Daily Papers

Assessing whether a molecule can be synthesised is a primary task in drug discovery. It enables computational chemists to filter for viable compounds or bias molecular generative models. The notion of synthesisability is dynamic as it evolves depending on the availability of key compounds. A common approach in drug discovery involves exploring the chemical space surrounding synthetically-accessible intermediates. This strategy improves the synthesisability of the derived molecules due to the availability of key intermediates. Existing synthesisability scoring methods such as SAScore, SCScore and RAScore, cannot condition on intermediates dynamically. Our approach, Leap, is a GPT-2 model trained on the depth, or longest linear path, of predicted synthesis routes that allows information on the availability of key intermediates to be included at inference time. We show that Leap surpasses all other scoring methods by at least 5% on AUC score when identifying synthesisable molecules, and can successfully adapt predicted scores when presented with a relevant intermediate compound.

Given a graph, the shortest-path problem requires finding a sequence of edges with minimum cumulative length that connects a source vertex to a target vertex. We consider a variant of this classical problem in which the position of each vertex in the graph is a continuous decision variable constrained in a convex set, and the length of an edge is a convex function of the position of its endpoints. Problems of this form arise naturally in many areas, from motion planning of autonomous vehicles to optimal control of hybrid systems. The price for such a wide applicability is the complexity of this problem, which is easily seen to be NP-hard. Our main contribution is a strong and lightweight mixed-integer convex formulation based on perspective operators, that makes it possible to efficiently find globally optimal paths in large graphs and in high-dimensional spaces.

We perform an empirical study of the behaviour of deep networks when fully linearizing some of its feature channels through a sparsity prior on the overall number of nonlinear units in the network. In experiments on image classification and machine translation tasks, we investigate how much we can simplify the network function towards linearity before performance collapses. First, we observe a significant performance gap when reducing nonlinearity in the network function early on as opposed to late in training, in-line with recent observations on the time-evolution of the data-dependent NTK. Second, we find that after training, we are able to linearize a significant number of nonlinear units while maintaining a high performance, indicating that much of a network's expressivity remains unused but helps gradient descent in early stages of training. To characterize the depth of the resulting partially linearized network, we introduce a measure called average path length, representing the average number of active nonlinearities encountered along a path in the network graph. Under sparsity pressure, we find that the remaining nonlinear units organize into distinct structures, forming core-networks of near constant effective depth and width, which in turn depend on task difficulty.

The presence of linear paths in parameter space between two different network solutions in certain cases, i.e., linear mode connectivity (LMC), has garnered interest from both theoretical and practical fronts. There has been significant research that either practically designs algorithms catered for connecting networks by adjusting for the permutation symmetries as well as some others that more theoretically construct paths through which networks can be connected. Yet, the core reasons for the occurrence of LMC, when in fact it does occur, in the highly non-convex loss landscapes of neural networks are far from clear. In this work, we take a step towards understanding it by providing a model of how the loss landscape needs to behave topographically for LMC (or the lack thereof) to manifest. Concretely, we present a `mountainside and ridge' perspective that helps to neatly tie together different geometric features that can be spotted in the loss landscape along the training runs. We also complement this perspective by providing a theoretical analysis of the barrier height, for which we provide empirical support, and which additionally extends as a faithful predictor of layer-wise LMC. We close with a toy example that provides further intuition on how barriers arise in the first place, all in all, showcasing the larger aim of the work -- to provide a working model of the landscape and its topography for the occurrence of LMC.

The paper proposes a novel machine learning-based approach to the pathfinding problem on extremely large graphs. This method leverages diffusion distance estimation via a neural network and uses beam search for pathfinding. We demonstrate its efficiency by finding solutions for 4x4x4 and 5x5x5 Rubik's cubes with unprecedentedly short solution lengths, outperforming all available solvers and introducing the first machine learning solver beyond the 3x3x3 case. In particular, it surpasses every single case of the combined best results in the Kaggle Santa 2023 challenge, which involved over 1,000 teams. For the 3x3x3 Rubik's cube, our approach achieves an optimality rate exceeding 98%, matching the performance of task-specific solvers and significantly outperforming prior solutions such as DeepCubeA (60.3%) and EfficientCube (69.6%). Additionally, our solution is more than 26 times faster in solving 3x3x3 Rubik's cubes while requiring up to 18.5 times less model training time than the most efficient state-of-the-art competitor.

Linear bandits have long been a central topic in online learning, with applications ranging from recommendation systems to adaptive clinical trials. Their general learnability has been established when the objective is to minimise the inner product between a cost parameter and the decision variable. While this is highly general, this reliance on an inner product structure belies the name of linear bandits, and fails to account for problems such as Optimal Transport. Using the Kantorovich formulation of Optimal Transport as an example, we show that an inner product structure is not necessary to achieve efficient learning in linear bandits. We propose a refinement of the classical OFUL algorithm that operates by embedding the action set into a Hilbertian subspace, where confidence sets can be built via least-squares estimation. Actions are then constrained to this subspace by penalising optimism. The analysis is completed by leveraging convergence results from penalised (entropic) transport to the Kantorovich problem. Up to this approximation term, the resulting algorithm achieves the same trajectorial regret upper bounds as the OFUL algorithm, which we turn into worst-case regret using functional regression techniques. Its regret interpolates between mathcal O(T) and {mathcal O}(T), depending on the regularity of the cost function, and recovers the parametric rate mathcal O(dT) in finite-dimensional settings.

