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Molecular Embedding-Based Algorithm Selection in Protein-Ligand Docking

arXiv.org Artificial Intelligence

Selecting an effective docking algorithm is highly context-dependent, and no single method performs reliably across structural, chemical, or protocol regimes. We introduce MolAS, a lightweight algorithm selection system that predicts per-algorithm performance from pretrained protein-ligand embeddings using attentional pooling and a shallow residual decoder. With only hundreds to a few thousand labelled complexes, MolAS achieves up to 15% absolute improvement over the single-best solver (SBS) and closes 17-66% of the Virtual Best Solver (VBS)-SBS gap across five diverse docking benchmarks. Analyses of reliability, embedding geometry, and solver-selection patterns show that MolAS succeeds when the oracle landscape exhibits low entropy and separable solver behaviour, but collapses under protocol-induced hierarchy shifts. These findings indicate that the main barrier to robust docking AS is not representational capacity but instability in solver rankings across pose-generation regimes, positioning MolAS as both a practical in-domain selector and a diagnostic tool for assessing when AS is feasible.



MASPRM: Multi-Agent System Process Reward Model

arXiv.org Artificial Intelligence

Practical deployment of Multi-Agent Systems (MAS) demands strong test-time performance, motivating methods that guide inference-time search and selectively spend compute to improve quality. We present the Multi-Agent System Process Reward Model (MASPRM). It assigns per-action, per-agent values to partial inter-agent transcripts and acts as an inference-time controller. MASPRM is trained from multi-agent Monte Carlo Tree Search (MCTS) rollouts without requiring step-level human annotations, by propagating returns to local targets. At inference, MASPRM guides step-level beam search and MCTS, focusing computation on promising branches and pruning early. On GSM8K and MATH, MASPRM-guided decoding with an outcome reward model (ORM) applied to the final answer, improves exact match (EM) over a single straight-through MAS pass by $+30.7$ and $+22.9$ points, respectively. A MASPRM trained on GSM8K transfers zero-shot to MATH without retraining, adding $8.4$ EM points at the same budget. MASPRM is a plug-in value model that estimates per-agent progress and complements verifier-style decoders, enabling more reliable, compute-aware multi-agent reasoning. Code: https://github.com/milad1378yz/MASPRM


Learning for Cross-Layer Resource Allocation in MEC-Aided Cell-Free Networks

arXiv.org Artificial Intelligence

Cross-layer resource allocation over mobile edge computing (MEC)-aided cell-free networks can sufficiently exploit the transmitting and computing resources to promote the data rate. However, the technical bottlenecks of traditional methods pose significant challenges to cross-layer optimization. In this paper, joint subcarrier allocation and beamforming optimization are investigated for the MEC-aided cell-free network from the perspective of deep learning to maximize the weighted sum rate. Specifically, we convert the underlying problem into a joint multi-task optimization problem and then propose a centralized multi-task self-supervised learning algorithm to solve the problem so as to avoid costly manual labeling. Therein, two novel and general loss functions, i.e., negative fraction linear loss and exponential linear loss whose advantages in robustness and target domain have been proved and discussed, are designed to enable self-supervised learning. Moreover, we further design a MEC-enabled distributed multi-task self-supervised learning (DMTSSL) algorithm, with low complexity and high scalability to address the challenge of dimensional disaster. Finally, we develop the distance-aware transfer learning algorithm based on the DMTSSL algorithm to handle the dynamic scenario with negligible computation cost. Simulation results under $3$rd generation partnership project 38.901 urban-macrocell scenario demonstrate the superiority of the proposed algorithms over the baseline algorithms.


SANDWICH: Towards an Offline, Differentiable, Fully-Trainable Wireless Neural Ray-Tracing Surrogate

arXiv.org Artificial Intelligence

Wireless ray-tracing (RT) is emerging as a key tool for three-dimensional (3D) wireless channel modeling, driven by advances in graphical rendering. Current approaches struggle to accurately model beyond 5G (B5G) network signaling, which often operates at higher frequencies and is more susceptible to environmental conditions and changes. Existing online learning solutions require real-time environmental supervision during training, which is both costly and incompatible with GPU-based processing. In response, we propose a novel approach that redefines ray trajectory generation as a sequential decision-making problem, leveraging generative models to jointly learn the optical, physical, and signal properties within each designated environment. Our work introduces the Scene-Aware Neural Decision Wireless Channel Raytracing Hierarchy (SANDWICH), an innovative offline, fully differentiable approach that can be trained entirely on GPUs. SANDWICH offers superior performance compared to existing online learning methods, outperforms the baseline by 4e^-2 radian in RT accuracy, and only fades 0.5 dB away from toplined channel gain estimation.


