.md
allaun 41fcbc3daa feat(init): initial BioSight commit — equation-to-DNA Φ encoding
BioSight encodes mathematical equations as 30-base hachimoji DNA
sequences for Adleman/Lipton-style DNA computing.

4-layer Φ mapping:
  Layer 1: F(E) — byte-class histogram on Δ₇
  Layer 3: τ(E) + δ(E) — parse tree structure
  Layer 4: 6 consistency rules → allele-specific PCR pass/fail

Independent phi/ modules:
  charclass, ast_parse, consistency, embed, output

Build: python3 -m py_compile — all modules clean
2026-06-23 18:27:35 -05:00

189 lines
5.9 KiB
Markdown
Raw Permalink Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

# SilverSight — Pure Equation Map
## 1. Fisher Geometry (Δ₇ → S⁷)
$$\Delta_7 := \{p \in \mathbb{R}^8 : p_i > 0,\; \sum_{i=1}^8 p_i = 1\}$$
$$T_p\Delta_7 := \{v \in \mathbb{R}^8 : \sum_{i=1}^8 v_i = 0\}$$
$$g_p(u,v) = \sum_{i=1}^8 \frac{u_i v_i}{p_i},\qquad u,v \in T_p\Delta_7$$
$$d_F(p,q) = 2\arccos\Bigl(\sum_{i=1}^8\sqrt{p_i q_i}\Bigr)$$
$$\psi : \Delta_7 \to S^7,\qquad \psi(p) = (\sqrt{p_1},\ldots,\sqrt{p_8})$$
$$g_p(u,v) = 4 \cdot g^{S^7}_{\psi(p)}(d\psi_p(u), d\psi_p(v))$$
$$d_F(p,q) = 2 \cdot d_{S^7}(\psi(p), \psi(q))$$
$$d_B(p,q) = \arccos\Bigl(\sum_{i=1}^8 \sqrt{p_i q_i}\Bigr)$$
$$\boxed{d_F(p,q) = 2\,d_B(p,q)}$$
$$\frac{1}{\pi} d_F(p,q) \leq d_{\text{chord}}(\Phi(p),\Phi(q)) \leq \frac{1}{2} d_F(p,q)$$
---
## 2. G1: Chaos Game Contraction
$$w_j(p) = \frac{A_j p + b_j}{1 + B_j},\qquad p \in \Delta_7$$
$$\Delta_7^{(\varepsilon_j)} := \{p \in \Delta_7 : p_i \geq (b_j)_i/(1+B_j)\},\qquad \varepsilon_j = \min_i (b_j)_i/(1+B_j) > 0$$
$$\widehat{w}_j(x) = \Phi(w_j(x^2)) = \frac{\sqrt{A_j x^2 + b_j}}{\sqrt{1+B_j}}$$
$$d_B(w_j(p), w_j(q)) \leq \frac{1}{\sqrt{1+B_j}} \, d_B(p,q)$$
$$d_F(w_j(p), w_j(q)) \leq \lambda_j \, d_F(p,q),\qquad \lambda_j = \frac{1}{\sqrt{1+B_j}} < 1$$
$$\lambda = \max_j \lambda_j < 1$$
$$\kappa_j(p) = \sup_{v \in T_p\Delta_7 \setminus \{0\}} \frac{\|dw_j|_p(v)\|_{F,w_j(p)}}{\|v\|_{F,p}}$$
$$\kappa_j(p) \leq \frac{1}{\sqrt{1+B_j}} \leq 1 - \frac{B_j}{2(1+B_j)}$$
$$\mathcal{A} = \bigcup_{j=1}^k w_j(\mathcal{A})$$
---
## 3. G2: Semantic Feature Collision Breaking
$$F(E)_i = \frac{f_i(E)}{|E|},\qquad f_i(E) = \sum_{\ell=1}^{L} \mathbf{1}_{\{\chi(e_\ell) = i\}}$$
