Solving Travelling Thief Problems using Coordination Based Methods

A travelling thief problem (TTP) is a proxy to real-life problems such as postal collection. TTP comprises an entanglement of a travelling salesman problem (TSP) and a knapsack problem (KP) since items of KP are scattered over cities of TSP, and a thief has to visit cities to collect items. In TTP, city selection and item selection decisions need close coordination since the thief's travelling speed depends on the knapsack's weight and the order of visiting cities affects the order of item collection. Existing TTP solvers deal with city selection and item selection separately, keeping decisions for one type unchanged while dealing with the other type. This separation essentially means very poor coordination between two types of decision. In this paper, we first show that a simple local search based coordination approach does not work in TTP. Then, to address the aforementioned problems, we propose a human designed coordination heuristic that makes changes to collection plans during exploration of cyclic tours. We further propose another human designed coordination heuristic that explicitly exploits the cyclic tours in item selections during collection plan exploration. Lastly, we propose a machine learning based coordination heuristic that captures characteristics of the two human designed coordination heuristics. Our proposed coordination based approaches help our TTP solver significantly outperform existing state-of-the-art TTP solvers on a set of benchmark problems. Our solver is named Cooperation Coordination (CoCo) and its source code is available from https://github.com/majid75/CoCo

Surrogate Assisted Optimisation for Travelling Thief Problems

The travelling thief problem (TTP) is a multi-component optimisation problem involving two interdependent NP-hard components: the travelling salesman problem (TSP) and the knapsack problem (KP). Recent state-of-the-art TTP solvers modify the underlying TSP and KP solutions in an iterative and interleaved fashion. The TSP solution (cyclic tour) is typically changed in a deterministic way, while changes to the KP solution typically involve a random search, effectively resulting in a quasi-meandering exploration of the TTP solution space. Once a plateau is reached, the iterative search of the TTP solution space is restarted by using a new initial TSP tour. We propose to make the search more efficient through an adaptive surrogate model (based on a customised form of Support Vector Regression) that learns the characteristics of initial TSP tours that lead to good TTP solutions. The model is used to filter out non-promising initial TSP tours, in effect reducing the amount of time spent to find a good TTP solution. Experiments on a broad range of benchmark TTP instances indicate that the proposed approach filters out a considerable number of non-promising initial tours, at the cost of omitting only a small number of the best TTP solutions.

A Cooperative Coordination Solver for Travelling Thief Problems

In the travelling thief problem (TTP), a thief undertakes a cyclic tour through a set of cities, and according to a picking plan, picks a subset of available items into a rented knapsack with limited capacity. The overall aim is to maximise profit while minimising renting cost. TTP combines two interdependent components: the travelling salesman problem (TSP) and the knapsack problem (KP). Existing TTP approaches typically solve the TSP and KP components in an interleaved fashion: the solution of one component is fixed while the solution of the other is changed. This indicates poor coordination between solving the two components, which may lead to poor quality TTP solutions. The 2-OPT heuristic is often used for solving the TSP component, which reverses a segment in the tour. Within the TTP context, 2-OPT does not take into account the picking plan, which can result in a lower objective value. This in turn can result in the tour modification to be rejected by a solver. To address this, we propose an extended form of 2-OPT in order to change the picking plan in coordination with modifying the tour. Items deemed as less profitable and picked in cities earlier in the reversed segment are replaced by items that tend to be equally or more profitable and not picked in cities later in the reversed segment. The picking plan is further changed through a modified form of the bit-flip search, where changes in the picking state are only permitted for boundary items, which are defined as lowest profitable picked items or highest profitable unpicked items. This restriction reduces the amount of time spent on the KP component, allowing more tours to be evaluated by the TSP component within a given time budget. The two modified heuristics form the basis of a new cooperative coordination solver, which is shown to outperform several state-of-the-art TTP solvers on a broad range of benchmark TTP instances.

Toxicity Prediction by Multimodal Deep Learning

Prediction of toxicity levels of chemical compounds is an important issue in Quantitative Structure-Activity Relationship (QSAR) modeling. Although toxicity prediction has achieved significant progress in recent times through deep learning, prediction accuracy levels obtained by even very recent methods are not yet very high. We propose a multimodal deep learning method using multiple heterogeneous neural network types and data representations. We represent chemical compounds by strings, images, and numerical features. We train fully connected, convolutional, and recurrent neural networks and their ensembles. Each data representation or neural network type has its own strengths and weaknesses. Our motivation is to obtain a collective performance that could go beyond individual performance of each data representation or each neural network type. On a standard toxicity benchmark, our proposed method obtains significantly better accuracy levels than that by the state-of-the-art toxicity prediction methods.

Diversified Late Acceptance Search

The well-known Late Acceptance Hill Climbing (LAHC) search aims to overcome the main downside of traditional Hill Climbing (HC) search, which is often quickly trapped in a local optimum due to strictly accepting only non-worsening moves within each iteration. In contrast, LAHC also accepts worsening moves, by keeping a circular array of fitness values of previously visited solutions and comparing the fitness values of candidate solutions against the least recent element in the array. While this straightforward strategy has proven effective, there are nevertheless situations where LAHC can unfortunately behave in a similar manner to HC. For example, when a new local optimum is found, often the same fitness value is stored many times in the array. To address this shortcoming, we propose new acceptance and replacement strategies to take into account worsening, improving, and sideways movement scenarios with the aim to improve the diversity of values in the array. Compared to LAHC, the proposed Diversified Late Acceptance Search approach is shown to lead to better quality solutions that are obtained with a lower number of iterations on benchmark Travelling Salesman Problems and Quadratic Assignment Problems.

Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction

Protein structure prediction (PSP) is computationally a very challenging problem. The challenge largely comes from the fact that the energy function that needs to be minimised in order to obtain the native structure of a given protein is not clearly known. A high resolution 20x20 energy model could better capture the behaviour of the actual energy function than a low resolution energy model such as hydrophobic polar. However, the fine grained details of the high resolution interaction energy matrix are often not very informative for guiding the search. In contrast, a low resolution energy model could effectively bias the search towards certain promising directions. In this paper, we develop a genetic algorithm that mainly uses a high resolution energy model for protein structure evaluation but uses a low resolution HP energy model in focussing the search towards exploring structures that have hydrophobic cores. We experimentally show that this mixing of energy models leads to significant lower energy structures compared to the state-of-the-art results.

A Hybrid Local Search for Simplified Protein Structure Prediction

Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino acids of the given protein. Local search algorithms can quickly find very good conformations by moving repeatedly from the current solution to its "best" neighbor. However, once such a compact hydrophobic core is found, the search stagnates and spends enormous effort in quest of an alternative core. In this paper, we attempt to restructure segments of a conformation with such compact core. We select one large segment or a number of small segments and apply exhaustive local search. We also apply a mix of heuristics so that one heuristic can help escape local minima of another. We evaluated our algorithm by using Face Centered Cubic (FCC) Lattice on a set of standard benchmark proteins and obtain significantly better results than that of the state-of-the-art methods.