Recent advances in protein backbone generation have achieved promising results under structural, functional, or physical constraints. However, existing methods lack the flexibility for precise topology control, limiting navigation of the backbone space. We present ProtPainter, a diffusion-based approach for generating protein backbones conditioned on 3D curves. ProtPainter follows a two-stage process: curve-based sketching and sketch-guided backbone generation. For the first stage, we propose CurveEncoder, which predicts secondary structure annotations from a curve to parametrize sketch generation. For the second stage, the sketch guides the generative process in Denoising Diffusion Probabilistic Modeling (DDPM) to generate backbones. During this process, we further introduce a fusion scheduling scheme, Helix-Gating, to control the scaling factors. To evaluate, we propose the first benchmark for topology-conditioned protein generation, introducing Protein Restoration Task and a new metric, self-consistency Topology Fitness (scTF). Experiments demonstrate ProtPainter's ability to generate topology-fit (scTF > 0.8) and designable (scTM > 0.5) backbones, with drawing and dragging tasks showcasing its flexibility and versatility.

Prompt learning is a popular fine-tuning method for vision-language models due to its efficiency. It requires a small number of additional learnable parameters while significantly enhancing performance on target tasks. However, most existing methods suffer from overfitting to fine-tuning data, yielding poor generalizability. To address this, we propose a new training objective function based on a Bayesian learning principle to balance adaptability and generalizability. We derive a prior over the logits, where the mean function is parameterized by the pre-trained model, while the posterior corresponds to the fine-tuned model. This objective establishes a balance by allowing the fine-tuned model to adapt to downstream tasks while remaining close to the pre-trained model.

Modern society is full of computational challenges that rely on probabilistic reasoning, statistics, and combinatorics. Interestingly, many of these questions can be formulated by encoding them into propositional formulas and then asking for its number of models. With a growing interest in practical problem-solving for tasks that involve model counting, the community established the Model Counting (MC) Competition in fall of 2019 with its first iteration in 2020. The competition aims at advancing applications, identifying challenging benchmarks, fostering new solver development, and enhancing existing solvers for model counting problems and their variants. The first iteration, brought together various researchers, identified challenges, and inspired numerous new applications. In this paper, we present a comprehensive overview of the 2021-2023 iterations of the Model Counting Competition. We detail its execution and outcomes. The competition comprised four tracks, each focusing on a different variant of the model counting problem. The first track centered on the model counting problem (MC), which seeks the count of models for a given propositional formula. The second track challenged developers to submit programs capable of solving the weighted model counting problem (WMC). The third track was dedicated to projected model counting (PMC). Finally, we initiated a track that combined projected and weighted model counting (PWMC). The competition continued with a high level of participation, with seven to nine solvers submitted in various different version and based on quite diverging techniques.

Causal analysis plays a foundational role in scientific discovery and reliable decision-making, yet it remains largely inaccessible to domain experts due to its conceptual and algorithmic complexity. This disconnect between causal methodology and practical usability presents a dual challenge: domain experts are unable to leverage recent advances in causal learning, while causal researchers lack broad, real-world deployment to test and refine their methods. To address this, we introduce Causal-Copilot, an autonomous agent that operationalizes expert-level causal analysis within a large language model framework. Causal-Copilot automates the full pipeline of causal analysis for both tabular and time-series data -- including causal discovery, causal inference, algorithm selection, hyperparameter optimization, result interpretation, and generation of actionable insights. It supports interactive refinement through natural language, lowering the barrier for non-specialists while preserving methodological rigor. By integrating over 20 state-of-the-art causal analysis techniques, our system fosters a virtuous cycle -- expanding access to advanced causal methods for domain experts while generating rich, real-world applications that inform and advance causal theory. Empirical evaluations demonstrate that Causal-Copilot achieves superior performance compared to existing baselines, offering a reliable, scalable, and extensible solution that bridges the gap between theoretical sophistication and real-world applicability in causal analysis. A live interactive demo of Causal-Copilot is available at https://causalcopilot.com/.

A wide range of LM applications require generating text that conforms to syntactic or semantic constraints. Imposing such constraints can be naturally framed as probabilistic conditioning, but exact generation from the resulting distribution -- which can differ substantially from the LM's base distribution -- is generally intractable. In this work, we develop an architecture for controlled LM generation based on sequential Monte Carlo (SMC). Our SMC framework allows us to flexibly incorporate domain- and problem-specific constraints at inference time, and efficiently reallocate computational resources in light of new information during the course of generation. By comparing to a number of alternatives and ablations on four challenging domains -- Python code generation for data science, text-to-SQL, goal inference, and molecule synthesis -- we demonstrate that, with little overhead, our approach allows small open-source language models to outperform models over 8x larger, as well as closed-source, fine-tuned ones. In support of the probabilistic perspective, we show that these performance improvements are driven by better approximation to the posterior distribution. Our system builds on the framework of Lew et al. (2023) and integrates with its language model probabilistic programming language, giving users a simple, programmable way to apply SMC to a broad variety of controlled generation problems.

