arXiv subjects

Max Ward

Publications and source records attributed to Max Ward.

9 recordsLinked to original sources

arXiv2025

A faster algorithm for efficient longest common substring calculation for non-parametric entropy estimation in sequential data

Non-parametric entropy estimation on sequential data is a fundamental tool in signal processing, capturing information flow within or between processes to measure predictability, redundancy, or similarity. Methods based on longest common substrings (LCS) provide a non-parametric estimate of typical set size but are often inefficient, limiting use on real-world data. We introduce LCSFinder, a new algorithm that improves the worst-case performance of LCS calculations from cubic to log-linear time. Although built on standard algorithmic constructs - including sorted suffix arrays and persistent binary search trees - the details require care to provide the matches required for entropy estimation on dynamically growing sequences. We demonstrate that LCSFinder achieves dramatic speedups over existing implementations on real and simulated data, enabling entropy estimation at scales previously infeasible in practical signal processing.

cs.DS↗

arXiv2025

mRNA Folding Algorithms for Structure and Codon Optimization

mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses significant challenges for drug storage and distribution, particularly in resource-limited regions. Co-optimizing RNA structure and codon choice has emerged as a promising strategy to enhance mRNA stability while preserving efficacy. Given the vast sequence and structure design space, specialized algorithms are essential to achieve these qualities. Recently, several effective algorithms have been developed to tackle this challenge that all use similar underlying principles. We call these specialized algorithms "mRNA folding" algorithms as they generalize classical RNA folding algorithms. A comprehensive analysis of their underlying principles, performance, and limitations is lacking. This review aims to provide an in-depth understanding of these algorithms, identify opportunities for improvement, and benchmark existing software implementations in terms of scalability, correctness, and feature support.

q-bio.BM↗

arXiv2025

Differentiable Folding for Nearest Neighbor Model Optimization

The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains $\approx13,000$ underlying thermodynamic parameters, and fitting these to both experimental and structural data is computationally challenging. Here, we leverage recent advances in $\textit{differentiable folding}$, a method for directly computing gradients of the RNA folding algorithms, to devise an efficient, scalable, and flexible means of parameter optimization that uses known RNA structures and thermodynamic experiments. Our method yields a significantly improved parameter set that outperforms existing baselines on all metrics, including an increase in the average predicted probability of ground-truth sequence-structure pairs for a single RNA family by over 23 orders of magnitude. Our framework provides a path towards drastically improved RNA models, enabling the flexible incorporation of new experimental data, definition of novel loss terms, large training sets, and even treatment as a module in larger deep learning pipelines. We make available a new database, RNAometer, with experimentally-determined stabilities for small RNA model systems.

q-bio.BM↗

arXiv2022

Scalable Edge Blocking Algorithms for Defending Active Directory Style Attack Graphs

Active Directory (AD) is the default security management system for Windows domain networks. An AD environment naturally describes an attack graph where nodes represent computers/accounts/security groups, and edges represent existing accesses/known exploits that allow the attacker to gain access from one node to another. Motivated by practical AD use cases, we study a Stackelberg game between one attacker and one defender. There are multiple entry nodes for the attacker to choose from and there is a single target (Domain Admin). Every edge has a failure rate. The attacker chooses the attack path with the maximum success rate. The defender can block a limited number of edges (i.e., revoke accesses) from a set of blockable edges, limited by budget. The defender's aim is to minimize the attacker's success rate. We exploit the tree-likeness of practical AD graphs to design scalable algorithms. We propose two novel methods that combine theoretical fixed parameter analysis and practical optimisation techniques. For graphs with small tree widths, we propose a tree decomposition based dynamic program. We then propose a general method for converting tree decomposition based dynamic programs to reinforcement learning environments, which leads to an anytime algorithm that scales better, but loses the optimality guarantee. For graphs with small numbers of non-splitting paths (a parameter we invent specifically for AD graphs), we propose a kernelization technique that significantly downsizes the model, which is then solved via mixed-integer programming. Experimentally, our algorithms scale to handle synthetic AD graphs with tens of thousands of nodes.

cs.CR↗

arXiv2022

Defending Active Directory by Combining Neural Network based Dynamic Program and Evolutionary Diversity Optimisation

