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Alessandro Micheli

Publications and source records attributed to Alessandro Micheli.

11 recordsLinked to original sources

Sequence-Informed Geometric Evaluation of RNA 3D Structures

Computational RNA structure pipelines generate many candidate conformations for the same sequence. Reliable evaluation therefore requires more than recognising plausible geometry, it requires determining whether that geometry is compatible with the sequence. We introduce SIRGE, a sequence-informed geometric evaluator that conditions structural representations on nucleotide embeddings from a pretrained RNA language model. Early results show that SIRGE outperforms established evaluators in Kendall--$\tau$ alignment, Top-1 selection, and Top-3 ranking. Controlled comparisons further show that sequence conditioning corrects errors made by an otherwise matched geometric model and improves target-level rank structure. These findings provide initial evidence that pretrained sequence representations supply ranking information that complements geometric reasoning.

q-bio.BM

Generative Modeling on Metric Graphs via Neural Optimal Transport

We introduce, to our knowledge, the first deep generative modeling framework for probability distributions continuously supported on compact metric graphs. Given source and target measures on a metric graph, our method embeds the graph into a smooth ambient space, solves an entropic Kantorovich problem via a neural semidual parameterization, and projects generated samples back onto the original graph. We study two embedded geometries: an extrinsic Euclidean realization and the intrinsic tropical Abel--Jacobi embedding into the Jacobian torus. In both cases, the resulting generator is graph-supported by construction. We prove that, in the joint limit of increasing neural expressivity, the learned generator converges weakly to a valid transport coupling between the original graph measures. Empirically, across a range of geometrically distinct graphs, our method matches or improves upon heuristic transport baselines based on discrete graph OT, while scaling more favorably. Finally, we demonstrate scalability on real-world urban mobility data by training our model on one million Uber pickup locations in Manhattan, New York City.

stat.ML

Entropic Riemannian Neural Optimal Transport

Many machine learning problems involve data supported on curved spaces such as spheres, rotation groups, hyperbolic spaces, and general Riemannian manifolds, where Euclidean geometry can distort distances, averages, and the resulting optimal transport (OT) problem. Existing manifold OT methods have pursued amortized out-of-sample maps, while entropic regularization has made discrete OT more scalable, but these advantages have remained largely disjoint. We propose Entropic Riemannian Neural Optimal Transport (Entropic RNOT), a unified framework that combines intrinsic entropic OT with amortized out-of-sample evaluation on Riemannian manifolds. Our method learns a single target-side Schrödinger potential through a neural pullback parameterization, recovers the induced Gibbs coupling, and uses the resulting conditional laws to construct intrinsic transport surrogates. These include barycentric projections on Cartan-Hadamard manifolds and heat-smoothed conditional surrogates on stochastically complete manifolds, the latter turning possibly atomic target laws into absolutely continuous ones. For fixed regularization $\varepsilon>0$, we prove that the proposed hypothesis class recovers the entropic optimal coupling in strong probabilistic metrics. As consequences, barycentric surrogates converge in $L^2$, while heat-smoothed surrogates are stable at fixed heat time and asymptotically unbiased as the heat time vanishes. The guarantees hold for compactly supported data on possibly noncompact manifolds. Empirically, our method matches or improves over Euclidean, tangent-space, and log-Euclidean baselines on benchmarks over $\mathbb{S}^2$, $\mathrm{SO}(3)$, $\mathrm{SPD}(3)$, $\mathrm{SE}(3)$, and $\mathbb{H}^2$, scales favorably relative to discrete manifold Sinkhorn, and in a protein-ligand docking application, refines poses on $\mathrm{SE}(3)$ without retraining or per-instance optimization.

stat.ML

Riemannian Neural Optimal Transport

Computational optimal transport (OT) offers a principled framework for generative modeling. Neural OT methods, which use neural networks to learn an OT map (or potential) from data in an amortized way, can be evaluated out of sample after training, but existing approaches are tailored to Euclidean geometry. Extending neural OT to high-dimensional Riemannian manifolds remains an open challenge. In this paper, we prove that any method for OT on manifolds that produces discrete approximations of transport maps necessarily suffers from the curse of dimensionality: achieving a fixed accuracy requires a number of parameters that grows exponentially with the manifold dimension. Motivated by this limitation, we introduce Riemannian Neural OT (RNOT) maps, which are continuous neural-network parameterizations of OT maps on manifolds that avoid discretization and incorporate geometric structure by construction. Under mild regularity assumptions, we prove that RNOT maps approximate Riemannian OT maps with sub-exponential complexity in the dimension. Experiments on synthetic and real datasets demonstrate improved scalability and competitive performance relative to discretization-based baselines.

cs.LG

NeuralSurv: Deep Survival Analysis with Bayesian Uncertainty Quantification

We introduce NeuralSurv, the first deep survival model to incorporate Bayesian uncertainty quantification. Our non-parametric, architecture-agnostic framework captures time-varying covariate-risk relationships in continuous time via a novel two-stage data-augmentation scheme, for which we establish theoretical guarantees. For efficient posterior inference, we introduce a mean-field variational algorithm with coordinate-ascent updates that scale linearly in model size. By locally linearizing the Bayesian neural network, we obtain full conjugacy and derive all coordinate updates in closed form. In experiments, NeuralSurv delivers superior calibration compared to state-of-the-art deep survival models, while matching or exceeding their discriminative performance across both synthetic benchmarks and real-world datasets. Our results demonstrate the value of Bayesian principles in data-scarce regimes by enhancing model calibration and providing robust, well-calibrated uncertainty estimates for the survival function.

