Jesper Ferkinghoff-Borg
Publications
Measuring Black-Box Confidence via Reasoning Trajectories: Geometry, Coverage, and Verbalization
Reliable confidence estimation enables safe deployment of chain-of-thought (CoT) reasoning through text-only APIs. Yet the dominant black-box baseline, self-consistency over K samples, is linearly expensive and ignores the geometry of the trace. We propose a black-box trajectory-confidence score: we embed a CoT as a sliding-window trajectory and measure its convergence to external answer anchors with a one-parameter softmax. The method needs no logits, hidden states, or supervised calibrators. Across six (benchmark, reasoner) settings on MedQA-USMLE, GPQA Diamond, and MMLU-Pro with Gemini 3.1 Pro and Claude Sonnet 4.6, fusing this score with coverage and verbalized-confidence channels at K=4 yields Pareto improvements over self-consistency at K=8 in 6/6 settings (median AUC 0.78 vs 0.71, deltaAUC=+0.075). A fixed-pick control (+0.060) and E5 cross-embedder replication rule out answer switching and single-vendor artifacts. Geometry peaks in the penultimate window across benchmarks and reasoners, and inverts at the terminal window on GPQA Diamond. Three unscaffolded regimes separate black-box confidence into a judge-mediated Coverage prior (C), within-trace Geometry (G), and a conditional Verbalization channel (V). Across 18 benchmark x reasoner x proposer settings, C and G provide independent signal in 18/18 and 16/18, while V contributes residual signal in 6/18. Swapping the judge from GPT-5-mini to Claude Sonnet 4.6 leaves G-only AUC unchanged (|delta|<=0.013) and shifts C-only AUC by at most +/-0.02 (kappa=0.82). Fusion beats the best single channel in 17/18 settings (median AUC 0.78, max 0.92).
MechPert: Mechanistic Consensus as an Inductive Bias for Unseen Perturbation Prediction
Predicting transcriptional responses to unseen genetic perturbations is essential for understanding gene regulation and prioritizing large-scale perturbation experiments. Existing approaches either rely on static, potentially incomplete knowledge graphs, or prompt language models for functionally similar genes, retrieving associations shaped by symmetric co-occurrence in scientific text rather than directed regulatory logic. We introduce MechPert, a lightweight framework that encourages LLM agents to generate directed regulatory hypotheses rather than relying solely on functional similarity. Multiple agents independently propose candidate regulators with associated confidence scores; these are aggregated through a consensus mechanism that filters spurious associations, producing weighted neighborhoods for downstream prediction. We evaluate MechPert on Perturb-seq benchmarks across four human cell lines. For perturbation prediction in low-data regimes ($N=50$ observed perturbations), MechPert improves Pearson correlation by up to 10.5\% over similarity-based baselines. For experimental design, MechPert-selected anchor genes outperform standard network centrality heuristics by up to 46\% in well-characterized cell lines.