$$\mathcal{N} := \{\text{bin-add}, \text{bin-sub}, \text{bin-mul}, \text{bin-div}, \text{bin-eq}, \text{un-neg}, \text{var}, \text{const}\}$$
$$\tau(E)_t = \frac{|\{n \in T(E) : \lambda(n) = t\}|}{|T(E)|},\qquad t \in \mathcal{N}$$
$$b_{t,t',i} := |\{(u,v) : \lambda(u) = t,\; \lambda(v) = t',\; \text{child index} = i\}|$$
$$M = \sum_{t,t',i} b_{t,t',i} = |T(E)| - 1$$
$$\delta(E)_{t,t',i} = b_{t,t',i} / M$$
$$\Phi(E) := (F(E),\; \tau(E)) \in \Delta_7 \times \Delta_{k-1}$$
$$\Phi_{+}(E) := (F(E),\; \tau(E),\; \delta(E)) \in \Delta_7 \times \Delta_{k-1} \times \Delta_{2k^2-1}$$
$$d^{\times}_F((p,r), (q,s)) = \sqrt{d^2_F(p,q) + d^2_F(r,s)}$$
$$d^F(\pi(x), \pi(y)) \leq d^{\times}(x, y)$$
$$d_F(F(E_1), F(E_2)) \leq \frac{C}{L}$$
$$d^{\times}_F(\Phi(E_1), \Phi(E_2)) \leq \sqrt{\frac{C_1^2}{L^2} + \frac{C_2^2}{N^2}}$$
---
## 4. G3: Eigensolid Fixed Point
$$C(p)_{2k-1} = C(p)_{2k} = \frac{p_{2k-1} + p_{2k}}{2},\qquad k = 1,2,3,4$$
$$M = \{p \in \Delta_7 : p_1 = p_2,\; p_3 = p_4,\; p_5 = p_6,\; p_7 = p_8\}$$
$$\phi(q_1,q_2,q_3,q_4) = \Bigl(\frac{q_1}{2},\frac{q_1}{2},\frac{q_2}{2},\frac{q_2}{2},\frac{q_3}{2},\frac{q_3}{2},\frac{q_4}{2},\frac{q_4}{2}\Bigr)$$
$$d_F(C(p), C(q)) \leq d_F(p,q)$$
**Strict iff** k: (p_{2k-1}, p_{2k}) not proportional to (q_{2k-1}, q_{2k})
$$I_{\text{loss}}(p) = \sum_{k=1}^4 s_k \cdot D_{KL}\Bigl(\bigl(\frac{p_{2k-1}}{s_k},\frac{p_{2k}}{s_k}\bigr) \,\big\|\, \bigl(\tfrac12,\tfrac12\bigr)\Bigr)$$
$$I_{\text{loss}}(p) = H(C(p)) - H(p)$$
$$C_{\mathcal{P}} = C_m \circ C_{m-1} \circ \cdots \circ C_1$$
**Nested:** P_{j+1} coarsens components of P_1,…,P_j C_𝒫² = C_𝒫
$$M_1 \supset M_2 \supset \cdots \supset M_m\quad (\text{nested})$$
$$S_*(p) = (p_1+p_2,\; p_3+p_4,\; p_5+p_6,\; p_7+p_8)$$
$$(A_j)_{2j-1,\ell} = (A_j)_{2j,\ell} = \begin{cases} \tfrac12 & \ell \in P_j, \\ \delta_{\ell,i} & i \notin P_j \end{cases}$$
---
## 5. Chentsov Reconstruction
$$h_9(p) = \sum_{i=1}^m \operatorname{Hess}(F)_p(e_i,e_i)$$
$$h_{\text{perm}}(p) = \sum_{i=1}^m \operatorname{Hess}(F)_p(e_i, e_{\pi(i)})$$
$$F(g_p^{(\alpha)}) = \alpha \cdot F(g_p^{(1)}) + (1-\alpha) \cdot F(g_p^{(0)})$$
$$g_p^{\text{mono}}(u,v) = \lambda(p) \cdot g_p^{\text{Fisher}}(u,v)$$