cs.LG

Diffusion Models for Inverse Problems in the Exponential Family

Diffusion models have emerged as powerful tools for solving inverse problems, yet prior work has primarily focused on observations with Gaussian measurement noise, restricting their use in real-world scenarios. This limitation persists due to the intractability of the likelihood score, which until now has only been approximated in the simpler case of Gaussian likelihoods. In this work, we extend diffusion models to handle inverse problems where the observations follow a distribution from the exponential family, such as a Poisson or a Binomial distribution. By leveraging the conjugacy properties of exponential family distributions, we introduce the evidence trick, a method that provides a tractable approximation to the likelihood score. In our experiments, we demonstrate that our methodology effectively performs Bayesian inference on spatially inhomogeneous Poisson processes with intensities as intricate as ImageNet images. Furthermore, we demonstrate the real-world impact of our methodology by showing that it performs competitively with the current state-of-the-art in predicting malaria prevalence estimates in Sub-Saharan Africa.

stat.ML

Deep Reinforcement Learning for Online Optimal Execution Strategies

This paper tackles the challenge of learning non-Markovian optimal execution strategies in dynamic financial markets. We introduce a novel actor-critic algorithm based on Deep Deterministic Policy Gradient (DDPG) to address this issue, with a focus on transient price impact modeled by a general decay kernel. Through numerical experiments with various decay kernels, we show that our algorithm successfully approximates the optimal execution strategy. Additionally, the proposed algorithm demonstrates adaptability to evolving market conditions, where parameters fluctuate over time. Our findings also show that modern reinforcement learning algorithms can provide a solution that reduces the need for frequent and inefficient human intervention in optimal execution tasks.

cs.LG

Fast and Slow Optimal Trading with Exogenous Information

We consider a stochastic game between a slow institutional investor and a high-frequency trader who are trading a risky asset and their aggregated order-flow impacts the asset price. We model this system by means of two coupled stochastic control problems, in which the high-frequency trader exploits the available information on a price predicting signal more frequently, but is also subject to periodic "end of day" inventory constraints. We first derive the optimal strategy of the high-frequency trader given any admissible strategy of the institutional investor. Then, we solve the problem of the institutional investor given the optimal signal-adaptive strategy of the high-frequency trader, in terms of the resolvent of a Fredholm integral equation, thus establishing the unique multi-period Stackelberg equilibrium of the game. Our results provide an explicit solution to the game, which shows that the high-frequency trader can adopt either predatory or cooperative strategies in each period, depending on the tradeoff between the order-flow and the trading signal. We also show that the institutional investor's strategy is considerably more profitable when the order-flow of the high-frequency trader is taken into account in her trading strategy.

q-fin.TR

Closed-Loop Nash Competition for Liquidity

We study a multi-player stochastic differential game, where agents interact through their joint price impact on an asset that they trade to exploit a common trading signal. In this context, we prove that a closed-loop Nash equilibrium exists if the price impact parameter is small enough. Compared to the corresponding open-loop Nash equilibrium, both the agents' optimal trading rates and their performance move towards the central-planner solution, in that excessive trading due to lack of coordination is reduced. However, the size of this effect is modest for plausible parameter values.

q-fin.MF

Evidence of Crowding on Russell 3000 Reconstitution Events

We develop a methodology which replicates in great accuracy the FTSE Russell indexes reconstitutions, including the quarterly rebalancings due to new initial public offerings (IPOs). While using only data available in the CRSP US Stock database for our index reconstruction, we demonstrate the accuracy of this methodology by comparing it to the original Russell US indexes for the time period between 1989 to 2019. A python package that generates the replicated indexes is also provided. As an application, we use our index reconstruction protocol to compute the permanent and temporary price impact on the Russell 3000 annual additions and deletions, and on the quarterly additions of new IPOs . We find that the index portfolios following the Russell 3000 index and rebalanced on an annual basis are overall more crowded than those following the index on a quarterly basis. This phenomenon implies that transaction costs of indexing strategies could be significantly reduced by buying new IPOs additions in proximity to quarterly rebalance dates.

q-fin.TR

Higgs self-coupling measurements using deep learning in the $b\bar{b}b\bar{b}$ final state

Measuring the Higgs trilinear self-coupling $λ_{hhh}$ is experimentally demanding but fundamental for understanding the shape of the Higgs potential. We present a comprehensive analysis strategy for the HL-LHC using di-Higgs events in the four $b$-quark channel ($hh \to 4b$), extending current methods in several directions. We perform deep learning to suppress the formidable multijet background with dedicated optimisation for BSM $λ_{hhh}$ scenarios. We compare the $λ_{hhh}$ constraining power of events using different multiplicities of large radius jets with a two-prong structure that reconstruct boosted $h \to bb$ decays. We show that current uncertainties in the SM top Yukawa coupling $y_t$ can modify $λ_{hhh}$ constraints by $\sim 20\%$. For SM $y_t$, we find prospects of $-0.8 < λ_{hhh} / λ_{hhh}^\text{SM} < 6.6$ at 68% CL under simplified assumptions for 3000~fb$^{-1}$ of HL-LHC data. Our results provide a careful assessment of di-Higgs identification and machine learning techniques for all-hadronic measurements of the Higgs self-coupling and sharpens the requirements for future improvement.

hep-ph