Reviews: Designing by Training: Acceleration Neural Network for Fast High-Dimensional Convolution

Neural Information Processing Systems

I am happy with the responses they have provided to my initial concerns which have improved the manuscript. I would encourage authors to add an appendix should they believe they can convey a more complete message without having to wait for drafting another another longer manuscript. They utilise the new Acceleration Network (AccNet) to express the approximation function of splatting/blurring/slicing (SBS) and generalise SBS by changing the architecture of AccNet. Upon finishing the training process, the proposed fast convolution algorithm can be derived from the weights and activation functions of each layer. They conducted various experiments that prove the effectiveness of the proposed algorithm.


Take a Step and Reconsider: Sequence Decoding for Self-Improved Neural Combinatorial Optimization

arXiv.org Artificial Intelligence

The constructive approach within Neural Combinatorial Optimization (NCO) treats a combinatorial optimization problem as a finite Markov decision process, where solutions are built incrementally through a sequence of decisions guided by a neural policy network. To train the policy, recent research is shifting toward a 'self-improved' learning methodology that addresses the limitations of reinforcement learning and supervised approaches. Here, the policy is iteratively trained in a supervised manner, with solutions derived from the current policy serving as pseudo-labels. The way these solutions are obtained from the policy determines the quality of the pseudo-labels. In this paper, we present a simple and problem-independent sequence decoding method for self-improved learning based on sampling sequences without replacement. We incrementally follow the best solution found and repeat the sampling process from intermediate partial solutions. By modifying the policy to ignore previously sampled sequences, we force it to consider only unseen alternatives, thereby increasing solution diversity. Experimental results for the Traveling Salesman and Capacitated Vehicle Routing Problem demonstrate its strong performance. Furthermore, our method outperforms previous NCO approaches on the Job Shop Scheduling Problem.


Identifying Easy Instances to Improve Efficiency of ML Pipelines for Algorithm-Selection

arXiv.org Artificial Intelligence

Algorithm-selection (AS) methods are essential in order to obtain the best performance from a portfolio of solvers over large sets of instances. However, many AS methods rely on an analysis phase, e.g. where features are computed by sampling solutions and used as input in a machine-learning model. For AS to be efficient, it is therefore important that this analysis phase is not computationally expensive. We propose a method for identifying easy instances which can be solved quickly using a generalist solver without any need for algorithm-selection. This saves computational budget associated with feature-computation which can then be used elsewhere in an AS pipeline, e.g., enabling additional function evaluations on hard problems. Experiments on the BBOB dataset in two settings (batch and streaming) show that identifying easy instances results in substantial savings in function evaluations. Re-allocating the saved budget to hard problems provides gains in performance compared to both the virtual best solver (VBS) computed with the original budget, the single best solver (SBS) and a trained algorithm-selector.


On Constructing Algorithm Portfolios in Algorithm Selection for Computationally Expensive Black-box Optimization in the Fixed-budget Setting

arXiv.org Artificial Intelligence

Feature-based offline algorithm selection has shown its effectiveness in a wide range of optimization problems, including the black-box optimization problem. An algorithm selection system selects the most promising optimizer from an algorithm portfolio, which is a set of pre-defined optimizers. Thus, algorithm selection requires a well-constructed algorithm portfolio consisting of efficient optimizers complementary to each other. Although construction methods for the fixed-target setting have been well studied, those for the fixed-budget setting have received less attention. Here, the fixed-budget setting is generally used for computationally expensive optimization, where a budget of function evaluations is small. In this context, first, this paper points out some undesirable properties of experimental setups in previous studies. Then, this paper argues the importance of considering the number of function evaluations used in the sampling phase when constructing algorithm portfolios, whereas the previous studies ignored that. The results show that algorithm portfolios constructed by our approach perform significantly better than those by the previous approach.


Stein Boltzmann Sampling: A Variational Approach for Global Optimization

arXiv.org Machine Learning

In this paper, we introduce a new flow-based method for global optimization of Lipschitz functions, called Stein Boltzmann Sampling (SBS). Our method samples from the Boltzmann distribution that becomes asymptotically uniform over the set of the minimizers of the function to be optimized. Candidate solutions are sampled via the \emph{Stein Variational Gradient Descent} algorithm. We prove the asymptotic convergence of our method, introduce two SBS variants, and provide a detailed comparison with several state-of-the-art global optimization algorithms on various benchmark functions. The design of our method, the theoretical results, and our experiments, suggest that SBS is particularly well-suited to be used as a continuation of efficient global optimization methods as it can produce better solutions while making a good use of the budget.