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节点 n6

OT-CFM velocity field in PCA for E9.5→E10.5 extrapolation

运行?一次完整的自动搜索或 Agent 会话,有自己的锁定配置和证据包。20261002-202908-search-t1-scr-D
父节点(种子,没有父节点)
子节点—
操作?种子:人写的起点;改进:在父节点上改;草稿:从头写;修复:修父节点的报错。草稿
状态生成失败
分数没有分数
审查未审查
用时?从运行开始到结束(或到现在)的挂钟时间。31 分
程序版本— (programs.git)
备注missing or empty solution/METHOD.md (method and knowledge sources are required)

方法说明?节点程序自带的 METHOD.md:这个程序做了什么、为什么。

没有 METHOD.md。

调研员的计划

名称OT-CFM velocity field in PCA for E9.5→E10.5 extrapolation
动机Node 4 (rank3 54.95) dominates via per-type constant shift but loses covariation (45.90 vs baseline 48.44) because all cells in a type get identical displacement. OT-CFM learns a state-dependent velocity field: cells within the same type receive different displacements based on their position in PCA space, potentially preserving covariation while still capturing directional change. Node 2/3 (moscot coupling, rank3 ~49) showed OT-based displacement helps over copy_last but the per-cell coupling displacement (κ=1) failed on X3 (26.4). CFM differs by learning a smooth vector field rather than using raw coupling barycenters, and by extrapolating with a damped step rather than full coupling displacement.
做法Steps: (1) Load E8.5 and E9.5 from view_io (two input stages). If only one stage available (proxy), fall back to copy_last. (2) Compute shared PCA on combined cells (HVG=2500, n_components=25). Store per-cell residuals in gene space. (3) Subsample min(3000, n) cells per stage. (4) Use torchcfm ExactOptimalTransportConditionalFlowMatcher(sigma=0.0). In training loop (2000 steps, Adam lr=1e-3): sample minibatch 256 pairs via fm.sample_location_and_conditional_flow(x0_batch, x1_batch); MLP v(x,t) with 2 hidden layers × 128 units, input dim=25+1 (state + time); loss = MSE(v(xt,t), ut). (5) Integrate: from all E9.5 cells in PCA, run 10 Euler steps from t=1.0 to t=1.0+alpha, alpha=0.5 (damped extrapolation; search range [0.3, 0.7, 1.0]). At each step dx = v(x,t)*dt/10. (6) Decode: project integrated PCA back to gene space via PCA components, add each cell's original residual (from E9.5), clip negatives to 0. Preserve sparsity pattern: where E9.5 cell was 0 and decoded value < small threshold (0.01), keep 0. (7) Output predicted E10.5 cells. vec-score after first successful run; if score < 46 (below copy_last), try alpha=0.3; if still bad, report failure. Total training budget: cap at 5 …
风险1) Extrapolation beyond t=1 is out-of-distribution for the trained field; velocity may diverge or produce unrealistic states. Mitigation: damp alpha to 0.5, monitor integrated trajectory norm; if PCA norm of output >> input, reduce alpha. Engineer should check after first integration. 2) With only 2 timepoints the field is weakly identified (k009 notes this); it may degenerate to near-constant per-region vectors. Check: compute within-type std of velocity; if < 10% of between-type std, mechanism not working. 3) Universal diffusion: field may just spread the cloud without correct direction. Check: compare output variance to input variance per PC; if ratio > 1.5 uniformly, field is diffusive. Compare against random-velocity control. 4) torchcfm/torchdyn import or API issues under time pressure. Mitigation: fallback to manual OT pairing via POT ot.emd on minibatches + straight-line CFM loss (x_t=(1-t)x0+t*x1, u=x1-x0), which is trivially implementable in pure PyTorch. 5) Memory: 3000×25 is tiny, no risk. Decode step (3000×2500 sparse) is fine.

