<p>It seems that the problem is in the model of chunker that you read in the first line. Probably, it uses wrong tokenizer, which is the source of <code>Bali.</code>, <code>I'</code>, <code>Widodo. I</code>, <code>" Abbott</code>, <code>"</code>. 
<code>pair</code> and <code>the Bali</code> can be explained by ordinary errors (taggers usually have not more than 80-90% precision). However, the source of such errors can also be explained by bad model - for example, it can be trained for another domain.</p>

<p>Btw, why do you use longpipe, but not <a href="http://nlp.stanford.edu/software/CRF-NER.shtml" rel="nofollow">Stanford NER</a>? It shows better results, as a rule; e.g. the first available (i.e. random) <a href="http://arxiv.org/ftp/arxiv/papers/1308/1308.0661.pdf" rel="nofollow">article</a>. 
Also, <a href="http://www.galalaly.me/index.php/2011/05/tagging-text-with-stanford-pos-tagger-in-java-applications/" rel="nofollow">here</a> is a good step-by-step tutorial for Standford NER.</p>
LingPipe Named Entity Recognizer outputs a lot of mismatches
<p>I'm trying to extract named entities (people, persons and organizations) using LingPipe and following <a href="http://alias-i.com/lingpipe/demos/tutorial/ne/read-me.html" rel="nofollow">this tutorial</a>. Here is the <a href="http://pastebin.com/YAUCWBMi" rel="nofollow">full text</a> that I am trying to extract names from and here is the code (exception handling omitted for brevity):</p>

<pre><code>Chunker chunker = readChunker("/path-to-chunker"); // custom method for
                                                     reading the model
String article = "Some long news article spanning multiple lines...";

Chunking chunking = chunker.chunk(article);
Set&lt;Chunk&gt; chunkingSet = chunking.chunkSet();
for (Chunk chunk : chunkingSet) {
   String name = article.substring(chunk.start(), chunk.end()));
   System.out.println(name);
}
</code></pre>

<p>And this is (part of) the output I get:</p>

<pre><code>Tony Abbott
Indonesia
Joko Widodo
Sukumaran
Andrew Chan
Bali.
pair
the Bali
Nusa Kambangan
Indonesian
Indonesian
I’
Widodo. I
” Abbott
Julie Bishop
Widodo
al-Jazeera
Sukumaran
Chan
Bishop
”
</code></pre>

<p>As you can see, there are a lot of mismatches/partial matches like <code>Bali.</code>, <code>pair</code>, <code>the Bali</code>, <code>I'</code>, <code>Widodo. I</code>, <code>" Abbott</code>, <code>"</code>. I assume library's NER is working just fine and the problem is that the above code is somehow misusing the classes/methods from this library. But I just can't seem to find what is wrong about the code? </p>

<p>Any ideas?</p>