We propose a scalable, approximate inference hypernetwork framework for a general model of history-dependent processes. The flexible data model is based on a neural ordinary differential equation (NODE) representing the evolution of internal states together with a trainable observation model subcomponent. The posterior distribution corresponding to the data model parameters (weights and biases) follows a stochastic differential equation with a drift term related to the score of the posterior that is learned jointly with the data model parameters. This Langevin sampling approach offers flexibility in balancing the computational budget between the evaluation cost of the data model and the approximation of the posterior density of its parameters. We demonstrate performance of the hypernetwork on chemical reaction and material physics data and compare it to mean-field variational inference.

The goal of Computer Adaptive Testing (CAT) is to reliably estimate an individual's ability as modeled by an item response theory (IRT) instrument using only a subset of the instrument's items. A secondary goal is to vary the items presented across different testing sessions so that the sequence of items does not become overly stereotypical -- we want all items to have an exposure rate sufficiently far from zero. We formulate the optimization problem for CAT in terms of Bayesian information theory, where one chooses the item at each step based on the criterion of the ability model discrepancy -- the statistical distance between the ability estimate at the next step and the full-test ability estimate. This viewpoint of CAT naturally motivates a stochastic selection procedure that equates choosing the next item to sampling from a model-averaging ensemble ability model. Using the NIH Work Disability Functional Assessment Battery (WD-FAB), we evaluate our new methods in comparison to pre-existing methods found in the literature. We find that our stochastic selector has superior properties in terms of both item exposure and test accuracy/efficiency.

Bayesian Federated Learning (BFL) enables uncertainty quantification and robust adaptation in distributed learning. In contrast to the frequentist approach, it estimates the posterior distribution of a global model, offering insights into model reliability. However, current BFL methods neglect continual learning challenges in dynamic environments where data distributions shift over time. We propose a continual BFL framework applied to human sensing with radar data collected over several days. Using Stochastic Gradient Langevin Dynamics (SGLD), our approach sequentially updates the model, leveraging past posteriors to construct the prior for the new tasks. We assess the accuracy, the expected calibration error (ECE) and the convergence speed of our approach against several baselines. Results highlight the effectiveness of continual Bayesian updates in preserving knowledge and adapting to evolving data.

Biological synapses effortlessly balance memory retention and flexibility, yet artificial neural networks still struggle with the extremes of catastrophic forgetting and catastrophic remembering. Here, we introduce Metaplasticity from Synaptic Uncertainty (MESU), a Bayesian framework that updates network parameters according their uncertainty. This approach allows a principled combination of learning and forgetting that ensures that critical knowledge is preserved while unused or outdated information is gradually released. Unlike standard Bayesian approaches -- which risk becoming overly constrained, and popular continual-learning methods that rely on explicit task boundaries, MESU seamlessly adapts to streaming data. It further provides reliable epistemic uncertainty estimates, allowing out-of-distribution detection, the only computational cost being to sample the weights multiple times to provide proper output statistics. Experiments on image-classification benchmarks demonstrate that MESU mitigates catastrophic forgetting, while maintaining plasticity for new tasks. When training 200 sequential permuted MNIST tasks, MESU outperforms established continual learning techniques in terms of accuracy, capability to learn additional tasks, and out-of-distribution data detection. Additionally, due to its non-reliance on task boundaries, MESU outperforms conventional learning techniques on the incremental training of CIFAR-100 tasks consistently in a wide range of scenarios. Our results unify ideas from metaplasticity, Bayesian inference, and Hessian-based regularization, offering a biologically-inspired pathway to robust, perpetual learning.

Causality and game theory are two influential fields that contribute significantly to decision-making in various domains. Causality defines and models causal relationships in complex policy problems, while game theory provides insights into strategic interactions among stakeholders with competing interests. Integrating these frameworks has led to significant theoretical advancements with the potential to improve decision-making processes. However, practical applications of these developments remain underexplored. To support efforts toward implementation, this paper clarifies key concepts in game theory and causality that are essential to their intersection, particularly within the context of probabilistic graphical models. By rigorously examining these concepts and illustrating them with intuitive, consistent examples, we clarify the required inputs for implementing these models, provide practitioners with insights into their application and selection across different scenarios, and reference existing research that supports their implementation. We hope this work encourages broader adoption of these models in real-world scenarios.