Active Directory (AD) is the default security management system for Windows domain networks. We study a Stackelberg game model between one attacker and one defender on an AD attack graph. The attacker initially has access to a set of entry nodes. The attacker can expand this set by strategically exploring edges. Every edge has a detection rate and a failure rate. The attacker aims to maximize their chance of successfully reaching the destination before getting detected. The defender's task is to block a constant number of edges to decrease the attacker's chance of success. We show that the problem is #P-hard and, therefore, intractable to solve exactly. We convert the attacker's problem to an exponential sized Dynamic Program that is approximated by a Neural Network (NN). Once trained, the NN provides an efficient fitness function for the defender's Evolutionary Diversity Optimisation (EDO). The diversity emphasis on the defender's solution provides a diverse set of training samples, which improves the training accuracy of our NN for modelling the attacker. We go back and forth between NN training and EDO. Experimental results show that for R500 graph, our proposed EDO based defense is less than 1% away from the optimal defense.

cs.NE↗

arXiv2022

Finding $(s,d)$-Hypernetworks in F-Hypergraphs is NP-Hard

We consider the problem of computing an $(s,d)$-hypernetwork in an acyclic F-hypergraph. This is a fundamental computational problem arising in directed hypergraphs, and is a foundational step in tackling problems of reachability and redundancy. This problem was previously explored in the context of general directed hypergraphs (containing cycles), where it is NP-hard, and acyclic B-hypergraphs, where a linear time algorithm can be achieved. In a surprising contrast, we find that for acyclic F-hypergraphs the problem is NP-hard, which also implies the problem is hard in BF-hypergraphs. This is a striking complexity boundary given that F-hypergraphs and B-hypergraphs would at first seem to be symmetrical to one another. We provide the proof of complexity and explain why there is a fundamental asymmetry between the two classes of directed hypergraphs.

cs.DM↗

arXiv2021

A Faster Algorithm for Maximum Independent Set on Interval Filament Graphs

We provide an algorithm requiring only $O(N^2)$ time to compute the maximum weight independent set of interval filament graphs. This also implies an $O(N^4)$ algorithm to compute the maximum weight induced matching of interval filament graphs. Both algorithms significantly improve upon the previous best complexities for these problems. Previously, the maximum weight independent set and maximum weight induced matching problems required $O(N^3)$ and $O(N^6)$ time respectively.

cs.DS↗

arXiv2021

Training Spiking Neural Networks Using Lessons From Deep Learning

The brain is the perfect place to look for inspiration to develop more efficient neural networks. The inner workings of our synapses and neurons provide a glimpse at what the future of deep learning might look like. This paper serves as a tutorial and perspective showing how to apply the lessons learnt from several decades of research in deep learning, gradient descent, backpropagation and neuroscience to biologically plausible spiking neural neural networks. We also explore the delicate interplay between encoding data as spikes and the learning process; the challenges and solutions of applying gradient-based learning to spiking neural networks (SNNs); the subtle link between temporal backpropagation and spike timing dependent plasticity, and how deep learning might move towards biologically plausible online learning. Some ideas are well accepted and commonly used amongst the neuromorphic engineering community, while others are presented or justified for the first time here. The fields of deep learning and spiking neural networks evolve very rapidly. We endeavour to treat this document as a 'dynamic' manuscript that will continue to be updated as the common practices in training SNNs also change. A series of companion interactive tutorials complementary to this paper using our Python package, snnTorch, are also made available. See https://snntorch.readthedocs.io/en/latest/tutorials/index.html .

cs.NE↗

arXiv2021

Efficient Network Analysis Under Single Link Deletion

The problem of worst case edge deletion from a network is considered. Suppose that you have a communication network and you can delete a single edge. Which edge deletion causes the largest disruption? More formally, given a graph, which edge after deletion disconnects the maximum number of pairs of vertices, where ties for number of pairs disconnected are broken by finding an edge that increases the average shortest path length the maximum amount. This problem is interesting both practically and theoretically. We call it the \emph{single edge deletion problem}. Our contributions include formally defining the single edge deletion problem and providing motivations from network analysis. Also, we give an algorithm that solves the problem much faster than a naive solution. The algorithm incorporates sophisticated and novel techniques, and generalises to the problem of computing the all-pairs shortest paths table after deleting each edge individually. This means the algorithm has deep theoretical interest as well as the potential for even wider applications than those we present here.

cs.DS↗