14Table 14.1 Comparative analysis of the translocation/dwell‐time (T/TD) and n...Table 14.2 Sensitivity limits for detection in the streptavidin‐biosensor mo...
List of Illustrations
1 Chapter 1Figure 1.1 A Penrose tiling. A non‐repeating tiling with two shapes of tiles...Figure 1.2 The Viterbi path. (Left) The Viterbi path is recursively defined,...Figure 1.3 Chunking on a dynamic table. Works for a HMM using a simple join ...Figure 1.4 Edge feature enhancement via HMM/EM EVA filter. The filter “proje...Figure 1.5 (Left) The general stochastic sequential analysis flow topology. ...
2 Chapter 2Figure 2.1 The Norwalk virus genome (the “cruise ship virus”).Figure 2.2 The start of the E. coli genome file, FASTA format.Figure 2.3 The Geometric distribution, P(X = k) = (1 − p)(k−1) p, with...Figure 2.4 The Gaussian distribution, aka Normal, shown with mean zero and v...
3 Chapter 3Figure 3.1 Codon structure is revealed in the V. cholera genome by mutual in...Figure 3.2 ORF encoding structure is revealed in the V. cholera genome by ga...Figure 3.3 (a) Topology index histograms shown for the V. cholerae CHR. I ge...Figure 3.4 Topology‐index histograms are shown for the Chlamydia trachomatis...Figure 3.5 Hash interpolated Markov model (hIMM) and gap/hash interpolated M...
4 Chapter 4Figure 4.1 Schematic for the finite state automaton used for acquisition of ...Figure 4.2 Sensitivity (SN) and Specificity (SP). For the predictor evaluato...Figure 4.3 Sensitivity (SN) and Specificity (SP) for other two conventions (...Figure 4.4 FSA with alternating SP:SN optimized tuning. Step 1: Acquire sign...Figure 4.5 Tuning on “start_drop_value for a collection of blockade signals ...Figure 4.6 Robust Spike feature extraction: radiated DNA. A time‐domain FSA ...Figure 4.7 SVM classification results with and without spike analysis. Addin...Figure 4.8 FSA acquisition flowchart.Figure 4.9 Prokaryotic gene structure discovered thus far.Figure 4.10 Two types of “stop” codon.Figure 4.11 Hypothesized splice signal upstream.Figure 4.12 Hypothesized splice signal downstream of stop upstream from true...
5 Chapter 6Figure 6.1 The most common stochastic sequential analysis flow topology. The...Figure 6.2 Graphical model for a first‐order Markov model.Figure 6.3 Graphical model for a standard hidden Markov model.Figure 6.4 The most probable state sequence.Figure 6.5 Viterbi path. Optimal path identification.Figure 6.6 Comparison of standard HMM and the clique‐generalized HMM. The up...Figure 6.7 HMM/EM Viterbi‐path level occupation feature extraction. Strong E...Figure 6.8 The binary classification performance using features extracted wi...Figure 6.9 Adaboost feature selection strengthens the SVM performance of the...Figure 6.10 If Adaboost operates from the 150 component manual set, a reduce...Figure 6.11 AdaBoosting to select 100 of the full set of 2600 features impro...
6 Chapter 7Figure 7.1 Top Panel. Sliding‐window association (clique) of observations an...Figure 7.2 The transition schematic for the HMM with duration (HMMD).Figure 7.3 Viterbi column‐pointer match de‐segmentation rule. Table 1 and Ta...
7 Chapter 8Figure 8.1 Map.Figure 8.2 Chart.Figure 8.3 Overlapping charts.Figure 8.4 Curve. Note: The parameterization λ defines different curves...Figure 8.5 Function.Figure 8.6 Tangent Bundle, where “cross‐section” of TM (gives intuitive noti...Figure 8.7 1 Forms and cotangent bundle. There is a duality between 1 forms ...Figure 8.8 Gradient 1 form.Figure 8.9 Parallel transport.
8 Chapter 9Figure 9.1 Single Neuron with step (threshold) activation function. The inpu...Figure 9.2 Perceptron update. The update rule shifts the position of the sep...Figure 9.3 Single Neuron, Sigma activation function: the inputs xk are multi...Figure 9.4 Neural Net, layered topology, fully connected between layers (“de...Figure 9.5 Link functions for GD (linear), EGU+/− (left and right curv...Figure 9.6 Link functions for BEG (sigmoid curve), where f(ω) =
9 Chapter 10Figure 10.1 Supervised learning: separability and maximum margin. Shown in t...Figure 10.2 Support vectors on margin boundary.Figure 10.3 (Left) One of the former positives (central to the positive clus...Figure 10.4 Separable solution with maximum width margin.Figure 10.5 Post‐training, have decision hyperplane. Now test data (ci...Figure 10.6 Two clusters, roughly, shown, with intra‐cluster distance shown ...Figure 10.7 Schematic for SVM‐based clustering, starting with randomly label...Figure 10.8 Sum of squared error (SSE) scoring. SSE, the total of the sum of...Figure 10.9 Perceptron update. The update rule shifts the position of the se...Figure 10.10 Decision boundary (solid line); with margin (region between dot...Figure 10.11 The solid circle is the decision boundary. In the implementatio...Figure 10.12 A possible modeling configuration for two‐cluster explicit situ...Figure 10.13 The Hoeffding inequality can be reduced to P[∣ν − μ ∣ > ɛ...Figure 10.14 Line Ax + By + C = 0 and a nearby point. D =