We present a fast algorithm for the design of smooth paths (or trajectories) that are constrained to lie in a collection of axis-aligned boxes. We consider the case where the number of these safe boxes is large, and basic preprocessing of them (such as finding their intersections) can be done offline. At runtime we quickly generate a smooth path between given initial and terminal positions. Our algorithm designs trajectories that are guaranteed to be safe at all times, and detects infeasibility whenever such a trajectory does not exist. Our algorithm is based on two subproblems that we can solve very efficiently: finding a shortest path in a weighted graph, and solving (multiple) convex optimal-control problems. We demonstrate the proposed path planner on large-scale numerical examples, and we provide an efficient open-source software implementation, fastpathplanning.

Large language models (LLMs) are powerful tools but are often expensive to deploy at scale. LLM query routing mitigates this by dynamically assigning queries to models of varying cost and quality to obtain a desired trade-off. Prior query routing approaches generate only one response from the selected model and a single response from a small (inexpensive) model was often not good enough to beat a response from a large (expensive) model due to which they end up overusing the large model and missing out on potential cost savings. However, it is well known that for small models, generating multiple responses and selecting the best can enhance quality while remaining cheaper than a single large-model response. We leverage this idea to propose BEST-Route, a novel routing framework that chooses a model and the number of responses to sample from it based on query difficulty and the quality thresholds. Experiments on real-world datasets demonstrate that our method reduces costs by up to 60% with less than 1% performance drop.

It has recently been conjectured that neural network solution sets reachable via stochastic gradient descent (SGD) are convex, considering permutation invariances (Entezari et al., 2022). This means that a linear path can connect two independent solutions with low loss, given the weights of one of the models are appropriately permuted. However, current methods to test this theory often require very wide networks to succeed. In this work, we conjecture that more generally, the SGD solution set is a "star domain" that contains a "star model" that is linearly connected to all the other solutions via paths with low loss values, modulo permutations. We propose the Starlight algorithm that finds a star model of a given learning task. We validate our claim by showing that this star model is linearly connected with other independently found solutions. As an additional benefit of our study, we demonstrate better uncertainty estimates on the Bayesian Model Averaging over the obtained star domain. Further, we demonstrate star models as potential substitutes for model ensembles. Our code is available at https://github.com/aktsonthalia/starlight.

We give a deterministic O(mlog^{2/3}n)-time algorithm for single-source shortest paths (SSSP) on directed graphs with real non-negative edge weights in the comparison-addition model. This is the first result to break the O(m+nlog n) time bound of Dijkstra's algorithm on sparse graphs, showing that Dijkstra's algorithm is not optimal for SSSP.

Autonomous driving is a key technology towards a brighter, more sustainable future. To enable such a future, it is necessary to utilize autonomous vehicles in shared mobility models. However, to evaluate, whether two or more route requests have the potential for a shared ride, is a compute-intensive task, if done by rerouting. In this work, we propose the Dynamic Longest Common Subsequences algorithm for fast and cost-efficient comparison of two routes for their compatibility, dynamically only incorporating parts of the routes which are suited for a shared trip. Based on this, one can also estimate, how many autonomous vehicles might be necessary to fulfill the local mobility demands. This can help providers to estimate the necessary fleet sizes, policymakers to better understand mobility patterns and cities to scale necessary infrastructure.

We present a randomized O(n^{3.5})-time algorithm for computing optimal energetic paths for an electric car between all pairs of vertices in an n-vertex directed graph with positive and negative costs. The optimal energetic paths are finite and well-defined even if the graph contains negative-cost cycles. This makes the problem much more challenging than standard shortest paths problems. More specifically, for every two vertices s and~t in the graph, the algorithm computes α_B(s,t), the maximum amount of charge the car can reach~t with, if it starts at~s with full battery, i.e., with charge~B, where~B is the capacity of the battery. In the presence of negative-cost cycles, optimal paths are not necessarily simple. For dense graphs, our new O(n^{3.5}) time algorithm improves on a previous O(mn^{2})-time algorithm of Dorfman et al. [ESA 2023] for the problem. The cost of an arc is the amount of charge taken from the battery of the car when traversing the arc. The charge in the battery can never exceed the capacity~B of the battery and can never be negative. An arc of negative cost may correspond, for example, to a downhill road segment, while an arc with a positive cost may correspond to an uphill segment. A negative-cost cycle, if one exists, can be used in certain cases to charge the battery to its capacity. This makes the problem more interesting and more challenging. Negative-cost cycles may arise when certain road segments have magnetic charging strips, or when the electric car has solar panels. Combined with a result of Dorfman et al. [SOSA 2024], this also provides a randomized O(n^{3.5})-time algorithm for computing minimum-cost paths between all pairs of vertices in an n-vertex graph when the battery can be externally recharged, at varying costs, at intermediate vertices.