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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 |
|---|---|---|
| k034 | Flow matching and Schrödinger bridges offline: torchcfm (OT-CFM, SF2M), metric FM, DSB | arXiv:2302.00482 (OT-CFM, Tong et al.); arXiv:2307.03672 ([SF]2M); arXiv:2405.14780 (metric flow matching); arXiv:2106.01357 (DSB) |
| k031 | Offline OT toolkit in the sandbox: moscot TemporalProblem, wot OTModel, POT, geomloss | 10.1038/s41586-024-08453-2 (moscot); 10.1016/j.cell.2019.01.006 (Waddington-OT) |
| k009 | Conditional / OT flow matching for population transport | arXiv:2210.02747 (Lipman et al., Flow Matching for Generative Modeling) |
计划里引用的来源
- 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)
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 |