代码改动?这个节点的程序和父节点程序的逐行差别:绿色是新增,红色是删除。

这个节点没有程序版本(没有生成代码)

调研来源?调研员查到并用到的知识条目和文献检索结果(只列标题和编号)。

用到的知识库条目

编号标题出处
k034Flow matching and Schrödinger bridges offline: torchcfm (OT-CFM, SF2M), metric FM, DSBarXiv:2302.00482 (OT-CFM, Tong et al.); arXiv:2307.03672 ([SF]2M); arXiv:2405.14780 (metric flow matching); arXiv:2106.01357 (DSB)
k031Offline OT toolkit in the sandbox: moscot TemporalProblem, wot OTModel, POT, geomloss10.1038/s41586-024-08453-2 (moscot); 10.1016/j.cell.2019.01.006 (Waddington-OT)
k009Conditional / OT flow matching for population transportarXiv:2210.02747 (Lipman et al., Flow Matching for Generative Modeling)

计划里引用的来源

分析结果?分析员写的 ANALYSIS.json:改了什么、各组分数怎么变、假设是否成立、经验和下一步建议。

没有分析结果(ANALYSIS.json)。

对话摘要?每个角色和大模型对话的统计:轮数、工具调用、用时、token 数和最后的回答摘录;原始记录只给路径。

只给统计和最后回答的摘录;完整对话请到原始记录位置里列出的文件看。

工程师

角色?调研员写计划、工程师改代码、分析员解读分数、审查员检查作弊。工程师 alibaba-token-plan-cn/qwen3.8-max
调用次数1 次(失败 1 次)
轮数?大模型一共回复了几轮(每轮可以调用多个工具)。17
工具调用?大模型调用读文件、执行命令等工具的次数,按工具名统计。共 21 次:bash 16、edit 4、write 1
用时30 分
token 数?输入 / 输出(含思考)的 token 数,来自接口返回的用量。输入 39,410 · 输出 6,710 · 思考 6,966
任务(第一行)按计划修改程序:OT-CFM velocity field in PCA for E9.5→E10.5 extrapolation
最后的回答(摘录)
GENESPACE+α=0.5 → 49.06, beats zero control (48.32). Tuning α and κ.
原始记录位置?完整对话记录在 Spark 上的文件路径;看板不复制原始内容。/home/spark-longxinyang/vec/runs/formal/20261002-202908-search-t1-scr-D/nodes/6/engineer.jsonl 94 KB
/home/spark-longxinyang/vec/runs/formal/20261002-202908-search-t1-scr-D/nodes/6/engineer.stderr

调研员

角色调研员 alibaba-token-plan-cn/qwen3.8-max
调用次数1 次
轮数1
工具调用共 0 次:—
用时1 分
token 数输入 9,198 · 输出 1,447 · 思考 1,357
任务(第一行)为节点 n6(草稿,父节点 nNone)写改进计划 PLAN.json,思路 ot_cfm
最后的回答(摘录)
lowMatcher); integrate from E9.5 with damped Euler steps to predict E10.5.",
  "vs_constant_shift": "Velocity is a function of cell state x (and time t): two cells of the same type at different PCA positions receive different displacement vectors. Node 4 applies one EB-shrunk mean-difference vector per cell type to all cells of that type. Here, within-type velocity dispersion should be substantial and correlated with cell position, not zero.",
  "mechanism_evidence": "Engineer should report: (a) within-type standard deviation of the predicted displacement vectors (norm of v(x,1)*alpha) averaged over types; compare to between-type mean displacement. If within-type std < 10% of between-type, the field collapsed to per-type constants. (b) Pairwise cosine similarity of displacements within a type (should be < 0.9 if truly state-dependent). (c) Four-group score decomposition vs copy_last and vs node 4: specifically whether covariation improves relative to node 4 while cell_state remains competitive. (d) PCA variance ratio output/input per dimension to detect universal diffusion.",
  "mechanism_off_control": "Run the same script with --velocity_mode zero: skip training and integration, output = E9.5 cells decoded back (i.e., copy_last equivalent). Expected: score ≈ node 1 (47-49). Additionally --velocity_mode random: replace learned v with Gaussian noise matched to the trained field's output variance; expected: worse than learned field on direction/DE if the field learned meaningful structure, similar on covariation. If learned ≈ random, mechanism did not engage.",
  "sources": ["arXiv:2302.00482 — Tong et al., OT-CFM: ExactOptimalTransportConditionalFlowMatcher API, minibatch-OT pairing, conditional flow regression (used for torchcfm API and training recipe)", "arXiv:2210.02747 — Lipman et al., Flow Matching: straight-line conditional paths x_t=(1-t)x0+t*x1, target u=x1-x0, time-conditioned vector field (used for fallback manual implementation and conceptual framing)"]
}
原始记录位置/home/spark-longxinyang/vec/runs/formal/20261002-202908-search-t1-scr-D/nodes/6/researcher.jsonl 6 KB
/home/spark-longxinyang/vec/runs/formal/20261002-202908-search-t1-scr-D/nodes/6/researcher.stderr