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Jesper Ferkinghoff-Borg

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Artificial Intelligence Biomolecules cond-mat.stat-mech physics.geo-ph

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preprint2026arXiv

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).

preprint2010arXiv

Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized

Understanding protein structure is of crucial importance in science, medicine and biotechnology. For about two decades, knowledge based potentials based on pairwise distances -- so-called "potentials of mean force" (PMFs) -- have been center stage in the prediction and design of protein structure and the simulation of protein folding. However, the validity, scope and limitations of these potentials are still vigorously debated and disputed, and the optimal choice of the reference state -- a necessary component of these potentials -- is an unsolved problem. PMFs are loosely justified by analogy to the reversible work theorem in statistical physics, or by a statistical argument based on a likelihood function. Both justifications are insightful but leave many questions unanswered. Here, we show for the first time that PMFs can be seen as approximations to quantities that do have a rigorous probabilistic justification: they naturally arise when probability distributions over different features of proteins need to be combined. We call these quantities reference ratio distributions deriving from the application of the reference ratio method. This new view is not only of theoretical relevance, but leads to many insights that are of direct practical use: the reference state is uniquely defined and does not require external physical insights; the approach can be generalized beyond pairwise distances to arbitrary features of protein structure; and it becomes clear for which purposes the use of these quantities is justified. We illustrate these insights with two applications, involving the radius of gyration and hydrogen bonding. In the latter case, we also show how the reference ratio method can be iteratively applied to sculpt an energy funnel. Our results considerably increase the understanding and scope of energy functions derived from known biomolecular structures.

preprint2004arXiv

Dynamics of Crystal Formation in the Greenland NorthGRIP Ice Core

The North Greenland Ice Core Project (NorthGRIP) provides paleoclimatic information back to at about 120 kyr before present (Dahl-Jensen and others, 2002). Each year, precipitation on the ice sheet covers it with a new layer of snow, which gradually transforms into ice crystals as the layer sinks into the ice sheet. The size distribution of ice crystals has been measured at selected depths in the upper 880 m of the NorthGRIP ice core (Svensson and others, 2003b), which covers a time span of 5300 years. The distributions change with time toward a universal curve, indicating a common underlying physical process in the formation of crystals. We identify this process as an interplay between fragmentation of the crystals and diffusion of their grain boundaries. The process is described by a two-parameter differential equation to which we obtain the exact solution. The solution is in excellent agreement with the experimentally observed distributions.