$$g_{ij}(p) = \frac{1}{p_i}\delta_{ij} + \frac{1}{p_m}$$
$$ds^2 = \sum_{i=0}^{m} \frac{(dp_i)^2}{p_i}$$
---
## 6. SOS Certificate (Merge Gate)
$$\text{gap}(x,m) = \text{sieve}(x,m) - \text{threshold}$$
$$K = \{x \in [2,90],\; m \in [3,13]\}$$
$$\text{gap}(x,m) = s_0(x,m) + s_1(x,m)(x-2) + s_2(x,m)(90-x) + s_3(x,m)(m-3) + s_4(x,m)(13-m)$$
$$s_i(x,m) = \sum_j q_{ij}(x,m)^2$$
$$\text{gap}(x,m) \geq 0 \text{ on } K \implies \text{merge gate}$$
**Baker (transcendence):**
$$\Lambda = \sum_{i=0}^{n} \beta_i \log \alpha_i \neq 0 \implies |\Lambda| > e^{-C \cdot \prod A_i \cdot \log B}$$
---
## 7. Sidon (Cross-Domain)
$$A \subset \mathbb{Z},\quad a+b=c+d \implies \{a,b\}=\{c,d\}$$
$$A_8 = \{2^i\}_{i=0}^7$$
$$h(N) = \max|A|,\quad A \subseteq \{1,\ldots,N\} \text{ Sidon}$$
$$h(N) \leq \lfloor\sqrt{2N}\rfloor + 1$$
$$S_p = \{x \in \mathbb{F}_{p^3}^\times / \mathbb{F}_p^\times : \operatorname{Tr}(x)=0\},\quad |S_p|=p+1$$
---
## 8. Braid / Spectral / Merge Gate
$$C \in \{0,\tfrac14,\tfrac12,\tfrac34\}^{8\times 8}$$
$$\varepsilon_{ij} = C_{ij}(\phi_i - \phi_j)$$
$$\text{crossStep}(s) = s \iff s \in \text{Eigensolid}$$
$$\text{gap}(s) = \bigwedge_{i,j \in \text{active}(s)} (i=j \lor |i-j|>1)$$
$$\text{merge}(s,e)_i = \min(1, s_i+e_i)$$
$$\text{res}(s,e) = |\{i : s_i \neq 0 \land e_i \neq 0\}|$$
$$\text{cross}(s,e) = \bigwedge_{i} \neg(s_i \neq 0 \land e_{i+1} \neq 0) \land \neg(e_i \neq 0 \land s_{i+1} \neq 0)$$
$$\text{gap}(s) \land \text{gap}(e) \land \text{res}(s,e)=0 \land \text{cross}(s,e) \implies \text{gap}(\text{merge}(s,e))$$
$$\text{byteGap}(n) = (n \land (n \gg 1)) = 0$$
$$\text{pack}(s) = \sum_{i=0}^{7} [s_i \neq 0] \cdot 2^i$$
---
## 9. Chiral / Q16_16
$$q = q_r + \varepsilon q_d,\quad \varepsilon^2 = 0$$
$$\chi = \frac{|q_r|^2}{|q_r|^2 + |q_d|^2},\quad |q_r|^2 + |q_d|^2 > 0$$
$$\chi > \tfrac12 \implies \text{compressive},\quad \chi < \tfrac12 \implies \text{anti-compressive},\quad \chi = \tfrac12 \implies \text{critical}$$
$$\text{Q16}(x) = \text{clamp}(-2^{31},\; \lfloor x \cdot 2^{16} \rfloor,\; 2^{31}-1)$$
$$a \oplus b = \text{clamp}(-2^{31},\, a+b,\, 2^{31}-1)$$
$$a \otimes b = \text{clamp}(-2^{31},\, \lfloor ab/2^{16} \rfloor,\, 2^{31}-1)$$