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Frédéric Cadet

Publications and source records attributed to Frédéric Cadet.

4 recordsLinked to original sources

Symmetry without a manifold: intrinsic dimension on orbits

The standard geometric derivation of neural scaling exponents takes the intrinsic dimension of a data manifold as its input. On modular addition in $\mathbb{Z}_p$ that derivation has no input. The exact algebraic solution is an orbit of $\mathbb{Z}_p$ acting by isometries. Transitivity alone makes the ratio statistic underlying the standard dimension estimator a point mass, so the estimator is undefined, and here the two nearest neighbour distances coincide exactly. Breaking the symmetry at scale $ε$ returns a number, but one that tracks $1/ε$ with no scale free plateau. We show that the failure is general, since on any finite orbit of a group acting by isometries the estimator reports the resolution at which the set is probed rather than a dimension. What replaces the power law is exponential in hidden width, $L(h)=L_\infty+A\exp(-c\,h^α)$, with $R^2$ between 0.982 and 0.995 against 0.857 to 0.906 for a power law admitting the same floor and fitted under the same protocol. Where the data supply is sufficient the rate belongs to the regulariser rather than to the group, since weight decay moves $c$ by a factor of 47 while group order moves it by 1.10, a residual below seed to seed resolution, for every fixed $α$ between 0.75 and 2. The critical width falls with group order rather than rising, against capacity counting that assigns a fixed number of neurons to each irreducible representation.

cs.LG↗

An Exactness Barrier for ZX-Calculus Optimization of Synthesized Clifford+T Circuits

Gate synthesis and circuit optimization are usually studied separately, and evidence on their interaction is contradictory: ZX-calculus rewriting removes a stable fraction of Solovay-Kitaev circuits, yet almost nothing from number-theoretically synthesized circuits. We show both behaviours follow from a single bound. For any optimizer that preserves the implemented element exactly--including all sound ZX rewriting with extraction--the achievable T-count is bounded below by the denominator exponent of the synthesized ring element. This exactness barrier is computable per instance and separates exact post-processing from approximation-aware resynthesis by a certified factor reaching 101x at recursion depth five. The two behaviours are then the barrier operating at different distances from the floor. For Solovay-Kitaev circuits we prove that the local ZX simplification layer (spider fusion and identity removal) computes exactly the free-product normal form of Z_2 * Z_8, giving exact per-instance compression and, under a calibrated ergodicity hypothesis, a depth-independent limit law confirmed on two independently constructed nets. For number-theoretically synthesized circuits the floor is already saturated: on single-qubit words automated ZX simplification attains it exactly, via a closed-form formula for minimal T-count in terms of phase linkage through the Z-axis normalizer. At two qubits and beyond the same valuation yields unconditional rigidity certificates, which on the quantum-Shannon-decomposition plus gridsynth pipeline certify 99.4-99.9% of the synthesized T-count as incompressible, with rigidity strengthening as accuracy tightens. This explains, and predicts the size of, the near-null optimization recently reported for that pipeline.

quant-ph↗

Using protein blocks to build custom fragment libraries from protein structures

The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous proteins but also in the recurrence of supersecondary motifs across unrelated proteins, underscoring the abundance and robustness of these structural units. Here, we present a novel pipeline for generating customized protein fragment libraries using protein blocks (PBs) - a structural alphabet that encodes local backbone conformations. Our method efficiently extracts structurally similar fragments from a curated, non-redundant protein structure database by converting three-dimensional structures into one-dimensional PB sequences. By integrating predicted PB sequences with the PB-ALIGN and PB-kPRED tools, our approach identifies relevant fragments independently of sequence homology. Fragment quality is further assessed using a new scoring function that combines secondary structure similarity and PB alignment metrics. The resulting libraries contain fragments of at least seven PBs (11 amino acid residues), covering over 70% of the local backbone structure. Our results demonstrate that PBs enable efficient mining of high-quality structural fragments from diverse protein spaces, including proteins with disordered regions. The pipeline is accessible as an online tool (PB-Frag, https://pbpred-us2b.univ-nantes.fr/pbfrag ).

q-bio.QM↗

A glance into the evolution of template-free protein structure prediction methodologies

Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure refinement protocols. A tremendous success has been witnessed in template-based modelling protocols, whereas strategies that involve template-free modelling still lag behind, specifically for larger proteins (> 150 a.a.). Various improvements have been observed in ab initio protein structure prediction methodologies overtime, with recent ones attributed to the usage of deep learning approaches to construct protein backbone structure from its amino acid sequence. This review highlights the major strategies undertaken for template-free modelling of protein structures while discussing few tools developed under each strategy. It will also briefly comment on the progress observed in the field of ab initio modelling of proteins over the course of time as seen through the evolution of CASP platform.

q-bio.QM↗